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Convergence of Genomics and the Land-Grant Mission:
Emerging Trends in the Application of
Genomics in Agricultural Research
A National Scientific Conference at Purdue UniversityWest Lafayette, IndianaSeptember 10-12, 2007
OFFICE OF THE DEAN W. R. Woodson
Glenn W. Sample Dean of Agriculture
Col lege o f Agr icu l ture
Agricultural Administration Building, Room 114 ■ 615 West State Street ■ West Lafayette, IN 47907-2053 (765) 494-8391 ■ Fax: (765) 494-7420
Welcome from Dean Randy Woodson
Welcome to this national conference on agricultural genomics and to Purdue University.
The genomics revolution and the Land Grant University mission are converging to generate new knowledge and create new opportunities important to our national agricultural R&D portfolio. Genomics research is well established in most of our basic agricultural laboratories. New knowledge is being generated, but there are limited opportunities for direct scientific exchanges across discipline boundaries, commodity interests, or target species, particularly for basic scientists to connect with applied scientists and stakeholders that represent the next links in the scientific discovery/technology development/implementation chain. Genomics consortia and associated research meetings are proliferating around the country, but typically cater to narrow discipline interests, specific commodities, or target species with little information exchange between research groups.
This conference is intended to address some of these concerns. The conference will feature invited presentations by recognized leaders in agricultural genomics and submitted posters from interested participants. Presentations on microbes, arthropods, plants, animals and ecological systems will be integrated into sessions addressing the following themes:
Transition from Model to Agricultural Species
Integrating Information Across Databases
Translational Challenges and Successes
Roundtable Discussion and Recommendations
The purpose of the meeting will be to share information, explore collaborations, and identify future research needs. This meeting promises to be a rare opportunity to exchange scientific expertise and experiences among genomics researchers and stimulate new discussions with applied researchers, stakeholders, and decision makers who do not normally interact with the genomics community. The goal of the conference is to promote synergisms across disciplines, commodities, and species on our campuses and across the country. A committee of recognized national leaders in molecular biology and genomics developed the program.
This meeting promises exciting and groundbreaking science, and we hope, a window into the future of genomics in agriculture. Enjoy the meeting and again welcome to Purdue University.
Randy Woodson, Glenn W. Sample Dean of Agriculture Purdue University
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ORGANIzING ANd STEERING COMMITTEES
Organizing Committee
The organizing committee is responsible for the scientific program of the conference. Its members are recognized scientific leaders with interests and expertise in agricultural genomics. The committee is coordinated by Dr. Sonny Ramaswamy who also serves as liaison to the steering committee.
• Dr. William Beavis, Chief Scientific Officer, National Center for Genome Resources, Santa Fe, NM • Dr. Richard Beeman, Research Entomologist, Biological Research Unit, Grain Marketing & Production Research Center, USDA-ARS, Manhattan , KS • Dr. Hans H. Cheng, Supervisory Research Geneticist, Avian Disease and Oncology Laboratory, USDA ARS, East Lansing, MI • Dr. Frank Collins, Professor, George and Winifred Clark Chair in Biological Science, Department of Biological Sciences, University of Notre Dame, IN • Dr. Rebecca W. Doerge, Professor, Departments of Agronomy and Statistics, Purdue University • Dr. Ronald D. Green, National Program Leader, Animal Production and Protection, USDA ARS • Dr. Kevin Hackett, National Program Leader, Crop Production and Protection, USDA ARS, Beltsville , MD • Dr. Molly Jahn, Professor, Plant Breeding and Plant Biology, Cornell University, NY • Dr. Stephen J. O’Brien, Principal Investigator, Chief of the Laboratory of Genomic Diversity and head of the Section of Genetics, NIH • Dr. Ronald L. Phillips, Regents’ Professor and McKnight Presidential Chair in Genomics University of Minnesota, MN • Dr. Sonny Ramaswamy, Associate Dean of Research and Director of Agricultural Research Programs, Purdue University, IN • Dr. Sam Reddy, Traits Platform Leader, Discovery Research, Dow AgroSciences, Indianapolis, IN • Dr. Mike J. Sanderson, Professor, Section of Evolution & Ecology, UC Davis, CA • Dr. James E. Womack, Distinguished Professor, Department of Veterinary Pathobiology, Texas A&M University, TX
Steering Committee
The steering committee initiated the conference concept and worked with the organizing committee to finalize the program, topics and speakers. This group will provide local arrangements support e.g. establishing the conference website, publicity, periodic announcements, registration, accommodation information, and other meeting logistics. Dr. Steve Yaninek serves as primary contact for this group.
• Dr. Andrew DeWoody, Department of Forestry and Natural Resources, Purdue University • Dr. Catherine Hill, Department of Entomology, Purdue University • Dr. Scott Jackson, Department of Agronomy, Purdue University • Dr. Bill Muir, Department of Animal Science, Purdue University • Dr. Barry Pittendrigh, Department of Entomology, Purdue University • Dr. Michael Scharf, Department of Entomology and Nematology, University of Florida • Dr. Jeff Stuart, Department of Entomology, Purdue University • Dr. Steve Yaninek, Department of Entomology, Purdue University
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ContentsGeneral Information and Logistics .......................................................................... 3
Monday .................................................................................................................... 5
Tuesday ................................................................................................................... 6
Wednesday .............................................................................................................. 8
Speakers ................................................................................................................. 10
Poster Abstracts ...................................................................................................... 62
Speaker/Author Index .............................................................................................. 83
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LOGISTICS ANd INFORMATION
RegistrationAll participants must register for the meeting. Registration badges are required for admission to all sessions, mixers, and other functions.
Monday 9:00 am - 5:00 pm Registration and Information Desk South Ballroom, West Entrance
Tuesday 7:30 am - 10:00 am Registration and Information Desk South Ballroom, West Entrance 10:00 am - 4:30 pm Stewart Center, Room 110
Wednesday 7:30 am - 10:30 am Stewart Center, Room 110
Messages, Program Changes, Lost & FoundMessage board for posting announcements: North BallroomProgram Changes: North BallroomLost & Found (turn in and retrieve): Union Club Hotel Desk
Local Support StaffConference and local support staff may be identified by the color of ribbon on their name badge:Purdue Conference Staff - Gold Purdue name badgeSteering Committee - White ribbonOrganizing Committee - Blue ribbonStudent Assistants - Gold ribbonSpeakers - Black ribbon
Audio/Visual EquipmentPreview Room – Purdue Memorial Union, Room 136 (Near the south entrance of the South Ballroom).
A dedicated laptop and LCD projector for PowerPoint presentations delivered on a CD or flash drive will be used. Plan to check and upload your presentation in the preview room as early as possible, but no later than half an hour before the start of your session.
Oral PresentationsPurdue Memorial Union – South BallroomTo keep interruptions to a minimum during presentations, please use designated entrance and exits posted in the North and South Ballrooms.
PostersPosters will be displayed in the Purdue Memorial Union, North Ballroom. Posters are to be set up by 12:00 pm on Monday, September 10th and will stay up until 1:00 pm on Wednesday, September 12th. All posters should be removed between 1:00 pm and 4:00 pm on Wednesday. Authors are requested to be present at their poster from 6:30 – 8:30 on Tuesday during the Poster Session and Mixer.
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Contents
AGENdA OVERVIEW
Monday, September 10, 2007 9:00 ----5:00 Registration .............................................................................. Foyer - South Ballroom 1:00 ----1:05 Welcome ...............................................................................................South Ballroom 1:05 ----2:00 Plenary I - Genomics for the applied geneticist ....................................South Ballroom 2:00 ----2:30 Status of agricultural genome sequencing projects ..............................South Ballroom 2:30 ----3:00 Genomics of plant pathogens ...............................................................South Ballroom 3:00 ----3:30 BREAK ..................................................................................................North Ballroom 3:30 ----4:00 Impact of sequencing the bovine genome ............................................South Ballroom 4:00 ----4:30 Agricultural insect pests ........................................................................South Ballroom 4:30 ----5:00 General Discussion ...............................................................................South Ballroom 6:30 ----9:00 CONFERENCE BANQUET, Keynote: Can the land-grant mission fulfillthepromisesofthegenomicsera? .................................North Ballroom
Tuesday, September 11, 2007 7:30---10:00 Registration and Information ................................................................South Ballroom10:00 ----4:30 Registration and Information ............................................ Stewart Center, Room 110 8:00 ----9:00 Plenary II - Recombineering: Creating genetical model organisms through genomics and reverse genetics ..................................South Ballroom 9:00 ----9:30 Comparative mammalian genomics: Evolutionary analyses of felids ..South Ballroom 9:30---10:00 Progress towards massively parallel, inexpensive automated gene synthesizers and other next generation genomic tools ...........South Ballroom10:00---10:30 BREAK .................................................................................................North Ballroom10:30---11:00 Use of high density SNP data and linkage disequilibrium to uncover evolutionary events, conformation form the cattle genome .....South Ballroom11:30---12:00 General Discussion ..............................................................................South Ballroom12:00----1:00 LUNCH BREAK ....................................................................................North Ballroom 1:00----2:00 Plenary III - Genomics and quantitative genetics .................................South Ballroom 2:00----3:00 Experimental approaches to annotate the Arabidopsis genome with the goal to integrate traits of agricultural importance ...............South Ballroom 3:00 ----3:30 BREAK .................................................................................................North Ballroom 3:30 ----4:00 Phylogenomics .....................................................................................South Ballroom 4:00 ----4:30 Comparative genomics of plants ..........................................................South Ballroom 4:30 ----5:00 General Discussion ..............................................................................South Ballroom 6:30 ----9:00 POSTER SESSION & MIXER ..............................................................North Ballroom
Wednesday, September 12, 2007 7:00---10:00 Registration and Information ............................................. Stewart Center, Room 110 8:00 ----9:00 Plenary IV - Retrotransposons and genome evolution .........................South Ballroom 9:00 ----9:30 Status and challenges of aquaculture genomics: Making reactions work without reagents ...........................................................................South Ballroom 9:30---10:00 Uncovering the mysteries of viral disease resistance in poultry through a combination of genomic and proteomic approaches ............South Ballroom10:00---10:30 BREAK .................................................................................................North Ballroom10:30--- 11:00 Identifying ecologically important genes ...............................................South Ballroom11:00--- 11:30 Genotoxic fallout from Chernobyl ..........................................................South Ballroom11:30--- 12:00 General Discussion ...............................................................................South Ballroom12:00---- 1:00 LUNCH BREAK ....................................................................................North Ballroom 1:00---- 5:00 Roundtable Discussion/Recommendation Session ..............................South Ballroom
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Monday, September 10, 2007
9:00 ----5:00 Registration and Information Purdue Memorial Union - South Ballroom, West Entrance
Transition from Model Organisms to Agriculturally Important Species (Part I)Moderator: Scott Jackson
Rapporteur: Jeff StuartPurdue Memorial Union – South Ballroom
1:00 ----1:05 Welcome, Sonny Ramaswamy, Associate Dean of Research and Director of Agricultural Research Programs, Purdue University, IN
1:05 ----2:00 Plenary I - Genomics for the applied geneticist, Ronald Phillips, Regents’ Professor and McKnight Presidential Chair in Genomics, Department of Agronomy and Plant Genetics, University of Minnesota, MN
2:00 ----2:30 Status of agricultural genome sequencing projects, Daniel Rokhsar, Program Head, Computational Genomics, Joint Genomics Institute, DOE, and Professor, Department of Molecular and Cell Biology, U.C. Berkeley, CA
2:30 ----3:00 Genomics of plant pathogens, Alan Collmer, Professor, Department of Plant Pathology, Cornell University, NY
3:00 ----3:30 BREAK - NORTH BALLROOM
3:30 ----4:00 Impact of sequencing the bovine genome, J.E. Womack, Distinguished Professor, Department of Veterinary Pathobiology, Texas A&M University, TX
4:00 ----4:30 Agricultural insect pests, Dick Beeman, USDA-ARS, Grain Marketing & Production Research Center, Manhattan, KS
4:30 ----5:00 General Discussion
6:30 ----9:00 CONFERENCE BANQUET - PURDUE MEMORIAL UNION (NORTH BALLROOM)
Purdue Welcome, Randy Woodson, Glenn W. Sample Dean of Agriculture, Purdue University
Keynote: CantheLand-grantmissionfulfillthepromisesofthegenomicsera? Roger N. Beachy, President, Donald Danforth Plant Science Center, St Louis, MO
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Tuesday
Tuesday, September 11, 2007
7:30 -- 10:00 Registration and Information Purdue Memorial Union - South Ballroom, West Entrance10:00 ----4:30 Stewart Center, Room 110
Transition from Model Organisms to Agriculturally Important Species (Part II)Moderator: Bill Muir
Rapporteur: Barry PittendrighPurdue Memorial Union – South Ballroom
8:00 ----9:00 Plenary II - Recombineering: Creating genetical model organisms through genomics and reverse genetics, L.B. Schook, Professor of Comparative Genomics, Gutgsell Endowed Chair; Professor of Pathobiology, College of Veterniary Medicine, University of Illinois Urbana-Champaign, IL
9:00 ----9:30 Comparative mammalian genomics: Evolutionary analyses of felids, Stephen J. O’Brien, Chief, Laboratory of Genomic Diversity. National Cancer Institute, Frederick, MD
9:30 -- 10:00 Progress towards massively parallel, inexpensive automated gene synthesizers and other next generation genomic tools, Michael Sussman, Professor, Department of Biochemistry, Director of UW Biotechnology Center, University of Wisconsin, WI
10:00 -- 10:30 BREAK - NORTH BALLROOM
10:30 -- 11:00 Use of high density SNP data and linkage disequilibrium to uncover evolutionary events,confirmationfromthecattlegenome,M.E. Goddard, Faculty of Land and Food Resources, University of Melbourne, Parkville, Victoria, Australia
11:00 -- 11:30 Associating plant phenotypes and genomes, Edward Buckler, USDA-ARS, Institute for Genomic Diversity, Cornell University, NY
11:30 -- 12:00 General Discussion
12:00 ----1:00 LUNCH BREAK
Integrating Information Across Databases: From Informatics to SemanticsModerator: Cate Hill
Rapporteur: Mike ScharfPurdue Memorial Union – South Ballroom
1:00 ----2:00 Plenary III - Genomics and quantitative genetics, William Beavis, Chief Scientific Officer, National Center for Genome Resources, Santa Fe, NM
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2:00 ----2:30 Experimental approaches to annotate the Arabidopsis genome with the goal to integrate traits of agricultural importance, Joseph R. Ecker, Plant Molecular and Cellular Biology Laboratory, Salk Institute, San Diego, CA
2:30 ----3:00 Arthropod databases, Frank H. Collins, Professor, George and Winifred Clark Chair in Biological Sciences, Department of Biology, University of Notre Dame, IN
3:00 ----3:30 BREAK
3:30 ----4:00 Phylogenomics, Michael J. Sanderson, Section of Evolution & Ecology, University of Arizona, AZ and University of California-Davis, CA
4:00 ----4:30 Comparative genomics of plants, Jeffrey Bennetzen, Norman and Doris Giles Professor, Department of Genetics, University of Georgia, GA
4:30 ----5:00 General Discussion
6:30 ----9:00 POSTER SESSION & MIXER - North Ballroom Appetizers and Cash Bar
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Wednesday
Wednesday, September 12, 2007
7:00 -- 10:00 Registration and Information Stewart Center, Room 110
Translational Challenges and SuccessesModerator: Andrew DeWoody
Rapporteur: Bill MuirPurdue Memorial Union – South Ballroom
8:00 ----9:00 Plenary IV - Retrotransposons and genome evolution, John F. McDonald, Chair, School of Biology, Georgia Tech University, GA
9:00 ----9:30 Status and challenges of aquaculture genomics: Making reactions work without reagents, Zhanjiang (John) Liu, Distinguished Alumni Professor and Director, Aquatic Genomics Unit, Department of Fisheries and Allied Aquacultures, Auburn University, AL
9:30---10:00 Uncovering the mysteries of viral disease resistance in poultry through a combination of genomic and proteomic approaches, Hans H. Cheng, Supervisory Research Geneticist, USDA-ARS, Avian Disease and Oncology Laboratory, East Lansing, MI
10:00---10:30 BREAK - NORTH BALLROOM
10:30---11:00 Identifying ecologically important genes, Hopi Hoekstra, John L. Loeb Associate Professor of Biology, Department of Organismic and Evolutionary Biology, Harvard University, MA
11:00---11:30 Genotoxic fallout from Chernobyl, R.J. Baker, Horn Professor, Department of Biological Sciences, Texas Tech University, TX
11:30---12:00 General Discussion
12:00----1:00 LUNCH BREAK
Roundtable Discussion / RecommendationsModerator: Sonny Ramaswamy
Rapporteur: Cate HillPurdue Memorial Union – South Ballroom
1:00----5:00 Roundtable Discussion / Recommendation Session
Agricultural genomics and stakeholder priorities, Nathan Fields, Director of Research & Business Development, National Corn Growers Association, Chesterfield, MO
Industry and LGU partnerships, John McLean, Director, Genomics Technology, Monsanto, St. Louis, MO
Genomics and plant breeding: Past, present, and future, Steve Thompson, Global Leader, Seeds & Traits R&D, Dow AgroSciences, LLC, Indianapolis, IN
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1:00----5:00 Roundtable Discussion / Recommendation Session (cont.)
Leading genomics to impact in the land-grant context, Irwin Goldman, Vice Dean, College of Agricultural and Life Sciences, University of Wisconsin, WI
Setting federal agricultural genomics research priorities, Patrick Schnable, Associate Director, Plant Sciences Institute; Director, Center for Plant Genomics; and Professor, Department of Agronomy, Iowa State University, IA
Round table wrap-up and recommendations, Sonny Ramaswamy, Associate Dean of Research and Director of Agricultural Research Programs, Purdue University, IN
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Speakers
Ph.D. : University of Arizona, 1967 M.S. : Oklahoma State, 1965 B.S. : Arkansas A&M, 1963 Developmental Leave: Harvard University, 1986 Faculty, Texas Tech University 1967 to present.
Dr. Baker, as part of a team led by Ron K. Chesser, has made more than 20 trips to Ukraine to study the Chernobyl environment and has published more than 20 papers concerned with the biodiversity and genetics of populations living in the most radioactive environments. His research
interests include modes and mechanisms of speciation of mammals, chromosomal evolution, and evolution of phyllostomid bats. He has been a strong proponent of the genetic species concept and the Bateson-Dobzhansky-Muller process of speciation. He has directed a museum that archives genetic resources as well as classical specimens. He strongly embraces the idea that the results from ecotoxicological studies should be supported by accurate exposure information and that biological material be archived for other scientists who may wish to enhance the value of studies or alternatively test published results. He has directed more than 30 Ph D students, including Andrew DeWoody, John Bickham, Terry Yates, Rodney Honeycutt, Ron Van Den Bussche, Jonathan Longmire, Kateryna Makova, Anton Nekrutenko, and Jeff Wickliffe. He has directed 5 Ph.D. dissertations concerned with Chernobyl.
R. J. Baker, Ph.d.Horn Professor, department of Biological Sciences, Texas Tech University, TX
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Time Magazine (May 1986) described the Chernobyl disaster as the “world’s worst environmental nuclear event.” It is certainly the most widely publicized nuclear accident. Paradoxically, the ecosystem in the most radioactive regions is vibrant and the biodiversity there is as great as would be predicted if the sites were uncontaminated by pollution. Our studies there for the most part do not support the hypothesis that negative genetic consequences resulting from multigenerational exposure, at least in rodents, exist. This is surprising because some species are receiving an annual cumulative dose that is equal to six times that of an acute lethal dose (LD50/30). Our team has continued to design experiments with the goal of providing meaningful information to resolve the question of the biological significance of living in such an environment. The scientific community is currently split with respect to the effects that the Chernobyl environment has had on species inhabiting the exclusion zone. Thus, questions concerning the ecological and human health effects associated with Chernobyl remain largely unresolved. Sequencing of small portions of the genome (i.e., single genes, mtDNA loci) is not sufficient for detecting a small increase in the mutation rate. However, a small but biologically significant increased mutational rate is expected to increase the genomic mutational load, resulting in increased birth defects and reduced fitness, especially in cases where a given deleterious mutation is present in the homozygous condition. Conversely, there are also biological responses in exposed organisms that may be expected to ameliorate negative consequences such as mutations. Radiation exposure of any magnitude is hypothesized to increase oxidative stress and the formation of reactive oxygen species (ROS). Physiological responses to natural endogenous levels of oxidative stress primarily involve antioxidants such as certain vitamins and radical scavenging proteins. It is plausible that such antioxidant mechanisms can respond to increased oxidative stress mediated by exogenous agents. A recent study that we have completed suggests that transcription of the gene encoding one such protein, superoxide dismutase, is increased in response to low dose-rate irradiation. It is also possible that additional mechanisms (e.g., DNA repair, damaged protein degradation, apoptosis) may be involved in either cellular or organ defense and, ultimately, organism protection. This suggests that models of risk assessment other than a simple, positive linear-effect relationship may need to be considered when reviewing effects resulting from relevant environmental exposure to ionizing radiation. An overview of studies and proposed experimentation capable of resolving this conflict will be discussed.
Genotoxic fallout from Chernobyl ABSTRACT:
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Speakers
Dr. Beachy is president of the Donald Danforth Plant Science Center in St. Louis, Missouri. He previously held academic positions at Washington University, St. Louis and The Scripps Research Institute, La Jolla, California. His research includes projects to reduce virus infection in plants via biotechnology and in studies of control of gene expression in plants. Beachy is a member of the U.S. National Academy of Sciences and a Fellow of the Academy of Microbiology, among others. He has several awards for his work, including the Wolf Prize in Agriculture. The Danforth Center has committed significant effort to
research in developing countries, including through private-public partnerships. Beachy is involved in a variety of efforts with regard to rationalizing regulations that control commercialization of agricultural biotechnology.
Roger N. Beachy, Ph.d.President, donald danforth Plant Science Center, St Louis, MO Member, National Academy of Sciences
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Can the land-grant mission fulfill the promises of the genomics era?
ABSTRACT:
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Speakers
Most often cited for his discovery of bias in estimates of genetic effects in QTL analyses of populations with poor power (the “Beavis Effect”), Dr. Beavis gained extensive experience in the application of statistical genetic methods during his twelve years at Pioneer-DuPont. Since joining NCGR in 1998, Dr. Beavis has been the principal investigator for a variety of bioinformatics projects, including The Arabidopsis Information Resource (TAIR), the Legume Information System (LIS), and the GeneX and GeneX-Lite gene expression systems. Most recently Dr. Beavis joined the faculty at Iowa State University as
the G.F. Sprague Chair of Crop Genomics and Sustainable Agriculture. Dr. Beavis earned a Ph.D. from Iowa State University in 1985. He holds a B.S. degree in range management from Humbolt State University, Arcata, California, and an M.S. degree in interdisciplinary biology-statistics from New Mexico State University in Las Cruces, NM. Since 2003, Dr. Beavis is also an adjunct professor in the Department of Mathematics and Statistics at the University of New Mexico and an adjunct scientist at Lovelace Respiratory Research Institute.
William Beavis, Ph.d.Chief Scientific Officer, National Center for Genome Resources, Santa Fe, NM
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Plant genome initiatives have promised future crop improvement based on fundamental information generated by these programs. While developmental and evolutionary biologists have taken advantage of omic data to generate testable hypotheses about fundamental molecular mechanisms, the same information is not being used by translational researchers nor by applied plant breeders. This is due, in part, to the proliferation of distributed, autonomous, and often ephemeral information resources and the failure to provide information from omic technologies in formats that are useful for translational researchers and plant breeders. To address the first challenge, we have been developing a Virtual Plant Information Network (VPIN) based on emerging middleware technology platforms resulting in powerful interoperable capabilities supporting integrative and comparative bioinformatics. To address the second challenge, we have begun to develop a decision support system that will utilize these integrated sources of information to assign values and/or relative risks to biomarkers in diagnostic kits that can be used for selection by the applied plant breeder.
Genomics and quantitative geneticsABSTRACT:
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Speakers
Dr. Beeman’s research emphasis is on the genetics and molecular biology of insect pests of stored products. He is currently involved in efforts to characterize genes that regulate resistance to insecticides and pathogens, develop DNA vectors for genetic engineering of pest and beneficial insects, discover and evaluate parasitic and lethal genes that occur naturally in pest insect populations, and develop molecular markers for population monitoring and resistance diagnosis.
PROJECT INFORMATIONPositional cloning of the maternally-acting, selfish gene, medea, in Tribolium castaneum - This poster documents the positional cloning of target genes in Tribolium by
chromosome walking in a BAC library. Two genes, aureate and the unique, maternal selfish gene medea, defined only by phenotypic effect, were cloned and mapped to the scabrous and highwire regions, respectively, using very high-resolution recombinational mapping. Confirmation will include molecular mapping of seven medea revertant (knockout) lesions induced by radiation, mapping of one spontaneous and one radiation-induced mutant lesion in aureate, expression analysis of the candidate genes in mutant beetles, and molecular characterization of gene mutations.
Tribolium molecular genetics - This site contains data and articles about the genetics of the red flour beetle, Tribolium castaneum, and related species. Work being done in Dr. Beeman’s laboratory involves both standard and molecular approaches.
Which phenoloxidase catalyzes insect cuticle tanning: laccase or tyrosinase? - Tanning, or sclerotization, is a vital process during insect development in which N-acylcatecholamines are oxidatively conjugated to cross-link proteins and stabilize the exoskeleton. The phenoloxidases laccase (Lac) and tyrosinase (Tyr) have been proposed to catalyze tanning, but evidence reported to date identifying the actual tanning enzyme has been inconclusive. To establish the involvement of either or both of these phenoloxidases in cuticle tanning, we performed RNA interference (RNAi) experiments using the red flour beetle, Tribolium castaneum. RNAi can be used to suppress specific messenger RNAs and generate loss-of-function phenotypes. We have knocked down phenoloxidase mRNAs and examined the phenotypes for effects on adult cuticle tanning. The results reported here demonstrate that laccase, and not tyrosinase, plays the major role in cuticle tanning.
dick Beeman, Ph.d.USdA-ARS, Grain Marketing and Production Research Center, Manhattan, KS
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The genome of a major grain pest, the red flour beetle, Tribolium castaneum, has been sequenced, assembled, annotated, and subjected to comparative genomic analysis. Large-scale EST projects have been conducted and microarray analyses initiated. The Tribolium genome is a “first,” both for beetles and for agronomic pest species. This species is unique among sequenced arthropods for its tolerance of dry environments and osmoregulatory physiology, omnivory and digestive physiology, pest status and capability for xenobiotic detoxification, extremely hard and thick exoskeleton, developmental indeterminacy, and particular strengths as a laboratory model for functional genomic inquiry. Annotation and functional analysis of the Tribolium genome has revealed many fascinating and unexpected features involving cuticle proteins, chitin metabolism, vasopressin and neuropeptide physiology, maternal-effect selfish genes, digestive physiology, and other aspects of Tribolium biology.
Agricultural insect pestsABSTRACT:
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Speakers
Dr. Bennetzen received his B.S. in Biology from the University of California at San Diego in 1974 and a Ph.D. in biochemistry from the University of Washington (Seattle) in 1980. As a postdoctoral fellow, he worked on a shared project between the laboratories of Dr. Michael Freeling (University of California-Berkeley) and Dr. Virginia Walbot (Stanford University). In 1981, he joined the International Plant Research Institute in San Carlos, CA. Dr. Bennetzen joined the Department of Biological Sciences at Purdue University as an assistant professor in 1983, where he later became an associate professor (1987) and
full professor (1991). Since 2003, he has been the Giles Professor of Molecular Biology and Functional Genomics in the Department of Genetics at the University of Georgia.
The Bennetzen laboratory has spent more than 25 years investigating the factors responsible for plant genome evolution. Early studies included the molecular cloning and characterization of transposable elements (e.g., the Mutator system of maize) and investigations of plant disease resistance gene evolution (e.g., the hyper-unstable Rp1 resistance gene cluster of maize). In the late 1980s, the Bennetzen lab began investigating genomic colinearity in the grasses, leading to the conceptualization of the single grass genome as a research model, and to discovery of the general structure and variation of complex plant genomes like maize. Most recently, this group has been characterizing the molecular mechanisms responsible for plant genome instability, lineage-specific differences in the aggressiveness of these processes, and the functional outcomes of genomic change.
Dr. Bennetzen was elected a member of the U.S. National Academy of Sciences in 2004 and as a fellow of the American Association for the Advancement of Science in 2005. His other awards include the Sigma Xi Research Award (1995) and Umbarger Professorship (1999) from Purdue University, the Nehru Centenary Professorship from the University of Hyderabad (2002), and a Georgia Research Alliance Professorship (2003).
Jeffrey Bennetzen, Ph.d.Norman and doris Giles Professor/Georgia Research Alliance Eminent Scholar, department of Genetics, University of Georgia, GA; Member, National Academy of Sciences
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The Angiosperms differ dramatically in genome size and arrangement but are generally conserved in gene content and evolved gene function. The great strength of comparative genomics is that it allows identification of both the genes that are responsible for the many shared properties of plants and the genes responsible for what makes each plant species unique. One particular family of plants, the grasses, provides a particularly fertile field of investigation, because the studied genomes have undergone very rapid rearrangement since the first grasses appeared 50-70 million years ago. Gene order has been largely conserved, although approximately 30% of the genes are no longer collinear when a distant comparison like maize versus rice is employed. Gene family numbers differ greatly, even between closely related species, partly as a function of high levels of polyploidy and partly because of a high frequency of tandem chromosomal segment duplication. Numerous gene fragments are found in plant genomes, many inside transposable elements (TEs) that have fused fragments from different genes into a sequence that yields chimeric transcripts and proteins after transcription and translation. This very high rate of de novo generation of candidate “exon-shuffled” genes appears to be unique to plants, perhaps because of the very high relative activity and diversity of plant TEs, but most of these potential genes (like most unselected DNA) are very rapidly removed by processes of unequal and illegitimate recombination. Although genomic instability appears to be high in all of the flowering plant genomes investigated so far, some genomes are much more unstable than others. Current studies are investigating the nature of these differences and the functional outcomes of genomic instability.
The comparative genomics of flowering plantsABSTRACT:
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Speakers
Dr. Buckler is a USDA-ARS researcher at Cornell University working on integrating quantitative genetics, genomics, and bioinformatics. Most of his work has focused on developing high -resolution association mapping in maize. His group has contributed to analysis of flowering time, starch production, vitamin A production, and central carbon metabolism.
He did his undergraduate work in biology and archaeology at the University of Virginia. He earned a Ph.D. in evolutionary genetics of maize at the University of
Missouri, and completed postdoctoral research in statistical genetics with Dr. Bruce Weir at North Carolina State University. He joined the USDA-ARS in 1998 with a position located in North Carolina State’s Department of Genetics. In 2003, his lab moved to Ithaca, NY with the USDA and Cornell University. He has won a Presidential Early Career Award and the Arthur Flemming Award.
Edward Buckler, Ph.d.USdA-ARS, Institute for Genomic diversity, Cornell University, NY
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Maize harbors tremendous natural diversity, which can be used for improvement. In our ongoing effort to characterize molecular and functional diversity in the maize genome, we have developed germplasm and analysis tools to carry out high-resolution association studies in maize. These association approaches have focused on developing and adapting structured association and family-based association methods. These association approaches have proven effective in identifying useful nucleotide polymorphisms in genes involved in carotenoids, aluminium tolerance, and kernel quality. However, while standard association mapping in maize provides high resolution, this approach can result in less statistical power. To exploit both high-resolution and statistical power, in collaboration with several other groups we are developing a platform for the dissection of complex traits in maize by utilizing nested association mapping approaches. Preliminary examples and statistical power of the maize nested association mapping population will be discussed. Large collaborative populations, association analysis, and genomic tools will be likely be able to revolutionize the study of complex traits.
Association mapping of diverse maize ABSTRACT:
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Speakers
Dr. Cheng is a supervisory research geneticist at the USDA- ARS Avian Disease and Oncology Laboratory in East Lansing, MI, where he serves as the lead scientist for the Genomics and Immunogenetics CRIS Project. The focus of this group is to identify and characterize genes of importance to the U.S. poultry industry, especially those involved in immunological and genetic resistance to Marek’s disease (MD) and avian leucosis virus (ALV). Highlights of Dr. Cheng’s research include the development of the East Lansing genetic map, the identification of QTL and genes conferring resistance to Marek’s disease,
and cloning and manipulation of infectious Marek’s disease virus BAC clones.
Dr. Cheng received his formal training from the Department of Microbiology, Michigan State University, where he received his B.S. in 1983, and from the Department of Molecular Biology, University of California-Berkeley, where he earned a Ph.D. in 1988 (Dr. Harrison Echols, advisor). Prior to joining USDA-ARS in 1992, Dr. Cheng spent 2 years as a NSF-funded postdoctoral fellow in Dr. Richard Michelmore’s laboratory, University of California-Davis, and as head of molecular biology for Petoseed, a vegetable seed company in Woodland, CA (Petoseed was acquired by Seminis in 1996, which later merged with Monsanto in 2005).
Dr. Cheng has been an active member in the scientific community. Some of his activities include being the U.S. Poultry co-coordinator, serving as a member of the National Animal Genome Preservation Committee, and serving on the editorial board for many journals. Also, he is an adjunct faculty member of the Genetics Program and the Veterinary School, Michigan State University.
Hans Cheng, Ph.d.Supervisory Research Geneticist, USdA-ARS, Avian disease and Oncology Laboratory, Michigan State University, MI
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Poultry is the third largest agricultural commodity in the U.S., and the largest producer and exporter of meat and egg products in the world. Several major issues confront the poultry industry today, with control of infectious diseases near the top of the list. Genomic technologies can identify the genetic basis for variation in complex traits like disease resistance and, thus, information that can be applied to enhance genetic gains through breeding. With this goal in mind, we have been implementing and integrating genomic approaches to interrogate genetic resistance to Marek’s disease (MD), a herpesvirus-induced T-cell lymphoma of chickens. First, QTL scans have been conducted in experimental and commercial resource populations, which provide information on relevant genomic regions. Unfortunately, like the situation in most other studies, QTL of the magnitude that we identified cannot be accurately resolved to provide viable positional candidate genes. Consequently, we have incorporated DNA microarrays to profile for transcripts that are differentially expressed between MD resistant and susceptible chicks, and two-hybrid assays to screen for Marek’s disease virus (MDV)-chicken protein-protein interactions. These latter approaches identify genes and pathways involved in MD resistance, which combined with genetic mapping can reveal positional candidate genes for genetic resistance. Furthermore, using more than one approach combines the strengths of each system and yields results of higher confidence, as well as reducing the number of targets to verify and characterize. These integrative genomic strategies have identified a number of genes that can be further interrogated by more traditional experimental approaches as well as the use of infectious BAC clones of the MDV genome, which are particularly useful for chicken-MDV protein interactions. These approaches can be applied to other complex traits, and our results indicate that molecular and genomic approaches will yield significant biological information that can be applied for agricultural improvement.
Uncovering the mysteries of viral disease resistance in poultry through a combination of genomic and proteomic approaches
ABSTRACT:
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Speakers
Dr. Collins received his Ph.D. from the University of California-Davis and carried out postdoctoral studies at the National Institute of Allergy and Infectious Diseases, NIH. The two broad areas of work in Dr. Collins’ laboratory are (1) genome-level studies of arthropod vectors of human pathogens and (2) field and laboratory research on malaria vectors, especially the mosquito Anopheles gambiae, which is the primary vector of malaria parasites in sub-Saharan Africa.
Dr. Collins’ laboratory directs a contract from the National Institutes of Health to develop and manage a Web-based bioinformatics resource center that provides scientists with access to all data related to the genomes of arthropod vectors. Management of this resource, called VectorBase (www.VectorBase.org), involves both developmental work in the areas of bioinformatics and computer science, as well as the direct analysis of the genomes that are displayed and managed by VectorBase. Much of the work in this area involves interdisciplinary links with faculty and students in the Department of Computer Science and Engineering in the Notre Dame College of Engineering.
In the area of direct work on the biology of malaria vectors, Dr. Collins’ lab now focuses on the development of molecular tools that will permit better resolution of questions about vector population ecology and ecological genetics, and the epidemiology of malaria transmission. The primary subjects of this work are the African malaria vectors A. gambiae and A. funestus. While most work in his group is laboratory based and emphasizes techniques of molecular biology, genetics, and genomics, Dr. Collins is also involved in a number of field studies with collaborators in Africa, and his group is planning to expand the field work to include malaria transmission in Indonesia.
Frank H. Collins, Ph.d.Professor, George and Winifred Clark Chair in Biological Sciences, University of Notre dame, IN
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The genomes of more than twenty arthropods have been sequenced to some level of completion, and a variety of different databases and associated genome browsers have been developed for presenting these genomes to the scientific community. The most widely used approaches include (i) the Chado schema and GBowse genome browser produced by the model organism database community, (ii) the Ensembl system developed and used by the European Bioinformatics Institute, (iii) the University of California at Santa Cruz system, and (iv) the Entrez genome browser system of NCBI. This talk will review the attributes of these different approaches to genome analysis and presentation.
Arthropod databasesABSTRACT:
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Dr. Collmer’s goal is to understand the molecular mechanisms that enable bacteria to attack plants. Much of his current work is focused on Pseudomonas syringae pv. tomato DC3000, which is a pathogen of tomato and the model plant Arabidopsis thaliana. Like many host-specific plant pathogens, P. syringae is a “stealth” parasite that can multiply for several days in host tissues before symptoms, such as necrotic spots, develop. Dr. Collmer has learned that the ability of P. syringae to multiply in the intercellular spaces of plant leaves and cause disease is dependent on a “type III” secretion system that injects
virulence effector proteins into host cells. Variants of this injector system are also used by many important animal pathogens (for example, Yersinia pestis, the plague pathogen) to deliver their virulence proteins. How many effector proteins are injected by P. syringae, what do they do inside plant cells to subvert host metabolism, and what other adaptations does this sophisticated parasite have for life in plants? To answer these questions, Dr. Collmer and a team of researchers from The Institute for Genomics Research, Cornell; Boyce Thompson Institute for Plant Research; and universities in Kansas, Missouri, and Nebraska have determined and annotated the complete sequence of the P. s. tomato genome, and they are developing a variety of biochemical, genetic, and cell biological tools to support a genome-wide study of virulence mechanisms. A more complete description of the objectives and progress of the P. syringae functional genomics project can be found at http://pseudomonas-syringae.org.
Alan Collmer, Ph.d.Professor, department of Plant Pathology, Cornell University, NY;Fellow, American Academy of Microbiology; Fellow, American Phytopathological Society
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Microbial pathogenesis is a highly multifactorial process involving seemingly redundant factors that have overlapping functions and are often difficult to identify because of their subtle contributions to virulence. Genomics has revolutionized the study of microbial pathogenesis by enabling iterative bioinformatic/experimental approaches that can reveal complete sets of virulence factors for careful analysis. Pseudomonas syringae pv. tomato DC3000 provides an excellent example of this approach. P. syringae is a bacterial pathogen of plants divided into ca. 50 pathovars based on host specificity. P. syringae virulence is dependent on its ability to inject 28 “effector” proteins into host cells via a type III secretion system (T3SS). The effectors and multiple accessory proteins that assist in the effector translocation process in DC3000 were identified based on sequence patterns associated with their expression and targeting to the T3SS. Experimental tests were then used to refine the bioinformatic searches and to validate effector candidates. Techniques were developed to construct polymutants lacking multiple effectors and to explore the ability of effectors to suppress plant defenses in novel gain-of-function assays. These experiments have yielded new insights into how P. syringae strains defeat plant defenses and how the interactions of effectors with plant defense systems control host specificity. Our functional genomics work also highlights the importance of fostering community effort toward understanding complex biological systems. This work will be discussed in the context of parallel advances made with Oomycetes and other important pathogens of plants.
Genomics of plant pathogensABSTRACT:
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Speakers
Dr. Ecker is a professor in the Plant Molecular and Cellular Biology Laboratory and the director of the Genomic Analysis Laboratory at The Salk Institute for Biological Studies in La Jolla, CA. He earned his Ph.D. in microbiology at the Pennsylvania State University College of Medicine and carried out postdoctoral studies with Ronald Davis at the Department of Biochemistry at Stanford University. He served on the faculty at the University of Pennsylvania (1987-00) before joining The Salk Institute for Biological Studies (2000). His research on the gaseous plant hormone ethylene has yielded basic
insights into the mechanisms of plant growth control and its application has resulted in technologies that delay fruit ripening and disease processes. His laboratory participated in mapping and sequencing of genome of the Arabidopsis thaliana and he continues to explore the encyclopedia of DNA elements in Arabidopsis through the development and application of technologies for genome-wide and systems biology analysis of plant gene function. He has been the recipient of multiple honors, including: the Kumho Science International Award in Plant Molecular Biology and Biotechnology (2001), the International Plant Growth Substances Association Distinguished Research Award (2004), and the American Society for Plant Molecular Biology Martin Gibbs Medal (2005). He was chosen as the Scientific American 50: Research Leader of the Year in Agriculture in 2004, and he was elected to the U.S. National Academy of Sciences in 2006. In 2007 he received the John J. Carty Award for the Advancement of Science from the U.S. National Academy of Sciences. Professor Ecker is an associate editor of PLoS Genetics and an editor of the Proceedings of the National Academy of Science. He currently serves as president of the International Society for Plant Molecular Biology.
Joseph Ecker, Ph.d.Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, San diego, CA; Member, National Academy of Science
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A precise and comprehensive understanding of DNA sequence and epigenetic variation in natural populations of a species will be essential for elucidating the basis of phenotypic variation. We have applied oligonucleotide tiling microarrays and next-generation ultra-high throughput DNA sequencing methods to identify DNA sequence and epigenetic variation in wild strains (accessions) of Arabidopsis thaliana that were chosen for maximal genetic diversity. The entire Arabidopsis Genome Initiative (AGI) reference genome sequence of A. thaliana Col-0 was tiled on high-density tiling microarrays at single-base resolution using more than a billion 25 base oligonucleotides. The arrays were hybridized with genomic DNA from 19 accessions, isothermally amplified DNA to minimize ascertainment biases. In addition, whole genome sequencing using a Solexa/Illumina Genetic Analyzer allowed more complete sequence coverage of the genomes of several strains (Col-0, Ler-1, Cvi-0, etc.), allowing independent assessment of the quality of the AGI Sanger and Perlegen array-based genome sequences. The degree of polymorphism and types of genes that harbor major effect polymorphisms in natural populations will be described. We are also using next-generation sequencing technology to develop methods for creating large populations of T-DNA insertion mutants in diverse genetic backgrounds as well as for determining the extent of epigenetic diversity in wild accessions. To understand genetic and epigenetic diversity and link the difference to important plant traits, a proposal for cost effective re-sequencing of 1,001 or more Arabidopsis genomes will be discussed. When coupled with community/worldwide phenotypic screens for traits of interest (e.g., drought tolerance, nitrogen utilization efficiency, increased biomass, enhanced disease and stress tolerance, etc.), this database would allow realization of whole genome association mapping studies and provide an unprecedented resource for understanding the genetic/epigenetic basis of phenotypic variation and a fundamental knowledge about important agricultural plant traits.
Mapping genotype into phenotype: The continuing need for a reference plant for the advancement of agriculture
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Nathan has been with the National Corn Growers Association (NCGA) since 2004 and currently leads that organization’s Research and Business Development (R&BD) activities. NCGA’s R&BD encompasses direct development of new technologies aimed at increasing the demand for corn, supporting technology development of new biotech and conventional methods to reduce input costs and create value added output traits, and political support and education of policy makers on basic research needs for the maize research community.
Under the Research and Business Development arm of NCGA, Nathan and a team of directors address issues including ethanol, production and stewardship, biotechnology, regulatory issues, economics, energy, and rural development. Responsibility is also shared with the Chesterfield based Communications and Member Services department and the Public Policy department based out of Washington D.C. All three divisions of NCGA are focused “to create and increase opportunities for corn growers.” Prior to his employment with NCGA Nathan worked in the Bio-Pharmaceutical industry managing Research and Development , Production and Process Development of pharmaceuticals, pharmaceutical exipients, custom bulk molecule synthesis, protein/DNA extraction and purification. His post-undergraduate work included involvement with the private sector effort on sequencing the human genome. Nathan graduated from the University of Illinois with a B.S. in biology and completed his masters in business administration (MBA) at Southern Illinois University Edwardsville.
Nathan Fields, Ph.d.director of Research and Business development, National Corn Growers Association, Chesterfield, MO
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The National Corn Growers Association Research and Business Development Team has maintained an active role in communicating with federal agencies and policy makers our research priorities from the producers perspective. With the growth of the National Plant Genome Initiative over the last ten years, the 2007 Farm Bill under development, and renewable fuels dominating agricultural press, we are more active than ever in pushing for basic research dollars. This presentation will be a review of NCGA research polices, the current status of several research programs within the federal government, current analysis of the new farm bill and the priorities set forth by our grass roots base.
Agricultural genomics and stakeholder prioritiesABSTRACT:
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CURRENT APPOINTMENT
• Professorial fellow in animal genetics, faculty of land and food
resources, University of Melbourne
• Victorian Department of Primary Industries, Attwood
TERTIARY EDUCATION AND ACADEMIC
QUALIFICATIONS
• 1968-72: B.V.Sc. (Hons), University of Melbourne
• 1973-77: Ph.D., University of Melbourne
Thesis Title: Genetic improvement of guide dogs for the blind.
CURRENT RESEARCH
• Application of genomics to genetic improvement of livestock. I lead a team of 20 working on dairy
cattle genomics, and I am program manager for the Beef Cattle CRC underpinning sciences
program.
• Selection of dairy cattle to maximise profitability.
AWARDS AND INVITATIONS TO SPEAK AT CONFERENCES
• 1999 - Urrbrae award for contribution to Australian agriculture
• 2003 - American Dairy Science Association, International Dairy Production Award.
• 2005 - Fellow of the Association for the Advancement of Animal Breeding and Genetics
• 2006 - Australian representative to international committee running the world congress on
genetics applied to livestock production
MEMBERSHIP OF INDUSTRY AND SCIENTIFIC BOARDS AND SOCIETIES
• Chairman, Genetics Committee, Australian Dairy Herd Improvement Scheme
• Member, Meat Livestock Australia national beef cattle genetics advisory committee
• Member, INTERBUL scientific advisory committee
M.E. Goddard, Ph.d. Professorial Fellow in Animal Sciences, Faculty of Land and Food Resources, University of Melbourne, Parkville, Victoria, Australia
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The variation in DNA sequence within and between our modern cattle breeds is a result of their evolutionary history and, therefore, can be used to infer aspects of that history. Assuming most polymorphisms are nearly neutral, the rate of heterozygous bases in a random animal depends on the past effective population size (Ne) and the mutation rate. The average heterozygosity is at least 0.0005 per base. Assuming a mutation rate of 10-8 per generation, this implies that Ne > 104, if it was constant. However, past Ne is most unlikely to have been constant, so we need a method to estimate Ne at different times in the past. Linkage disequilibrium (LD), as measured by the r2 statistic, also depends on past Ne, but, because it is eroded by recombination, the higher the recombination rate (c) between the markers, the shorter the time in the past it reflects. Using this relationship, we have estimated that Ne has decreased from between 104 and 105 before domestication to 103 after domestication 10,000 years ago to 102 in modern breeds such as Holstein. We can also use LD between breeds to estimate the time of their divergence. Using a data set of 10000 SNPs genotyped in both Angus and Holstein cattle, we estimated their time of divergence to be approximately 300 generations ago. Since this time, Ne in both breeds has declined from about 2000 to 100 and both these sources of information together predict that both breeds have experienced inbreeding of F=0.3 since divergence. This can be compared with an estimate of inbreeding made from differences in allele frequency of F=0.16. These estimates of Ne since domestication imply that Bos taurus cattle have experienced inbreeding (F) of approximately 0.5 since domestication. This conclusion is supported by the finding that mutant alleles at polymorphic sites are almost as common as ancestral alleles, where mutant and ancestral alleles were distinguished by genotyping species related to B. taurus, i.e., yak, banteng and bison. This information also showed that about 10% of B. taurus polymorphisms have existed since these species shared a common ancestor with B. taurus over1 million years ago. For this to occur, the Ne in cattle over the last 1 million years must have been >50,000. The LD information, prevalence of ancestral and mutant alleles, and heterozygosity levels support a hypothesis that the Ne of B. taurus cattle has declined from 50,000 before domestication, to 1000-2000 after domestication, to 100 in modern breeds. Consequently, many of the neutral polymorphisms found in cattle today are very old, but they represent only a fraction of the variation that existed before domestication. This reduction in population size has caused a decrease in the effectiveness of natural selection, leading to an increase in the frequency of DNA substitutions that change an amino acid, most of which are slightly deleterious.
New knowledge of the evolution of domestic cattle from genomics
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• B.S. in agricultural science, University of Illinois • M.S. in crop science, North Carolina State University • Ph.D. in plant breeding and plant genetics, University
of Wisconsin• Postdoctoral research associate in maize genetics,
University of Illinois
Dr. Goldman joined the faculty of the College of Agricultural and Life Sciences at the University of Wisconsin-Madison in 1992. Currently, he is the vice
dean of the college as well as a professor in the Department of Horticulture. His teaching responsibilities include two courses in plant breeding and genetics, and a course on vegetable crops. He is responsible for breeding and genetic research of cross-pollinated vegetable crops, primarily carrot, onion and beet.
Irwin Goldman, Ph.d.Vice dean, College of Agricultural and Life Sciences; andProfessor, department of Horticulture, University of Wisconsin-Madison, WI
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The land-grant concept presented to the American public for the first time the radical idea that higher education should be practical. One hundred forty-five years of this practicality in more than 100 land-grant institutions across the United States has completely transformed the educational landscape in this country. Our land-grants have fostered the growth of many key elements of American society by promoting democracy, engaging citizens in public policy issues, enhancing business, economy, and improved standards of living, bringing scientific agriculture to the forefront, and perhaps most significantly giving a very wide spectrum of students and opportunity to learn and develop their minds. Through this phenomenal period, scientists at land-grant institutions have led technologies forward by being able to combine the power of fundamental inquiry with practical application. The land-grant mission is every bit as relevant today as it was at its inception. The genomic revolution of the past 15 years is a perfect example of how the duality of fundamental knowledge acquisition and practical application can be brought to bear on problems and opportunities that reside in the land-grant context.
Among the many issues facing agriculture and natural resource management in this century, the production of alternative fuels and consequent reduction in harmful greenhouse gases is at or near the top of everyone’s list. The University of Wisconsin-Madison, together with its partner Michigan State University and additional scientific partners at DOE National Laboratories (Pacific Northwest and Oak Ridge National Labs), other universities (University of Florida, Illinois State University, Iowa State University), and biotechnology companies (Lucigen Corporation), has recently been awarded funding from the Department of Energy for the Great Lakes Bioenergy Research Center (GLBRC). The focus of the center will be to conduct fundamental, genomics-based research to remove bottlenecks in the biofuel pipeline. Genomics-based strategies will facilitate development of plant germplasm with improved yields of easily degraded polysaccharides within cell walls and to increase the yields of hydrocarbons in biomass tissues. Genomic technologies will also be crucial in the development of new physical and biological ways to process existing and improved plant biomass, efforts to create novel biological or chemical ways to convert plant material into H2, electricity, or other chemical feedstocks that can replace fossil fuels, and to develop economically viable and environmentally responsive practices for the biomass-to-bioenergy pipeline.
The land-grant tradition would dictate that the GLBRC will be as responsive to the cutting edge of energy technology companies as it is to the traditional constituents of the land-grant institution. Genomic technologies will play a key role in serving the wide spectrum of stakeholders characteristic of our institutions, and be a cornerstone of our success in translating practical knowledge to the people of the U.S.
Leading genomics to impact in the land-grant contextABSTRACT:
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Speakers
Dr. Hoekstra received her B.A. in integrative biology from University of California-Berkeley. She completed her Ph.D. in 2000 as a Howard Hughes Predoctoral Fellow at the University of Washington. For her dissertation, Dr. Hoekstra worked on the evolution of sex chromosome polymorphisms in South American field mice (genus Akodon). For this work, she was awarded the Ernst Mayr Prize from the Society for the Study of Evolution. She then moved to the University of Arizona as a NIH postdoctoral fellow where she studied the genetic basis of adaptive melanism in lava-dwelling pocket mice. This
work has been featured in several textbooks and highlighted in The New York Times. In 2003, she was awarded the Young Investigator’s Prize from the American Society of Naturalists. The same year, she became an assistant professor of biological sciences at University of California-San Diego. In 2007, she moved to Harvard University, where she is a John L. Loeb Associate Professor of Biology in the Department of Organismic and Evolutionary Biology and curator of mamma logy at the Museum of Comparative Zoology. She has recently received a Young Investigator Award from the Arnold and Mabel Beckman Foundation. She also serves as an associate editor for Evolution and is a member of the National Evolutionary Synthesis Center (NesCent) advisory board.
Dr. Hoekstra and her lab study the evolutionary genetics of natural populations. Currently, they are interested in the genetics of adaptation (morphology, behavior, reproduction, and development) and speciation in wild populations. More specifically, their research focuses on understanding how variation is generated and maintained in natural populations with a particular interest in the role of natural selection in shaping adaptive genetic and phenotypic variation. To address these questions, they use an integrative approach combining molecular genetic techniques, theoretical modeling, experimental tests, breeding studies, and field work.
Hopi Hoekstra, Ph.d.John L. Loeb Associate Professor of Biology, department of Organismic and Evolutionary Biology, Harvard University, MA
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Ecological genetics has entered the genomic era, with one of its main goals to identify genes underlying ecologically important traits. In this talk, I will discuss several ways to connect genotype to phenotype in non-model systems. I illustrate these approaches using natural populations of mice (Peromyscus polionotus) that have recently colonized the sandy dunes of Florida’s Gulf and Atlantic Coasts. In this novel environment, these “beach mice” have evolved many new traits relative to their mainland counterparts, most strikingly a unique pigmentation driven by natural selection for crypsis. I first discuss how we identified the genes responsible for this rapid color adaptation and then describe how this approach can be extended to other phenotypic traits (from morphology to behavior) and to other species. In particular, I will draw parallels to studies on both wild plants and to agricultural species to highlight both recent successes and ongoing challenges. Finally, I will examine the question of what having “the genes” in hand can really tell us about ecology and adaptation in nature.
Identifying ecologically important genesABSTRACT:
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Speakers
Dr. Liu is currently a Distinguished Alumni Professor in Genomics and director of the Aquatic Genomics Unit at Auburn University. He obtained his Ph.D. in 1989 at the University of Minnesota, and since has been conducting research in the area of aquatic genomics. His research has been funded mostly by USDA-NRI and Sea Grant, as well as NSF and several other federal agencies. He is the editor for Marine Biotechnology and serves on editorial board for Aquaculture, Animal Biotechnology, and Reviews in Aquaculture. He is serving as the aquaculture coordinator for the U.S . National Animal Genome Project and serving
on the National Scientific Advisory Panel for the Oceans and Human Health Initiative. He has served on many expert panels for many international and national activities. He is a member of the steering committee of the International Network on Genetics in Aquaculture (INGA). He has published more than 160 peer reviewed papers and written many reviews and book chapters. He is the editor as well as an author of thirteen chapters for Aquaculture Genome Technologies. His research objectives are to use genomic approaches to improve performance traits of catfish. His major research accomplishments to date include development of tens of thousands of molecular markers, construction of a genetic linkage map of catfish, construction of a BAC contig-based physical map of catfish, generation of hundreds of thousands of ESTs of catfish and oysters, development and application of microarray technology in catfish, and development of genetically improved, synthetic catfish breeds by using channel catfish and blue catfish inter specific hybrids.
zhanjiang (John) Liu, Ph.d.distinguished Alumni Professor in Genomics; and director of Aquatic Genomics Unit, department of Fisheries and Allied Aquacultures, Auburn University, AL
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Major progress has been made in aquaculture genomics, in spite of the late start. To date, framework genetic linkage maps have been constructed for major aquaculture fish and shellfish species; BAC-based physical maps have been constructed in Atlantic salmon, tilapia, and channel catfish. Integration of genetic linkage and physical maps are underway for Atlantic salmon and catfish. Large numbers of ESTs have been generated for several major aquaculture species, including catfish, Atlantic salmon, rainbow trout, tilapia, oysters, and shrimps. Microarray platforms have been developed for the analysis of genome expression in salmonids, catfish, oysters, and the shrimps. Genome repeat structures are well studied in catfish, salmonids, and several other aquaculture species, laying grounds for whole genome sequencing. A draft genome sequence is being produced for tilapia, and white papers have been developed advocating whole genome sequencing for the genomes of Atlantic salmon, rainbow trout, catfish, oysters, and shrimps.
In spite of the above progress, aquaculture genomics is facing great challenges. The greatest challenge is not technical but financial. As large numbers of species (over 300 species) are involved in aquaculture, genome studies of aquaculture species require great efficiency. Genome studies in aquaculture species, however, also have many advantages. The high fecundity of many aquaculture species allows production of large full-sib and half-sib families suitable for analysis of performance traits. Large resource families allow heavy selection pressure to be applied that not only enhance likelihood for the detection of linkage disequilibrium, but also allow rapid progress in breeding programs. As the focus of aquaculture genomics should be on performance traits-related issues, efficient and accurate phenotypic evaluations and genotyping systems are crucially important. To meet these challenges, greater efforts in phenomics must be devoted, including development of biochemical and molecular indicators of performance traits. Efficient marker platforms must be developed, especially the SNP platforms. As a nation, we must continue the course of generating draft genome sequences for major agricultural species, including aquaculture species, and yet much can be accomplished using existing genome resources and innovative technologies such as the 454 and Solexa sequencing technologies. Once the efficient SNP platforms are developed, when coupled to the use of large resource families, rapid progress is anticipated in aquaculture genomics toward the development of genome-based technologies for practical applications and genetic enhancement using marker-assisted selection and other related technologies.
Status and challenges of aquaculture genomics: Making reactions work without reagents
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Speakers
Dr. McDonald is chair of the School of Biology at the Georgia Institute of Technology and chief scientific officer of the Ovarian Cancer Institute in Atlanta. Prior to assuming his current positions, Dr. McDonald was a faculty member in the Department of Genetics at the University of Georgia, serving as department head from 1998-04. He received his Ph.D. in genetics from the University of California-Davis in 1978 and was an NIH postdoctoral fellow at the University of California-San Diego (LaJolla) from 1979-80 before taking a faculty position at Iowa State University in 1980. Dr. McDonald
is former editor of the journal Genetica and of several books, including two on the role of transposable elements in evolution. He is author of over 100 scientific publications and co-author of the genetics textbook The Science of Genetics (Saunders Press). In 2004, Dr. McDonald was elected a fellow of the American Association for the Advancement of Science.
John F. Mcdonald, Ph.d.Chair, School of Biolog, Georgia Tech University, GAChief Scientifc Officer, Ovarian Cancer Institute, Atlanta, GA
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Once considered “junk DNA” of little or no biological significance, retrotransposons have, in recent years, taken on a new aura of scientific respectability among both molecular and evolutionary biologists. The contribution of retrotransposons to gene and genome evolution has been both direct and indirect. Evidence in support of the direct contribution of retrotransposons to the evolution of genes and their regulation was initially the gratuitous by-product of detailed molecular analyses of individual genes. In recent years, more widespread evidence is emerging from the comparative analyses of sequenced genomes. While the direct contribution of retrotransposons to genome evolution is easier to document, the indirect contribution may have been of equal or greater consequence. By way of example, I will summarize the results of some recently acquired evidence on the direct impact of retrotransposons on human and chimpanzee evolution and on the indirect role of retrotransposons in the evolution of dosage compensation in Drosophila. Some potential implications for agricultural research will be discussed.
Retrotransposons and genome evolutionABSTRACT:
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Speakers
John McLean currently serves as director of the Genomics Technology Program for Monsanto Company, with responsibility for the generation of trait product vectors and quality assurance of transgenic events. He also has matrix leadership of Monsanto’s plant transgenic pipelines (corn, soy, cotton, and canola) and is responsible for pipeline speed, capacity, cost, innovation, data system strategy, and investment. During McLean’s tenure, Monsanto has strengthened its industry-leading ability to discover and test new product candidates.
McLean is a 28-year veteran of Monsanto with broad experience in research, process engineering, business development, business management, information technology, and strategy. He received his M.S. degree in Chemical Engineering Practice from the Massachusetts Institute of Technology and his MBA degree from Washington University. Prior to joining the Biotechnology team in January of 2001, he was the IT lead responsible for building the application and bioinformatics capability integral to Monsanto’s combined Ag and Pharma Genomics initiative. As Director, Strategy and Operations Lead for the Biotechnology research group, McLean accelerated efforts to create value via external collaborations, participated in trait portfolio and enabling technology strategic decisions, and enhanced operational excellence of the global Biotechnology group via redesign of research teams/processes, expansion of patent science, championing innovation and introduction of quality systems (ISO, Six Sigma, and LEAN).
John McLean director, Genomics Technology, Monsanto, St. Louis, MO
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This presentation will provide an overview of Monsanto’s seed and trait product portfolio, focusing on new trait targets in our research pipeline. I will review the modular design and growing capacity of the biotech plant pipelines by which we screen and advance product candidates.
Given this context, the majority of time will be used to discuss our interest in collaborating with land-grant universities to bring new value to agriculture. In reviewing our university relationships, I will encourage discussion on how we can improve collaboration effectiveness, both via research scope selection and partnering processes. Included will be a review of how Monsanto has worked with land-grant universities to negotiate and sign master service agreements (MSAs). Initially used for field trials, many of our university cooperators have taken the MSA use a step further, now using it for service arrangements as well. This is only one way that Monsanto is working daily to become a better research partner.
Industry and land-grant university partnershipsABSTRACT:
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Speakers
Dr. O’Brien has been chief of the Laboratory of Genomic Diversity (formerly Laboratory of Viral Carcinogenesis) at the National Cancer Institute (NCI), National Institutes of Health (NIH), since 1986. Dr. O’Brien is the author or co-author of over 450 scientific articles and the editor or co-editor of fourteen volumes. Dr. O’Brien received his B.S. in biology in 1966 from St. Francis College, which presented him with a Distinguished Alumni Award in 1994. He earned a Ph.D. in genetics from Cornell University in 1971 and served a postdoctoral fellowship at the National Institute of Aging before joining the National Cancer Institute in 1972 .
Dr. O’Brien is internationally recognized for his research contributions in human and animal genetics, evolutionary biology, AIDS, retrovirology, and species conservation. In collaboration with his students, fellows, and colleagues, his list of achievements include: gene mapping of over 100 human genes, including scores of cancer oncogenes; development of the domestic cat gene map as a model for comparative genome analyses; discovery of the remarkable genetic uniformity of the African cheetah, a prelude to genetic assessment of endangered species; solving the century-old evolutionary riddle of the giant panda’s evolutionary history; discovery of epidemic prevalence of feline immunodeficiency (AIDS) virus among wild cat species; and description of the first human gene to affect HIV-1 infection and AIDS progression, CCR5. His group has now identified eight distinct human genetic variants that influence the outcome of exposure to HIV.
Dr. O’Brien was elected to the American Academy of Arts and Science in 1994, to the Explorer’s Club in 1988, and to the Cosmos Club in 1987. He has served as President of the NCI Assembly of Scientists as chairman of the International Committee on Comparative Gene Mapping for the Human Genome Organization (HUGO). He is the editor of Genetic Maps: Locus Maps of Complex Genomes (Cold Spring Harbor Laboratory Press), executive editor of the Journal of Heredity (American Genetics Association), associate editor for Isozyme Bulletin, Genomics, Mammalian Genome, Molecular Phylogenetics and Evolution, and Cosmos.
Stephen J. O’Brien, Ph.d.Chief, Laboratory of Genomic diversity, National Cancer Institute, NIH, Frederick, Md
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The genome sequence (1.9-fold coverage) of an inbred Abyssinian domestic cat was recently assembled, mapped, and annotated with a comparative approach that involved cross-reference to annotated genome assemblies of six mammals (human, chimpanzee, mouse, rat, dog, and cow). The results resolved chromosomal positions for 663,480 contigs, 20,285 putative feline gene orthologues, and 133,499 conserved sequence blocks (CSBs). Additional annotated features include repetitive elements, endogenous retroviral sequences, nuclear mitochondrial (numt) sequences, micro-RNAs, and evolutionary breakpoints that suggest historic balancing of translocation and inversion incidences in distinct mammal lineages. Large numbers of single nucleotide polymorphisms (SNPs), deletion insertion polymorphisms (DIPs), and short tandem repeats (STRs), suitable for linkage or association studies were characterized in the context of the long stretches of chromosome homozygosity. These comparative insights shed new light on the tempo and mode of gene/genome evolution in mammals, promise several research applications for the cat, and also illustrate that a comparative approach using more deeply covered mammals provides an informative, preliminary annotation of a light coverage mammal genome sequence. The applications and potential for the genome sequence in research questions will be discussed.
Comparative mammalian genomics: Evolutionary analyses of felids
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Speakers
Dr. Phillips is Regents Professor and McKnight Presidential Chair in Genomics, University of Minnesota. He earned B.S. and M.S. degrees from Purdue University and a Ph.D. from the University of Minnesota; his postdoctoral training was at Cornell University. Purdue awarded him an honorary doctorate in 2000. He served as chief scientist of the USDA (1996-98) in charge of the National Research Initiative Competitive Grants Program. Awards include fellow of AAAS, ASA, and CSSA, the Purdue University Agriculture Distinguished Alumni Award; the DeKalb Genetics Crop Science Distinguished Career Award; and
the Crop Science Society of America Research Award. Dr. Phillips served as president of the Crop Science Society of America, and as chair of the Council of Scientific Society Presidents and of AAAS Section O (Agriculture, Food, and Renewable Resources). In 1991, he was elected a member of the National Academy of Sciences and is former chair of the Plant, Soil and Microbial Sciences. section. He currently serves on the Scientific Advisory Board of the Donald Danforth Plant Science Center and on the board of trustees of the International Rice Research Institute of the Philippines, and he recently was a non-resident fellow of the Noble Foundation. Dr. Phillips received the 2007 prestigious Wolf Prize in Agriculture in Israel.
Throughout his career, Dr. Phillips has coupled the techniques of plant genetics and molecular biology to enhance our understanding of the basic biology of cereal crops and to improve these species by innovative methods. He is a founding member and former director of the Plant Molecular Genetics Institute of the University of Minnesota and a founder of the Microbial and Plant Genomics Institute. Dr. Phillips teaches a course in plant genetics and is invited to teach it or present the results of his research at numerous university, governmental, and industrial institutions in the U.S. and abroad.
Ronald Phillips, Ph.d.Regents Professor and McKnight Presidential Chair in Genomics, department of Agronomy and Plant Genetics, University of Minnesota, MN;Member, Microbial and Plant Genomics Institute;Member, National Academy of Sciences,
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An applied geneticist is defined as a person who explains their research in terms of the ultimate application, whether the current research is basic or applied. Because 50% of the gains in crop productivity are generally attributed to genetic improvement, any additional knowledge of genetics is important to the applied geneticist. Genomics is providing genetic insights in an unprecedented manner. DNA sequencing increased more than 500-fold during the past 10 years, with an associated reduction in costs. The applied geneticist is now working under a new paradigm, where the complete genetic code of an organism will be known together with the capacity to measure gene expression across the entire genome and knowledge of the function of many if not all of the genes. This opens the possibility of many new approaches, most of which require the coupling of lab and field. Genotyping is of little use to the applied geneticist without efficient and accurate phenotyping.
Many transgenic and non-transgenic methods are evolving, such as marker-assisted selection, RNAi silencing leading to root-knot nematode resistance, reduction of cotton gossypol levels, and cytoplasmic male-sterile lines. TILLing (targeting induced local lesions in genomes) is identifying hundreds of alleles at a locus in wheat, representing more genetic diversity than described for that locus in the past 25 years. The cloning of the Ph1 (Pairing homoeologous) gene will likely lead to controlled recombination in crosses of wheat with wild relatives. Measurement of genetic diversity is marking the bottlenecks in varietal development throughout the years.
Innovative ideas related to human health also will be in the hands of the applied geneticist, such as low linolenic and high omega-3 soybeans, cholera vaccines, human insulin production, low mycotoxin corn, lower allergenic peanuts, high antioxidant activity with cancer-fighting potential, high folate tomato, high vitamin A rice (golden rice), and antibody production. Yield enhancing traits include drought-tolerant crops and the submergence gene in rice, important for flood-prone areas.
Ralph Waldo Emerson said “Do not follow where the path may lead. Go instead where there is no path and leave a trail.” We now can clearly see that the convergence of genomics and the land-grant mission is taking us on a new path.
Genomics for the applied geneticistABSTRACT:
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Speakers
Dr. Rokhsar’s research interests center on collective phenomena and ordering in condensed matter and biological systems. In the past, he has worked on high-temperature superconductivity, quantum antiferromagnetism, the fullerenes, and liquid crystals. His current interests include the theoretical and computational modeling of molecular, cellular, and collective properties of biological systems, as well as the behavior of quantum fluids such as cold atomic gases and high temperature superconductors.
Current projects involve the mammalian visual system, a complex system that is “self-organizing,” in the sense that the connections between cells in the retina and brain arise
spontaneously in the developing animal. These organized connections are not “hardwired” but instead arise from a complex program of intercellular signaling. In particular, as the retina develops, it exhibits spontaneous electrical activity that propagates across patches in a wavelike manner; these waves have been implicated in the formation of ordered maps between the retina and the cortex. In collaboration with neuroscientists Marla Feller and Carla Shatz, Dan Butts and Dr. Rokhsar have developed models for the interactions between cells in the developing retina. Their goal is both to model the specific behavior of the developing ferret retina for close comparisons with experiment, and to use such models to better understand the principles that govern real neural networks and systems.
The three-dimensional structure of a protein is typically specified by its amino acid sequence. This three-dimensional folded or “native” structure, in turn, allows the protein to fulfill its biological function, which may be enzymatic, structural, mechanical, etc. For many proteins, the folded structure is the equilibrium state under physiological conditions, and they are typically stable by 5-15 kT. By heating them, changing the pH, or adding certain chemicals to the water in which they are dissolved, proteins can be unfolded in a “cooperative” or first-order transition. When such unfolded or “denatured” proteins are returned to physiological conditions, refolding typically occurs rapidly (on the order of milliseconds) and reproducibly. How does this process occur? What are the general principles by which proteins can find their stable folded states? How is this information encoded in their sequence? To answer these questions, Vijay Pande, Nik Putnam, Jarrod Chapman, and Dr. Rokhsar are developing and studying models that range from simplified lattice polymers to complete molecular dynamics with solvent, as well as new analysis techniques to characterize the folding process.
daniel Rokhsar, Ph.d.Program Head, Computational Genomics, U.S. department of Energy Joint Genome Institute;Professor, department of Molecular and Cell Biology, University of California-Berkeley, CA
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Status of agricultural genome sequencing projectsABSTRACT:
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Speakers
Dr. Sanderson’s research applies statistical and computational techniques to problems in phylogenetics and evolution. Until recently, the empirical side of these studies focused on specific taxa: legumes (especially Astragalus and relatives), angiosperms, and seed plants. In the last few years, however, his research has shifted toward computational phylogenetic problems at the scale of the “tree of life,” with an empirical emphasis on all green plants. Across these various levels ,he has been attracted to phylogenetic problems that pose methodological obstacles or present unusual quantitative challenges. The same is true of the evolutionary problems he has addressed, most of which concern quantitative analyses of rates of molecular evolution (especially in relation to divergence time problems) or taxonomic diversification.
In the next five years, Dr. Sanderson will concentrate on computational problems aimed specifically at developing software tools to mine the sequence databases for phylogenetic analyses. GenBank archives data on more than 100,000 species (a surprisingly large fraction of described species diversity), but it is extremely “sparse,” composed almost entirely of small blocks of homologous data across relatively small sets of organisms. His lab has begun to outline strategies for optimal extraction of complete phylogenetic data sets from such sparse databases (Sanderson et al., 2003; Sanderson & Driskell, 2003) and has worked extensively on the problem of assembling the trees that result from these discrete analyses via supertree methods. The main goal of the research is to use these and similar algorithms to characterize the potential phylogenetic information content of sequence databases and to develop software to make “high-throughput” phylogenomics a reality.
Michael J. Sanderson, Ph.d.Section of Evolution and Ecology, University of Arizona, Az and University of California-davis
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Genomic sequence data is providing new sources of information to reconstruct evolutionary relationships of plants and infer the processes responsible for their diversity. Although methods of phylogenetic inference are well suited to comparative sequence data, the scale of the data sets emerging from genome projects and the peculiarities of genome structure (such as repeated genome duplications in plants) apparent at this scale present new challenges to these efforts. Using exemplar data sets from angiosperm EST libraries, BAC-end sequencing projects, and data mining surveys of GenBank, I describe some of the problems and prospects of using such data to improve understanding of plant phylogeny. Significant obstacles common to all types of phylogenomic sets include homology assessment, treatment of orthology-paralogy relationships, and fragmentation of data into subsets with heterogeneous signals. Two that will be highlighted in detail are the proper incorporation of gene and genome duplication patterns into phylogenetic inference procedures and the accurate resolution of conflicting gene trees stemming from the confounding processes of divergence, introgression, and lineage sorting in closely related plant species. Although genome scale data will undoubtedly provide the power to resolve among distinct historical explanations, they will require concomitant advances in theory and algorithms. At present, many proposed solutions are highly experimental and await much needed work to validate them in the context of emerging data sets.
PhylogenomicsABSTRACT:
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Speakers
Dr. Schnable received his BS from Cornell University in 1981 and was awarded a PhD from Iowa State University in 1986 for his studies of the Mu transposon with Peter Peterson. Following a post-doctoral appointment with Heinz Saedler at the Max Planck Institute in Cologne, he was appointed to the faculty at Iowa State University in 1988. He is currently a professor in the departments of Agronomy and Genetics, Development & Cell Biology. He also serves as the Associate Director of Iowa State University’s Plant Sciences Institute and as the founding director of ISU’s Center for Plant Genomics.
Dr. Schnable manages a vigorous research program that emphasizes interdisciplinary approaches to understanding plant biology. His own expertise is in the areas of genetics, molecular biology and genomics, but he collaborates with researchers in diverse fields, including biochemistry, plant breeding, plant physiology, bioinformatics, computer science and engineering. His wide-ranging research interests include heterosis, meiotic recombination, cytoplasmic male sterility and the development of new genomic technologies and bioinformatics approaches to understanding the maize genome.
Dr. Schnable serves on variety of scientific advisory boards and is an elected member of the American Association for the Advancement of Science Section Committee of the Agriculture, Food and Renewable Resources Section and is chair of the Maize Genetics Executive Committee.
Patrick Schnable, Ph.d.Associate director, Plant Sciences Institute; director, Center for Plant Genomics; and Professor, department of Agronomy, Iowa State University, IA
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Investments in genomics are advancing agricultural research. Yet Federal funding for agricultural genomics research is in a state of flux. Interests in biofuels have created new funding opportunities at the DOE and other agencies. The National Research Council is reviewing the National Plant Genome Initiative, including the NSF Plant Genome Program, which over the past decade has transformed the agricultural genomics landscape. Changes in the USDA-NRI program will also be reviewed. Central to these discussions are the roles of model species, the balance between large centralized projects versus individual investigator projects, and overall funding levels for agricultural genomics research.
Setting federal agricultural genomics research prioritiesABSTRACT:
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Speakers
Dr. Schook attended Albion College and received his Ph.D. from Wayne State School of Medicine. After postdoctoral training at the Institute for Clinical Immunology in Switzerland and the University of Michigan, he has held faculty positions at the Medical College of Virginia and the University of Minnesota. He is currently professor of animal sciences, pathobiology, nutritional sciences, and surgical oncology and serves as the theme leader for regenerative biology and tissue engineering at the Institute for Genomic Biology, University of Illinois at Urbana-Champaign. He is a recipient of NIH, Swiss National Fund and Pardee Fellowships, was named a UIUC University
Scholar, received the Funk Award for Meritorious Achievements in Agriculture, the H. H. Mitchell Award for Graduate Teaching and Research, and the Pfizer Animal Health Research Award, and is an elected fellow of the American Association for the Advancement of Science. He has also been appointed a Fellow at the National Center for Supercomputer Applications and the Academy for Entrepreneurial Leadership, and has an affiliate faculty appointment at the Beckman Institute for Advanced Science and Technology.
He currently serves on the board of directors for the Illinois Biotechnology Organization and the Agricultural Biotechnology International Conference Foundation and was formerly on the Governing Board on Food and Agriculture at BIO. Dr. Schook has also served in several key leadership roles at the USDA and NRC in animal genomics, and chairs the executive steering committee of the Alliance for Animal Genome Research, and is project director for the International Swine Genome Sequencing Consortium.
His scholarly activities include more than 200 publications and 6 edited books, and, he is the founding editor of Animal Biotechnology. He has given over 175 seminars and presentations to international congresses and universities around the world. In addition to serving as the major advisor to 11 M.S. and 19 Ph.D. students, he has mentored 15 postdoctoral fellows and 25 undergraduate students. He has received over $20 million in sponsored research from government and industry sources, and his research focuses on genetic resistance to disease, the interactions of nutrition on innate immunity, and using genomics to create animal models for biomedical research.
Lawrence Schook, Ph.d.Professor of Comparative Genomics, Gutgsell Endowed Chair; and Professor of Pathobiology, College of Veterinary Medicine, University of Illinois Urbana-Champaign, IL; Professor of Surgical Oncology, College of Medicine, University of Illinois at Chicago, IL; Theme Leader (Regenerative Biology and Tissue Engineering), Institute of Genomic Biology; Fellow, American Association for the Advancement of Science
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Biomedical research utilizes animal models to elucidate human disease processes at the cellular and molecular level, and for the development of new therapies. Traditionally, mammalian models have been limited to the mouse, primarily because of well characterized genetic lines and the ability to manipulate the genome to directly test hypotheses regarding casual mutations and disease phenotypes. The emerging availability of genome sequences of other mammals (bovine, canine, equine, feline, and porcine) now permits utilization of the mammal in which the phenotype best approximates the human condition. Equally important is the use of somatic cell nuclear cloning coupled with targeted germline manipulation to create animals to resolve the molecular mechanisms of the disease state.
The pig has emerged as an important biomedical mammalian model due to its physiology which is close to humans; access to its genomic sequence; and the ability to perform targeted genetic manipulation using fetal fibroblast lines in conjunction with cloning by nuclear transfer. Three examples will be presented. The first will demonstrate the utility of a porcine genetically defined tumor model that recapitulates human tumorgenesis; secondly, using pigs with genetic risk factors for development of cardiovascular disease as a function of nutrition; and thirdly, characterizing alternative splice variants associated with neurological disease. These examples were selected based on the observation that current existing mouse models do not demonstrate the same phenotypes observed in human patients. Finally, the use of technologies (recombineering) to utilize genome information to create appropriate animal models will be illustrated.
dNA-based animal models: Creating the sppropriate vlinical phenotypic model
ABSTRACT:
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Speakers
At the University of Wisconsin over the past two decades, Dr. Sussman has become recognized as a leading expert on signal transduction and genomics in plants. His research interests have focused on using the model higher plant, Arabidopsis thaliana, for understanding the role of plasma membrane proteins in signal transduction and solute transport. His laboratory was the first to report on unique protein kinases found only in plants and protists and on the plasma membrane proton pump, which provides the driving force for the uptake of all nutrients. To help understand the in situ role played by these important proteins, his laboratory has pioneered the development of
genome-wide reverse genetics techniques. Specifically, they have utilized an insertional mutagenesis scheme to isolate “knockout” plants, starting with the sequence for any one of the ca. 30,000 genes in Arabidopsis. For example, recent results from Dr. Sussman’s lab demonstrate that the plant homologue for a brain potassium channel is performing a nutritional role in plants, i.e., is responsible for the uptake of potassium from soil.
More recently, Dr. Sussman has been developing new genomic technology instrumentation. For example, together with Prof. Franco Cerrina in the College of Engineering, Dr. Sussman is codeveloper of a new instrument known as a MAS (Maskless Array Synthesizer), which makes “gene chips” that can analyze hundreds of thousands of genes at once. The MAS is unique because it eliminates the requirement for expensive masks used in traditional DNA chip technology, thus making this elegant technology accessible to all scientists. Another recent body of work concerns using isotope-assisted tandem mass spectrometry to analyze the metabolome and phosphroteome of mutant plants and animals.
Dr. Sussman’s awards have included a Fulbright research fellowship for a sabbatical in Belgium, a McKnight Foundation award, and recently, a UW-Madison WARF Kellett Mid-Career Award. In 1996 Dr. Sussman was appointed Interim Director of the UW Biotechnology Center (UWBC), and in 1997, he was appointed as director. The UWBC is a campuswide facility devoted to research, outreach, and service in the area of biotechnology and genomic science and instrumentation. UWBC currently has an operating budget of approximately $8 million per year and 100 employees.
Michael Sussman, Ph.d.Professor, department of Biochemistry, and director of U.W. Biotechnology Center, University of Wisconsin, WI
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Recent advances in DNA sequencing and DNA chips are providing a “democratization” of genomic technologies, in that they are placing in the hands of individual laboratories and scientists sophisticated genomic tools that used to only be available through large core facilities. In this talk, Dr. Sussman will describe some of these new technologies as well as others that are on the cusp of success. For example, recent gene synthesis from oligonucleotides has become more commonplace and is available through the private sector or in individual laboratories via purchase of synthetic oligonucleotides. However, these procedures are still costly and time consuming, with a typical gene costing at least 50 cents per base pair, and three weeks delivery time. By eluting oligonucleotides from de novo-synthesized, high-density oligonucleotide arrays, there are opportunities for reducing the price of gene synthesis by one or two orders of magnitude. If these succeed, the need to perform time consuming, enzyme-based, cut and paste methods for DNA cloning could be greatly reduced or eliminated. Other advances in mass spectrometric and NMR-based analyses of the metabolome will also be described in the context of a systems biology approach for linking the metabolome and transcriptome in a comprehensive and experimentally determined manner. Identifying the 30,000 or so small molecules comprising the plant metabolome may be as important a goal for future progress as sequencing DNA was for genomics.
Next generation genomic technologiesABSTRACT:
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Speakers
CAREER HISTORY
• 2007-present: Functional Leader for Seeds & Traits R&D
• 2004-07: Seeds & Traits GBU R&D leader; functional leader
for Breeding and Trait Genetics & Technologies
• 2002-03: Seeds GBU R&D Leader; functional leader for
Breeding and Trait Genetics & Technologies
• 1998-01: Global leader for Trait Development and Plant
Breeding (Plant Breeding added fall 1999)
• 1997 - 1998: Field Development Leader for Biotechnology
and Plant Genetics, responsible for Supercede corn and Nexera
canola breeding programs
• 1988-96: Director, Crop Research, United AgriSeeds/DowElanco, member of management staff
of United AgriSeeds
• 1986-88: Director, Plant Breeding, United AgriSeeds
• 1982-84: Corn breeder, Southwest France, Ciba-Geigy
COMMUNITY, INDUSTRY & CORPORATE LEADERSHIP ACTIVITIES
• Chair American Seed Trade Assocation Corn Variety Identification Subcommittee
• Dow AgroSciences Sangamo Steering Team
• Board of Directors Illinois Foundation Seeds
• Co-chair PBI (Plant Biotechnology Institute) Alliance with Dow AgroSciences
• Dow AgroSciences R&D Management Team
EDUCATION
• University of Minnesota, St. Paul, MN, Ph.D. in Plant Breeding, 1982
• University of Minnesota, St. Paul, MN, M.S. in Cytogenetics, 1980
• Hamline University, St. Paul, MN, B.A. in Chemistry, 1975
• President’s Scholarship Program, National Merit Scholar, Phi Beta Kappa
Steve Thompson, Ph.d.Global Leader, Seeds & Traits R&d, dow AgroSciences, LLC, Indianapolis, IN
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New genomic tools promise to revolutionize plant breeding, bringing power and precision to create and manipulate genetic variability. Plant breeding is grounded in fields such as Mendelian genetics, cytogenetics, quantitative genetics, plant physiology, and biochemistry that can be considered ancestors of plant genomics. Advances in molecular biology and information technologies associated with genomics have fueled advances in breeding.
Many of today’s breeding tools are of recent vintage. The first papers about the use of isozymes to assess genetic diversity appeared in the 1980s. Since then, marker systems and their applications have evolved as new technologies, such as restriction enzymes and PCR, have become available. The uses of molecular markers for germplasm characterization and the introgression of simply inherited traits are firmly established. We are now tackling complex traits.
Cytogenetics and quantitative genetics have been revitalized by advances in genomics. Now more than ever people understand the importance of crop germplasm and the use of wild relatives and unadapted germplasm in crop improvement. Understanding genomic relationships between crops and their relatives enables more effective exploitation of these sources of useful variability. Densely saturated genetic/physical maps enable the precise transfer genes from wild relatives while minimizing loss of fertility and other penalties associated with residual genome segments. Knowledge of gene function gained through genomic technologies such as activation tagging allow us to develop metabolic models that explain phenotype in place of the simplifying assumptions of quantitative genetics, such as independent, anonymous genes of equal effect.
Variability created within plant genomes via mutagenesis and transformation has been from random genomic events. Future manipulations will be guided by the comprehensive knowledge of genome structure and function, and new genomic technologies such as zinc finger-mediated gene targeting will enable us to make precise changes in existing genes and regulatory elements.
A comprehensive knowledge of genome structure and function will help address the BIG questions of plant breeding concerning the nature of GxE, heterosis, combining ability, and epistasis. Answers to these questions and the ability to harness the potential of plants will require data collection from thousands of progenies grown at hundreds of locations and sophisticated algorithms for analysis and decision making enabled by massive data-crunching capabilities. This computational power, together with the ability to make precise genomic changes, provides hope that plant breeding will be able to keep pace with accelerating societal needs.
Genomics and plant breeding: Past, present, and futureABSTRACT:
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Speakers
Dr. Womack holds the title of Distinguished Professor at Texas A&M University and is the W. P. Luse Professor of Pathobiology in the College of Veterinary Medicine. He is a member of the faculty of Genetics and holds a joint academic appointment in the Department of Medical Biochemistry and Genetics. He is director of the Center for Animal Biotechnology and Genomics. Dr. Womack holds degrees from Abilene Christian University (B.S.1964) and Oregon State University (Ph.D.,1968). He serves as coordinator for the USDA-NRSP8 Cattle Genome Program and has served as President of the
International Society for Animal Genetics, the American Genetics Association, and the Texas Genetics Society. He is a member of the National Academy of Sciences USA, a fellow in the AAAS, and recipient of the 1994 CIBA Prize for research in animal health and the 2001 Wolf Prize in agriculture. He has published, with students and associates, more than 300 peer-reviewed articles in scientific journals. His research interests are comparative genomics, mapping the bovine genome, and the genetic basis of disease resistance in mammals.
James E. Womack, Ph.d.distinguished Professor, department of Veterinary Pathobiology, Texas A&M University, TX;Fellow, American Association for the Advancement of Science; Member, National Academy of Sciences
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Approximately one year ago, the Bovine Genome Sequencing Project (http://genome.gov/12512284) released the third version of the bovine genome assembly, Btau_3.1, which is a 7.15X mixed assembly that combines whole genome shotgun (WGS) sequence with BAC sequence. The sequence, predominantly from a Hereford female, is available in GenBank, EMBL, and DDBJ. Sequencing skims for single nucleotide polymorphism (SNP) discovery were generated from random shotgun libraries from individual animals of Holstein, Angus, Brahman, Limousin, and Jersey breeds.
While it is still early to evaluate the impact of the availability of whole genome sequence on cattle research, several trends have become immediately apparent. For one, the cow is now a full partner in comparative genomic biology, contributing to multi-species comparisons that define evolutionary breakpoints in chromosomes and associated molecular and biological parameters of those breakpoints. omparisons of whole genome sequence between different mammalian species has revealed a large number of conserved non-coding sequences, suggestive of regulatory elements which are potentially important to differential gene expression and trait development. On another comparative front, the bovine represents a highly conserved mammalian clade which includes other species of economic importance, i.e., sheep, goats, buffalo, deer. The cattle sequence, when used with species-specific maps in these other species, provides an excellent tool for improvement of health and productivity of additional livestock species of global significance.
The whole genome sequence provides a catalogue of SNPs which are now available for analysis on chips for high-throughput genome scans and trait mapping. The measure of linkage disequilibrium and the association of haplotypes with phenotypes is an immediate asset to trait mapping and gene discovery. In addition to their value in gene mining, SNP chips will be invaluable to more clearly defining breed origins and diversity.
Impact of sequencing the bovine genomeABSTRACT:
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Efforts to address the emerging educational and technological needs of the genomics era/revolution have resulted in faculty embracing the need for collaboration across disciplines at North Carolina A&T State University. Through a collaborative endeavor of four departments in the School of Agriculture and Environmental Sciences a concerted effort was undertaken to meet the demands for a diverse, well trained workforce. The approach used consisted of several interrelated activities; an identification of areas of interest, the submission of grants for capacity building, increasing the instrumentation and infrastructure, establishment of a bioinformatics learning facility, course development, faculty and staff development, graduate fellowship support and development of a graduate level certificate program in agricultural biotechnology and genomics. These approaches, each in line with School and University-wide initiatives in biotechnology, reflect state wide recognition for workforce training in biotechnology. A multidisciplinary collaboration between animal, plant microbial and social scientists, infused with IT training and an awareness of the land-grant mission is being undertaken. Research experiences and supplemental training in collaboration with genomics and bioinformatics centers supplement on campus activities. These efforts will help advance the integration of new sciences, highly skilled personnel, provide support for biotech research, embellish undergraduate and graduate training, and expedite outreach efforts. The many advantages and positive impacts of this unique collaborative effort in agricultural biotechnology and genomics will be shared.
Contact Information: Millie Worku, Department of Animal Sciences, North Carolina A&T State University, 1601 East Market St, Greensboro, NC 27411. USA; Phone: 336-334-7615; Fax: 336-334-7288; Email: [email protected]
Mulumebet Worku1, Benjamin Gray2, Donald McDowell2
ABSTRACT: Agricultural Education and Collaboration: Addressing Emerging Needs of the Genomics Era/Revolution
1Departments of Animal Sciences, NC A&T State University, Greensboro, NC, USA 2Agribusiness, Applied Economics and Agriscience Education, NC A&T State University, Greensboro, NC, USA
Simple sequence repeats (SSR) have become markers of choice in plant genetic analysis because of their high variability and reproducible patterns. This study was undertaken to evaluate correlation between SSR length and the level of polymorphism in rice (Oryza sativa L.). The rice SSRs were divided into 7 classes based on their repeat length and 201 random SSR primers were developed representing both genic and intergenic regions from the 12 rice chromosomes. The level of polymorphisms with these 201 primers was tested in 8 rice genotypes. There was a direct relationship between the length of the SSR and level of polymorphism in SSR length range of 10-50bp. The highest polymorphism (1.88 alleles per locus) was obtained in the repeat length range below 70 bp, but subsequently there was a decline in the level of polymorphism with higher SSR length of more than 70bp, which stabilized at about 1.6 alleles per locus in the eight genotypes analyzed. Based on the results for 201 SSR primers, 45 additional SSR primers were designed from the genomic sequence of chromosome 11 for validation. It was observed that the average alleles per locus increased to 2.05. The highest level of polymorphism was detected with the primers based on tri- and di-nucleotide repeats. Particularly, the repeat motifs TAA, GTT and ATT showed the maximum polymorphism information content. These findings are important for the identification of polymorphic SSR loci in specific regions of the genome for QTL mapping and marker-assisted breeding.
Contact Information: Harvinder singh, Lab-50,LBS-Building, National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, Pusa, New Delhi, 110012, India; Phone: +91-9810304088; Fax+91-11-25843984; Email: [email protected]
N.K. Singh1, Harvinder Singh2
ABSTRACT: Relationship between the Length of SSR and level of Polymorphism in Rice (Oryza sativa L.)
1Indian Initiative for Rice Genome Sequencing, National Research Centre on Plant Biotechnology,Indian Agricultural Research Institute.New Delhi, 110012, India2Biological sciences, Birla Institute of Technology and Sciences, Pilani, 333031, (Raj.) India.
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Drosophila melanogaster, the fruit fly, and the nematode, Caenorhabditis elegans, have been essential in furthering our understanding of ethanol sensitivity and are classic invertebrate models of alcoholism. Ethanol studies with other invertebrates, such as the honey bee (Apis mellifera), could be invaluable for comparative studies with these animal models. A quantitative trait locus (QTL) mapping experiment was designed to identify loci and candidate genes influencing ethanol sensitivity in honey bees. Ethanol exposure and consumption assays revealed high-sensitive and low-sensitive (tolerant) bee strains in our apiary. We bred these lines together to produce a hybrid F1 queen and mated her back to a parental line. The resulting backcross mapping population was tested for ethanol sensitivity and frozen on dry ice. DNA was extracted from this population and used to produce AFLP (amplified fragment length polymorphism) genetic markers. A linkage map was constructed with over 500 AFLP and STS (sequence-tagged site) markers. QTL mapping software (QTX Mapmanager, MapQTL) was used to statistically associate the inheritance of genetic markers with ethanol sensitivity data in individuals of the backcross population. This process identified three significant QTL from two different linkage groups with LOD (log of odd) scores of 2.35, 2.25, and 1.8 at their peaks. Markers from these QTL were cloned into bacterial vectors and sequenced. BLAST (basic local alignment search tool) was utilized with BeeBase and NCBI databases to localize our QTL regions in the honey bee genome. Ethanol sensitivity candidate genes were identified influencing neuronal membrane permeability and detoxification.
Contact Information: Andrew Ammons, Department of Entomology, Purdue University, 901 W. State St., West Lafayette, IN 47907 USA; Phone: 765-494-6747; Fax: 765-494-0535; Email: [email protected]
Andrew Ammons1, Christine Emore1, Greg Hunt1
ABSTRACT: Quantitative Trait Loci and Candidate Genes Influencing Ethanol Sensitivity in Honey Bees
1Department of Entomology, Purdue University, West Lafayette, IN, USA
By changing leaf chemistry exposure to elevated CO2, an important element of global change, may fundametally alter the relationship between plants and herbivorous insects. Under natural field conditions, elevated CO2 not only increased susceptibility of soybean (Glycine max) to herbivory by the invasive species Japanese beetle (Popillia japonica), but also enhanced the performance of these beetles. To understand the mechanisms governing increased susceptibility to herbivores, we determined gene expression and activity of cysteine proteinase inhibitors (CystPIs) of soybeans grown in under otherwise typical field conditions but with free-air CO2 enrichment. In addition, we determined the expression of genes that regulate the accumulation of the defense hormones jasmonic acid and ethylene. Elevated CO2 not only down-regulated cystpi, lox8, lox7 and acc-s transcripts, but also decreased the activity of CystPIs. Moreover, beetle attack increased CystPIs activity and transcripts on plants grown either on elevated or ambient CO2, but with lower levels of induction in plants grown under elevated CO2. Although the activity was higher in younger than older leaves, elevated CO2 decreased constitutive levels of CystPIs and reduced beetle-elicited CystPIs activity of both young and fully expanded leaves. Interestingly, the cysteine activity in the gut of Japanese beetles that fed on soybean crop grown under elevated CO2 was higher than those that fed on plants grown on ambient CO2. Our results suggest that elevated CO2 increased the susceptibility of soybean to invasive insects by down-regulating the expression of hormones related with defense, which down-regulate the important defense CystPIs against beetles.
Contact information: Jorge A. Zavala, Institute for Genomic Biology, University of Illinois, 1206 W Gregory Dr., Urbana – Champaign, IL 61801, USA; Email: [email protected]
Jorge A. zavala1, Clare L. Casteel1,2, May R. Berenbaum1,3, Evan H. De Lucia1,2
ABSTRACT: Elevated CO2 Affects Leaf Preferences within Soybean Plants by down-regulating Molecular and Activity of Cysteine Proteinase Inhibitors.
1Institute for Genomic Biology, University of Illinois, Urbana – Champaign, USA 2Department of Plant Biology, University of Illinois, Urbana – Champaign, USA3Department of Entomology, University of Illinois, Urbana – Champaign, USA
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The cotton family of germplasm (Gossypium) is comprised of cultivated tetraploid species and wild/uncultivated diploid species. The multitude of valuable natural traits in the diploid species is not readily available to cotton breeders because they will not readily cross pollinate with the cultivated types. Furthermore, when this type of cross can be made, it requires a long time with standard breeding techniques to develop a new variety. This collaborative project was initiated to take advantage of specialized crossing techniques developed by the Gembloux University in Belgium plus the advanced cotton molecular marker capability within TG&T, and the breeding skills within PhytoGen to transfer the Reniform nematode resistance trait from the diploid species, G. longicalyx, into a proprietary PhytoGen variety.
Contact Information: Ed King, Dow AgroSciences, Seeds & Traits R&D, Indianapolis, IN,USA 46268 USA; Phone: 317-337-4924; Fax: 317-337-4266; Email: [email protected]
J. Pellow1, M. McPherson1, S. Kumpatla2, D. Anderson3
ABSTRACT: developing the Ability to Capture Traits From diploid Gossypium Species
1Phytogen/Dow AgroSciences, Leland, MS, USA 2Dow AgroSciences, Indianapolis, IN, USA3Phytogen/Dow AgroSciences, Corcoran, CA, USA
Hessian fly (Mayetiola destructor) females typically produce offspring of only one sex. In order to map the genetic factor controlling this trait, individual gynogenic and androgenic females were fingerprinted using AFLP-PCR. A BAC clone (Mde37d21) containing a marker (2709) linked to the sex factor was then physically positioned near the end of the long arm of the polytene chromosome A1 by FISH. This analysis revealed two chromosome A1 inversions associated with this trait. BAC clones Mde37d21 and Hf5d5 were diagnostic for these inversions. These were used to examine the karyotypes of 82 families produced by individual females collected from eight different populations. Three variants of the A1 chromosome were observed, A1AX, A1GY1 and A1GY2. A1AX was present in every individual examined and was homozygous in every male. Females were either homozygous A1AX or heterozygous for A1AX and one of other two A1 variants. Heterozygous A1AX/A1GY1 and A1AX/A1GY2 females were both observed in four populations, but never within the same all-female family. Experimental matings were performed to determine the segregation pattern of theses inversions. Females heterozygous for the inversions were gynogenic (female-producers), and females that lack the inversions were androgenic (male-producers). Matings between males and gynogenic females produced both gynogenic (heterogametic) and androgenic (homogametic) females.
The results of this study allowed us to conclude that sex determination in the Hessian fly is controlled by autosome A1 chromosome inversions. These inversions have three properties associated with the primitive Y chromosome: 1) they carry the “master switch” for sex determination, 2) they appear to suppress genetic recombination, and 3) they are nearly always in a heterozygous condition.
Contact Information: Jeffrey J. Stuart, Department of Entomology, Purdue University, West Lafayette, IN 47907, USA; Email: [email protected]
Thiago Benatti1, R. Aggarwal1, J. Wailling2, C. Zhao1, Jeffrey Stuart1
ABSTRACT: A Primitive Y Chromosome with Unique Behaviors in the Genome of the Hessian Fly
1Department of Entomology, Purdue University, West Lafayette, IN 47907, USA2Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
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The introduction of molecular marker technologies has improved the pace and precision of genetics. Simple sequence repeats (SSRs) are widely used molecular markers for the analysis of both plant and animal genomes. While SSRs once developed are very useful tools, their development requires the generation of DNA sequence information, which is a rate limiting and expensive step. Sequences from many genomes are continuously made freely available in the public databases and the utilization of such sequences through bioinformatics approaches permits rapid, high-throughput and economical marker development. These approaches are especially attractive in crops like cotton where polymorphism is low requiring the development of a large number of markers. We have developed a high-throughput SSR mining tool, RepeatFetcher, and have mined a total of 43,953 ESTs and 2,525 genomic sequences from GenBank, belonging to two cotton species, Gossypium hirsutum and Gossypium arboreum. This resulted in the identification of over three thousand sequences containing mono-, di-, tri- and tetra nucleotide SSR repeats and the development of 700+ markers in a span of eight weeks. The marker development process using this computational approach is extremely rapid and saves considerable amount of time and resources by eliminating expensive and labor-intensive library construction, screening and sequencing required to generate DNA sequence information. This tool has been successfully used for mining in more than 50 dicot species since then. The approach and the results from this project will be presented.
Contact Information: Siva Kumpatla, Dept. of Trait Genetics & Technologies, Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN 46268, USA; Phone: 317-337-3422; Fax:317-337-5989; Email: [email protected]
Siva P. Kumpatla1, Manali R. Shah1, Steven A. Thompson1
ABSTRACT: Bioinformatics Approach for High-throughput development of SSR Markers in Gossypium Species
1Dept. of Trait Genetics & Technologies, Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN, USA
The Hessian fly (Mayetiola destructor) is an important pest of wheat (Triticum spp.). We have developed a physical map of the Hessian fly genome by employing high-throughput fingerprinting of bacterial artificial chromosomes (BACs). The BAC DNA was digested with five different enzymes and labeled with SNaPshot Primer Extension Kit. The restricted fragments were sized using ABI 3730 capillary DNA analyzer. DNA fingerprints of 13,614 BAC clones were generated that provided ~12-X coverage to the Hessian fly genome. The BAC fingerprints were assembled into contigs using FPC (v. 8) software at a cutoff value of 1e-29 and a tolerance value of 5. These analyses assembled 264 contigs with 4542 BACs (~4.3-X coverage) ranging in length from 8 to 73 BACs per contig.
The Hessian fly polytene chromosomes were divided into 26 regions numbered from A to Z. Each of the 264 contigs was assigned to a particular region of the polytene chromosome using fluorescent in situ hybridization (FISH). Microsatellite (SSR) markers and salivary gland derived Expressed Sequence Tags (ESTs) were integrated onto their respective contigs.
Contact Information: Jeff Stuart, Department of Entomology, Purdue University, 901 W. State St., West Lafayette, IN 47906 USA; Phone: 765-494-4561; Fax: 765-494-0535; Email: [email protected]
Rajat Aggarwal1, T. Benatti1, J.P. Fellers2, M-S. Chen3, C. Zhao1, B.J. Schemerhorn1, S. Hulbert4, Jeff Stuart1
ABSTRACT: An FPC-Based Integrated Genetic and Physical Map of the Hessian Fly Genome
1Department of Entomology, Purdue University, West Lafayette, IN, USA 2USDA-ARS and Department of Plant Pathology, Kansas State University, Manhattan, KS, USA 3USDA-ARS and Department of Entomology, Kansas State University, Manhattan, KS, USA 4Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
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Fructans, oligomers of fructose, are synthesized by approximately 15% of flowering plant species and a small number of bacterial species. Plants in the Poaceae family synthesize graminan-type fructans, which are branch-types containing both ß (2,1) and ß (2,6)- linked fructofuranosyl units. The objective of this research was to study the gene expression of enzymes of fructan biosynthesis under cold stress: sucrose:sucrose 1-fructosyltransferase (1-SST) and Fructan:fructan fructosyltransferase (1-FFT) as well as degradation upon warming: fructan exohydrolase (1-FEH). Two-week-old wheat seedlings (Triticum aestivum L. cv Patterson) grown at 25°C, in a 12-hour-light period were transferred to cold temperature (10°C), to induce fructan biosynthesis. After 5 days in the cold, plants were transferred to 25°C in a 12-hour-light period for 3 days to monitor fructan degradation. Plants were harvested two times a day: After 12 hours in the dark and after 9 hours in the light. Fructan in blade and shoot tissues were measured as fructose equivalents by assay with anthrone. Under cold induction, fructan concentration in both tissues increased continuously, and decreased sharply in 25°C within 3 days. Expression study determined by quantitative real-time PCR showed that 1-SST and 1-FFT genes were highly regulated in the first day of cold induction in both blade and shoot tissues compared to expression of the control group at 25°C. During the fructan degradation study at 25°C, 1-SST and 1-FFT expression decreased to reach the same level observed in the control group within 24 hours. However, 1-FEH expression in blade and shoot tissues was different. Significance of the results 1-FEH will be discussed.
Contact Information: Pasajee Kongsila, Department of Agronomy, Purdue University, 915 W. State St., West Lafayette, IN 47906 USA; Phone: 765-494-9138; Email: [email protected]
Pasajee Kongsila1, Thomas L. Housley1, Joseph M. Anderson1
ABSTRACT: Real Time Quantitaive PCR of Wheat Fructan Genes Induced by Cold
1Department of Agronomy, Purdue University, West Lafayette, IN, USA
Juvenile hormone (JH) plays a critical role in regulating insect metamorphosis and reproduction. Juvenile hormone esterase (JHE) is one of the JH-specific metabolizing enzymes that are mainly responsible for the degradation of JH. JHE has been identified from fruit fly and few other insects. However, JHEs from important human disease vectors, such as yellow fever mosquito (Aedes aegypti), have not been identified. When we used bioinformatic tools searching in the genome database of NCBI, we found that there were ten putative JHEs of Ae. aegypti. Similarity comparison analysis of these putative JHEs showed that only three of them, EAT43357, EAT43353 and EAT43354, shared high similarity with JHE of fruit fly. To determine which putative JHE(s) encode for a functional enzyme, the expression of the three putative JHE genes were quantified and JHE enzyme activity from the whole bodies of mosquitoes was measured during the larval-pupal metamorphosis stage. The three putative JHE genes were expressed differently. Only the expression pattern of the EAT43357 gene correlates well with the developmental profile of JHE enzymatic activity, and they both have a maximum level prior the larval-pupal metamorphosis, suggesting that this gene may encode for a functional JHE enzyme. Functional tests of putative JHE genes were performed using a baculovirus protein expression system to produce the recombinant proteins of three putative JHEs. Only the recombinant protein of EAT43357 exhibited JHE enzymatic activity confirming that EAT43357 encodes for a functional JHE enzyme. We designated this gene as AaJHE (JHE of Ae. aegypti).
Contact Information: Hua Bai, Department of Entomology, University of Kentucky, S-225 Agricultural Science Center North, Lexington, KY 40546 USA; Phone: 859-257-1134; Email: [email protected]
Subba Reddy Palli1, Parthasarathy Ramaseshadri1, Hua Bai1
ABSTRACT: Identification and Characterization of Juvenile Hormone Esterase of Yellow Fever Mosquito, Aedes aegypti
1Department of Entomology, University of Kentucky, Lexington, KY, USA
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The western corn rootworm beetle, Diabrotica virgifera virgifera (Coleoptera: Chrysomelidae), is a major pest of corn in the United States. A principal method of management is crop rotation, as this insect typically completes its entire life cycle in corn. However, the western corn rootworm has adapted to crop rotation as a control method in much of Illinois and Indiana. Rotation-resistant females lay eggs in fields that are in annual rotation with corn, namely soybean. The mechanism for this behavioral adaptation is likely to be related to heightened levels of flight and locomotory activity, increasing the odds that rotation-resistant females enter non-corn crops. A molecular marker is needed to clearly distinguish between rotation-resistant and susceptible individuals. Previously, a cDNA library of heads of gravid females was used to construct a microarray of expressed sequence tags (ESTs) at the University of Illinois. We used microarray analysis to compare the two behavioral types for differential gene expression. A total of 20 ESTs show at least a twofold expression difference at a stringent level of significance. Potential markers for the rotation-resistance trait will be discussed with regard to reproducibility with quantitative RT-PCR and significance of expression differences.
Contact information: Lisa Knolhoff, Department of Entomology, University of Illinois, 505 S. Goodwin Ave., 320 Morrill Hall, Urbana IL 61801 USA; Phone: 217-333-0489; Fax: 217-244-3499; Email: [email protected]
Lisa M. Knolhoff1, Kim K. O. Walden1, Susan T. Ratcliffe2, David W. Onstad3, Hugh M. Robertson1
ABSTRACT: The Use of Microarrays to Find a Marker for Rotation Resistance in the Western Corn Rootworm
1Department of Entomology, University of Illinois, Urbana, USA2Department of Crop Sciences, University of Illinois, Urbana, USA3Department of Natural Resources and Environmental Science, University of Illinois, Urbana, USA
Ticks in the family Ixodidae (hard ticks) transmit the greatest variety of pathogens of any invertebrate vector and are second only to mosquitoes as vectors of human disease. In the U.S., the black legged or Lyme disease tick, Ixodes scapularis, transmits the causative agents of Lyme disease, babesiosis and human granulocytic anaplasmosis. The I. scapularis genome has recently been sequenced to six-fold coverage with funding from the National Institutes for Allergy and Infectious Diseases (NIAID) and the National Institutes of Health (NIH). Sequencing was conducted by the Broad Institute and The Institute for Genomic Research (TIGR). This project is the first to sequence a medically significant tick species and a member of the subphylum Chelicerata. Over 19 million shotgun reads and more than 200,000 ESTs have been sequenced to date. The complete sequencing of 40 Bacterial Artificial Chromosomes (BACs) and end sequencing of approximately 160,000 BAC clones has also been undertaken as part of this effort. All data types associated with the I. scapularis project including genomic sequence, ESTs, genome assemblies and annotations will be made available to the scientific community through the NIAID funded VectorBase at http://www.vectorbase.org/index.php. An overview of the Ixodes genome project is provided and preliminary studies of I. scapularis genome organization are presented.
Contact Information: Catherine A. Hill, Department of Entomology, Purdue University, 901 W. State St., West Lafayette, IN 47906 USA; Phone 765-496-6157; Email: [email protected]
Jason M. Meyer1, Janice P. Van Zee1, Nicholas S. Geraci1, Felix D. Guerrero2, Jeffrey J. Stuart1, Stephen K. Wikel3, Bruce Birren4, Vish M. Nene5, Frank H. Collins6, Catherine A. Hill1
ABSTRACT: Sequencing the Genome of Ixodes Scapularis – the Lyme disease Tick
1Purdue University, West Lafayette, IN, USA2USDA-ARS Knipling-Bushland, Kerrville, TX, USA3University of Connecticut Health Center, Farmington, CT, USA4The Broad Institute, Cambridge, MA, USA5The J. Craig Venter Institute, Rockville, MD, USA6University of Notre Dame, Note Dame, IN, USA
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Lower termites of the genus Reticulitermes are the most common and economically destructive termites in the US and Europe. All lower termites feed on an exclusive “lignocellulose” diet composed of the recalcitrant polymers lignin, cellulose, and hemicellulose. Amazingly, these termites are able to digest and receive ample nourishment from this nutritionally poor diet. This is made possible by unique gut physiology and enzymes produced by both termites and their gut endosymbionts (prokaryotic and eukaryotic). Through recent research efforts, some enzymes that participate in termite cellulose digestion have been identified. However, our understanding of the entire lignocellulose digestion / assimilation process in termites remains largely incomplete, especially for economically important species like R. flavipes. This lack of understanding has hindered the development of safe, effective, termite-specific termiticides and contributes to the degradation of urban landscapes. Additionally, termites and their gut symbionts are a potentially important source for novel, highly relevant enzymes with applications in the rapidly expanding biorefinery industry.
The broad goals of this research are to sequence the R. flavipes gut metagenome and to use this information to build genomic tools and resources that will assist the scientific community in developing (a) more effective and environmentally sound termiticides, as well as (b) novel enzymes for use in plant cell wall deconstruction and bioethanol production. Our investigations are combining high-throughput cDNA sequencing from a symbiont-free normalized gut library with state-of-the-art picotiter plate “454” symbiont metagenome sequencing. This poster overviews our research approaches and presents preliminary sequencing results.
Contact Information: Michael E. Scharf, Entomology & Nematology Department, PO Box 110620, University of Florida, Gainesville, FL, 32611-0620 USA, Phone: 352-392-1901; Fax: 352-392-0190; Email: [email protected]
Aurélien Tartar1, Xuguo Zhou1, Faith M. Oi1, William G. Farmerie2, Drion G. Boucias1, Michael E. Scharf1
ABSTRACT: Metagenomic dissection of Lignocellulose Utilization in Termites
1Entomology & Nematology Department, University of Florida, Gainesville, FL, USA2Genomics Core Facility, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
Ixodid ticks (subphylum Chelicerata, class Arachnida, suborder Ixodida) are obligatory hematophagous ectoparasites of worldwide medical and veterinary importance. They transmit a variety of viruses, bacteria and protozoa and cause direct damage to their host via attachment and feeding. Our research team is analyzing the genomes of several Ixodid ticks to improve understanding of tick biology and transmission of tick-borne diseases. Our previous work has revealed that species of hard ticks (family Ixodidae) and soft ticks (family Argasidae) have relatively large genomes with haploid genome sizes ranging from 1 to more than 7Gbp. Preliminary evidence suggests that repetitive DNA and possibly segmental duplications may contribute significantly to the genome size of ixodid ticks. However, genome composition and organization have been largely unstudied in the Ixodida to date.
Gene and segmental duplication events are recognized as major driving forces in eukaryotic evolution providing biological variants, generating biodiversity and consequently reproductive barriers. In this study we used bioinformatics approaches to investigate the frequency of gene duplication events in four species of hard ticks, namely the prostriate tick Ixodes scapularis (Lyme disease tick) and the metastriate ticksAmblyomma variegatum (lone start tick), Rhipicephalus annulatus (common name) and Rhipicephalus (Boophilus) microplus (southern cattle tick). Non-synonymous substitution rates were used to estimate the timing of putative gene duplication events in each species. Our data suggest that a significant fraction of the expressed genome may have recently duplicated in all four species. This work contributes to our understanding of genome evolution in the pro- and metastriate lineages and complements ongoing efforts to sequence and analyze pro- and metastriate ticks.
Contact information: Janice Van Zee - Department of Entomology, Purdue University, 901 W. State St., West Lafayette, IN 47906 USA; Phone: 765-496 1513; Fax: 765-496 1219; Email: [email protected]
Catherine Hill1, Jessica Schlueter2, Janice P. Van zee1
ABSTRACT: Gene duplication and Genome Organization of the Ixodidae
1Department of Entomology, Purdue University, West Lafayette, IN, 47909, USA2Agronomy Department, Purdue University, West Lafayette, IN, 47909, USA
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The long-term goal of this project is to develop a spray to control Escherichia coli O157:H7 on beef, using metabolic intermediates that will affect the expression levels of the global regulator FlhD/FlhC. This study aims at understanding global gene regulation around FlhD/FlhC under conditions that mimic refrigerated storage of beef. Wild-type bacteria and FlhC mutants were grown at 10ºC in beef extract medium for ten days. Few flagellar genes appeared regulated or even expressed. Since the bacteria were motile at this temperatures (1 cm per day on beef broth swarm plates), the most likely reason for the absence of the flagellar genes could be the early growth phase (OD600 of 0.35) at which the bacteria had been harvested. Among the genes that appeared regulated were cell division genes and genes of aerobic respiration. These results were consistent with previous experiments where FlhD/FlhC regulated cyoABCDE.
In addition, seven transcriptional regulators were regulated. These results strongly support the global regulatory role of FlhD/FlhC. Interestingly, the eivG gene, which constitutes part of a degenerative type III secretion system and lies in a seven gene operon, is positively regulated by FlhC (18 fold). A second group of genes that appeared regulated by FlhC includes two unknown proteins that are encoded by the prophages CP-933O and CP-933C. One of these genes was positively affected by FlhC (24 fold) and the other was negatively regulated (0.46 fold). A large number of genes encoding for proteins of unknown functions were also regulated.
Contact Information: Birgit Pruess, Department of Veterinary and Microbiological Sciences, North Dakota State University, 1523 Centennial Blvd., Fargo, ND 58105 USA; Phone: 701-231-7848; Fax: 701-231-9692, Email: [email protected]
Birgit Prüß1, Preeti Sule1
ABSTRACT: Gene Regulation of Escherichia coli O157:H7 in Beef Extract Medium include Type III Secretion and Phage related Genes
1Department of Veterinary and Microbiological Sciences, North Dakota State University, Fargo, ND, USA
The Hessian fly, the wheat midge, and the rice gall midge are among the most important insect pests of cereals worldwide. Plant resistance is the most effective method of control, however, the use of resistant cultivars leads to the development of biotypes that can survive on formerly resistant cultivars. How these insects hijack their host plant’s development to feed and protect the larvae is unknown. However, it is believed salivary secretions from the larvae are the signals that cause abnormal plant growth in susceptible plants or elicit a defense response in resistant plants. We have created a database of genes expressed in the salivary glands of these insects. From this database we have been able to identify genes that are similar between the species and genes that are unique to each species. These results are allowing us to understand how these pests hijack a susceptible plant’s development as well as the signals a resistant plant recognizes to defend itself.
Contact Information: Richard Shukle, USDA-ARS, Department of Entomology, Purdue University, 901 W. State St., West Lafayette, IN 47907 USA; Phone: 765-494-6351; Fax: 765-494-5105; Email: [email protected]
Omprakash Mittapalli1, Jagadish Bentur2, Jonathan Neal3, Ming-Shun Chen4, Jeffery Stuart3, Ian Wise5, Richard Shukle6
ABSTRACT: Comparison of Gene Expression in the Salivary Glands of Three Major Insect Pests of Cereals
1Max Planck Institute for Chemical Ecology, Department of Molecular Ecology, Beutenberg Campus, Hans Knöll-Straße 8, Jena, Germany2Directorate of Rice Research, Rajendranagar, Hyderbad, India3Dept. of Entomology, 901 W. State Street, Purdue University, W. Lafayette, IN4USDA-ARS, Dept. of Entomology, 123 Waters Hall, Kansas State University, Manhattan, KS5Agriculture and Agri-food Canada, Cereal Research Center, Winnipeg, MB, Canada6USDA-ARS, Dept. of Entomology, 901 W. State Street, Purdue University, W. Lafayette, IN
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Fusarium head blight (FHB), caused by the fungi Fusarium graminearum and Fusarium culmorum, is a worldwide disease of wheat (Triticum aestivum L.). The Chinese cultivar, Ning7840, is one of a few wheat cultivars with resistance to FHB. GeneCallingTM, an open-architecture, mRNA-profiling technology, was used to identify differentially expressed genes induced or suppressed in spikes after infection by Fusarium graminearum in wheat line Ning7840. One-hundred-twenty-five individual cDNA fragments representing transcripts differentially expressed in wheat spikes were identified. Based on BLASTN and BLASTX analyses, putative functions were assigned to some of the unigenes: 28 were assigned function in primary metabolism and photosynthesis, seven were involved in defense response, 14 in gene expression and regulation, 24 encoded proteins associated with structure and protein synthesis, 42 lacked homology to sequences in the database, and three genes were similar to cloned multidrug resistance or disease resistance proteins. Real-time quantitative reverse-transcription PCR indicated that of 51 genes tested, 19 showed 2-fold or greater induction or suppression in the FHB resistant wheat cultivar Ning7840 in contrast to the water-treated control. The remaining 32 genes were not significantly induced or suppressed in Ning7840 compared to the control. Subsequently, these 19 induced or suppressed genes were examined in the wheat line KS24-1 containing FHB resistance derived from Lophopyrum elongatum and Len, a FHB-susceptible wheat cultivar. The temporal expression for some of these sequences encoding resistance proteins or defense-related proteins showed FHB (resistance-specific) induction, suggesting that these genes play a role in protection against toxic compounds in plant - fungal interactions. On the basis of comprehensive expression profiling of various biotic or abiotic response genes revealed by real-time PCR in this study and other supporting data, we hypothesized that the plant - pathogen interactions may be highly integrated into a network of diverse biosynthetic pathways.
Contact information: Lingrang Kong, Department of Agronomy, Purdue University, 915 W. State St., West Lafayette, IN 47907 USA; Phone 765-496-3081; Fax: 765-496-2926; Email: [email protected]
Lingrang Kong1, Herbert W. Ohm1, Joseph M. Anderson1,2
ABSTRACT: Expression Analysis of defense-Related Genes in Wheat in Response to Infection by Fusarium graminearum
1Agronomy Department and 2United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Purdue University, 915 W. State St., West Lafayette, IN 47907, USA
The midgut proteome of Drosophila melanogaster was compared in larvae fed dietary Bowman-Birk inhibitor (BBI) versus larvae fed control diet. By using 2 Dimensional Gel Electrophoresis (2-DE), nine differentially-expressed proteins were observed, which were associated with enzymes or transport functions such as: sterol carrier protein X-like thiolase (SCPX), ubiquitin-conjugating enzyme (UBC), endopeptidase, receptor signaling protein kinase, ATP-dependent RNA helicase, and α-tocopherol transport. Quantitative Real-Time PCRs (qRT-PCRs) verified differential expression of transcripts coding for six of the proteins observed from the proteomic analysis. BBI evidently affects expression of proteins associated with protein degradation, transport, and fatty acid catabolism. We then tested the hypothesis that SCPX was critical for the Drosophila third instars’ response to BBI treatment. Inhibition of SCPX caused the third instars to become more susceptible to dietary BBI.
Contact Information: Hongmei LI, Department of Entomology, Purdue University, 901 W. State St., West Lafayette, IN 47906 USA; Phone: 765-494-8713; Fax: 765-494-0535; Email: [email protected]
Hong-Mei Li1, Larry L. Murdock1, William Muir2, Jun Xie3, Jing Wu3, Lijie Sun1, Brandi J. Schemerhorn4, Barry R. Pittendrigh1
ABSTRACT: Changes in drosophila Melanogaster Midgut Proteins in Response to dietary Bowman-Birk Inhibitor
1Department of Entomology, Purdue University, West Lafayette, IN, USA2Department of Animal Science, Purdue University, West Lafayette, IN, USA3Department of Statistics, Purdue University, West Lafayette, IN, USA4USDA-ARS, Department of Entomology, Purdue University, West Lafayette, IN, USA
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Adaptations in mammary tissue gene expression networks were studied in response to a S. uberis IMI during mid-lactation (~90 days post-partum). Ten multiparous Holstein cows were inoculated with 5,000 cfu of S. uberis (O140J) into one rear mammary quarter. At 20 h post-inoculation, before the expected peak in clinical signs, both rear mammary quarters (i.e. infected (YES) and control (NO) quarters) of all cows were biopsied for gene expression analysis. A 13,257 bovine oligonucleotide (70-mers) microarray and qPCR were used for transcript profiling. Annotation was based on similarity searches using BLASTN and TBLASTX against human, mouse, and bovine UniGene databases, the human genome, and the cattle TIGR database. Data were analyzed with the MIXED procedure of SAS. Infection (YES vs. NO) resulted in 2,104 differentially expressed genes (FDR < 0.05). Ingenuity Pathway Analysis® (IPA) identified interleukin-10 (IL-10) signaling (n = 22), IL-6 signaling (25), peroxisome proliferator-activated receptor signaling (18), NF-kappa-ß signaling (21) and apoptosis signaling (21) as some of the top canonical pathways affected by IMI. Among genes up-regulated with infection (1,082), IPA identified inflammatory disease (34), cellular movement (48), immune response (47), cell signaling (57), molecular transport (23) and vitamin and mineral metabolism (23) as some of the most enriched molecular functions. Down-regulated genes (1,020) were associated with lipid metabolism (12), cellular transport (11), small molecule biochemistry (12), carbohydrate metabolism (6), connective tissue development and function (5) and tissue morphology (5). Results indicate that IMI affects a broad specrum of gene expression networks in mammary tissue.
Contact Information: Kasey M. Moyes, Department of Animal Science, University of Illinois, 258 Animal Sciences Laboratory MC-630, 1207 W. Gregory Dr., Urbana, IL 61801 USA; Phone: 217-333-0466; Fax: 217- 333-7088; Email: [email protected]
J. J. Loor1, K. M. Moyes1, M. Bionaz1, D. E. Morin1, S. L. Rodriguez-Zas1, R. E. Everts1, H. A. Lewin1,2, J. K. Drackley1
ABSTRACT: Gene Expression Networks in Bovine Mammary Tissue during a Streptococcus uberis (S. uberis) Intrammamary Infection (IMI) Challenge
1Department of Animal Sciences, University of Illinois, Urbana, USA2Institute for Genomic Biology, University of Illinois, Urbana, USA
Mammary parenchyma (PAR) and fat pad (FAT) development appear to be responsive to pre-weaning level of nutrition. We evaluated adaptations in gene expression networks simultaneously in PAR and FAT in heifers fed milk replacers designed to support different rates of growth. Tissues from calves (n = 6/diet) fed control (20:20, protein: fat, fed at 450 g/d), high-protein/low-fat (28:20, HPLF, fed at 970 g/d), HP high-fat (28:28, HPHF, fed at 970 g/d), or a HPHF+ (fed at 1,460 g/d) diet were used. A 13,257 bovine oligonucleotide (70-mers) array was used for gene expression profiling. Annotation was based on similarity searches using BLASTN and TBLASTX against human, mouse, and bovine UniGene databases, the human genome, and the cattle TIGR database. Over 1,400 genes were affected (FDR ≤ 0.05) by diet in PAR or FAT. When comparing the different diets to control, feeding HPLF resulted in the most drastic changes in gene expression, with 119 and 357 differentially expressed genes (DEG) having ≥1.5-fold change in PAR and FAT. Within FAT of calves fed HPLF vs. control, Ingenuity Pathway Analysis® (IPA) identified small molecule biochemistry and cellular growth and proliferation as the most enriched molecular functions among up-regulated DEG. Similarly, IPA analysis of down-regulated DEG identified small molecule biochemistry as well as lipid metabolism as most-enriched functions in FAT. Overall, results indicate that mammary gene networks are responsive to enhanced nutrient supply designed to achieve greater growth rates prior to weaning.
Contact Information: Paola Piantoni, Department of animal Sciences, University of Illinois, 1207 W. Gregory Dr., Urbana, IL 61801 USA; Phone: 217-265-8497; Fax: 217-333-8286; Email: [email protected]
J. J. Loor1, P. Piantoni1, D. Graugnard1, K. M. Daniels2, R. E. Everts1, S. L. Rodriguez-Zas1, H. A. Lewin1,3, R. M. Akers2
ABSTRACT: Intensified-Growth Nutrition during the Pre-Weaning Period Affects Gene Expression Networks in Mammary Parenchyma and Fat Pad of Heifer Calves
1University of Illinois, Urbana, IL, USA 2Virginia Tech, Blacksburg, VA, USA3Institute for Genomic Biology, University of Illinois, Urbana, USA
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Ecotilling is a powerful genetic analysis tool. It can provide rapid identification of naturally occurring Single Nucleotide Polymorphisms (SNPs) and small insertion/deletions (indels) in a pool of accessions for a gene of interest. This technique eliminates the time consuming and expensive procedure of sequencing all individuals of a population in order to mine for DNA polymorphisms. Ecotilling was used to identify DNA polymorphisms such as SNPs and indels in a population of mung bean (Vigna radiata). Initially, V. sublobata was used as the reference DNA and compared to each member of the population classified as V. radiata to detect interspecific polymorphic sites. Additionally, accessions in the population were pooled together in a 1:1 ratio to identify intraspecific SNPs among V. radiata accessions. Numerous SNPs and indels were detected in all genes when comparing V. sublobata to V. radiata suggesting that the species sublobata and radiata are distinct. However, when accessions of V. radiata were mixed together and digested with CEL I, very few SNPs and indels were detected, suggesting that accessions classified as V. radiata have limited genetic diversity. Morphology data from flowers and pod descriptors lend support to limited diversity in the USDA mung bean germplasm collection.
Contact Information: Noelle Barkley, USDA-ARS PGRCU, 1109 Experiment Street, Griffin, GA 30223 USA, Phone: 770-412-4035; Fax: 770-229-3323; Email: [email protected]
Noelle Barkley1, Ming Li Wang1, Graves Gillaspie1, Rob Dean1, Gary Pederson1, Tracie Jenkins2
ABSTRACT: Mining SNPs and Indels in Mung Bean (Vigna radiata) by Ecotilling
1USDA-ARS Plant Genetic Resources Conservation Unit, Griffin, GA, USA2Department of Entomology, University of Georgia, Griffin, GA, USA
Microarray experiments are popular tools in functional genomics and many techniques have been developed for evaluating their results. The data are typically analyzed to find genes which are significantly expressed, or groups of genes which show similar expression across multiple related experiments. In addition, gene expression information has been used to directly predict the function of genes. Our approach is designed to find gene functions, as opposed to genes, which are connected with patterns in microarray data and derive understanding of regulatory activity from these associations. This means that predictive techniques are not appropriate. Identifying functional patterns among the resulting group or groups of genes is a separate step that is not supported by standard clustering techniques. Here an algorithm is presented for identifying functional groups that are preferentially regulated based on gene expression data. The algorithm is applied to a published set of microarray data (Oshima et al. 2002, Mol. Microbiol.), which studied the two-component sensor systems of Escherichia coli. The presence of patterns by identifying neighboring relationships is quantified among profiles using a product measure. If a gene has more neighbors with a similar expression profile than would be expected by random chance then the existence of a pattern is supported. The number of neighbors, for all genes that share the function, is summarized in a histogram. Using this histogram, the significance of the relationship between expression data and the functional annotation is evaluated. The algorithm output is used to develop hypotheses for agricultural studies.
Contact Information: Megan K. Townsend, Department of Veterinary and Microbiological Sciences, North Dakota State University, 1523 Centennial Blvd., Fargo, ND 58105 USA; Phone: 701-231-6741; Fax: 701-231-9692; Email: [email protected]
Birgit M. Prüß1, Megan K. Townsend1, Jianfei Wu2, Anne M. Denton2
ABSTRACT: Finding Relationships Between Protein Functions and Gene Expression data
1Department of Veterinary and Microbiological Sciences, North Dakota State University, Fargo, ND, USA 2Department of Computer Science, North Dakota State University, Fargo, ND, USA
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Targeted transgene integration via homologous recombination occurs at a very low frequency in plant cells compared to random integration, making gene targeting in plants via homologous recombination impractical. Most recently, substantial increases in the frequency of homologous recombination have been observed following the induction of DNA double stranded breaks in host cells and apparent stimulation of cellular repair mechanisms. Restriction enzymes whose recognition sites are rare in the plant genome have been shown to stimulate homologous recombination following the formation and repair of DNA double stranded breaks in the host DNA. Strategies to achieve targeted DNA double stranded breaks have been developed by fusing zinc finger DNA binding proteins with sequence-independent nuclease domains derived from Type II restriction endonucleases. In the present study, a target DNA sequence was stably integrated into tobacco cell cultures using Agrobacterium. This target sequence contained specific zinc finger protein recognition/binding sites, along with a non-functional test gene to be corrected. A few selected transgenic events containing a single integrated copy of the target sequence were re-transformed using Agrobacterium strains harboring different T-DNAs. One Agrobacterium strain contained a donor DNA sequence comprising the bases necessary to correct the non-functional test gene, flanked by sequences homologous to the pre-integrated target DNA. A second Agrobacterium strain contained a gene encoding a zinc finger nuclease that specifically recognized a binding site in the integrated target sequence. Gene targeting via site-directed homologous recombination was demonstrated as evidenced by the re-constitution of a functional test gene and was confirmed via molecular and biochemical analyses.
Contact Information: Charles Cai, Molecular Biology and Biochemistry, Dow AgroSciences, 306/A1-2108, 9330 Zionsville Rd., Indianapolis, IN 46268, USA; Phone: 317-337-5813; Fax: 317-337-3228; Email: [email protected]
Charles Cai1, Lisa Baker1, Teresa Bauer1, Ryan Blue1, Trevor Collingwood2, Russell DeKelver2, Philip Gregory2, Adam Miller1, Jeffrey Miller2, Fyodor Urnov2, Andy Worden1, Joseph F. Petolino1
ABSTRACT: Site-directed Homologous Recombination in Tobacco Cell Cultures via zinc Finger Nucleases
1Dow AgroSciences, Indianapolis, IN, USA2Sangamo BioSciences, Richmond, CA, USA
The human body louse, Pediculus humanus (Class Insecta; Order Phthiraptera; Suborder Anoplura) is an obligate, blood-feeding ectoparasite of humans. It is a serious pest of human health worldwide because it causes irritation and social embarrassment, and it transmits the causative agents of louse-borne relapsing fever and epidemic typhus. The P. humanus genome was sequenced and assembled in 2007, providing an important resource to understand P. humanus biology and identify new methods for control of lice and louse-borne diseases.
In this study, we used bioinformatic and phylogenetic approaches to identify, annotate and classify the repertoire of G Protein-Coupled Receptors (GPCRs) in the P. humanus genome. GPCRs are a super-family of seven trans-membrane spanning receptors; their interaction with a wide variety of extra-cellular ligands initiates intra-cellular signal transduction cascades. GPCRs function in a range of sensory and neurological processes and are potential targets for development of novel insecticides. Pediculus has orthologs of many non-sensory and visual GPCRs identified in other invertebrates, and a smaller repertoire of these receptors compared to holometabolous insects suggesting conservation of GPCR-mediated processes across insect lineages. Our analysis has provided important insights into the evolution of insect GPCRs that facilitate our ongoing investigations for novel pediculicide targets.
Contact Information: Emily Kraus, Department of Entomology, Purdue University, 901 West State Street, West Lafayette, IN 47907 USA; Phone: 765-496-1513; Fax: 765-496-1219; Email: [email protected]
Emily C. Kraus1, J. Pagel VanZee1 , Catherine A. Hill1
ABSTRACT: G Protein-Coupled Receptors in the Genome of the Body Louse, Pediculus humanus
1Purdue University, Department of Entomology, West Lafayette, IN, 47907
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Embryonic development rate is associated with embryo survivability, juvenile growth, and adult age at sexual maturity in salmonid fishes. We have identified a major embryonic development rate quantitative trait locus (QTL), accounting for greater than 20% of the variation in this trait, in line crosses of rainbow and steelhead trout (Oncorhynchus mykiss). We tested whether this and other detected QTL exhibit significantly different additive effects in different maternal cytoplasmic environments (MCE), and have begun to identify candidate genes and their expression in this region. Doubled haploid progeny were produced by androgenesis (all-paternal inheritance) from F1 progeny of a line cross between an Oregon State University (OSU) female Shasta-type rainbow trout clonal line and a Clearwater River (CW) steelhead clonal line. Eggs from eight different females were irradiated to destroy the maternal nuclear DNA component, and then fertilized with sperm from one OSUxCW F1 individual. Time from fertilization to hatch was recorded for each individual reared in a constant 11°C environment. Six QTL were associated with development rate, and both MCE and QTLxMCE significantly contributed to variation in development rate. Additive effects of the major QTL were not significantly different among MCE, but some minor effect QTL did exhibit significant QTLxMCE. We have subsequently mapped three potential candidate genes to the region and followed the expression of these genes during embryonic development. Further dissection of this region will reveal the genetic mechanisms controlling multiple traits, and will have important implications for selective breeding of rainbow trout for multiple aquaculture production traits.
Contact information: Krista M. Nichols, Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907 USA; phone: 765-496-6848; fax: 765-494-0876; Email: [email protected]
Krista M. Nichols1,4, Karl W. Broman2, Scott A. Gahr3, Caird E. Rexroad III3, Kyle Sundin4, Jennifer Young4, Ruth B. Phillips5, Megan Duge1, Paul A. Wheeler4, Gary H. Thorgaard4
ABSTRACT: The Genetic Architecture of development Rate in Rainbow Trout: QTL, QTL x Maternal Environment, and Candidate Gene Expression
1Departments of Biological Sciences and Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907 2Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205-2179 3USDA-ARS, National Center for Cool and Cold Water Aquaculture, Kearneysville, WV 25430 4School of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA 99164
Wheatgrass species such as Thinopyrum and Lophopyrum have become sources of useful traits for wheat, particularly disease resistance to Barley and Cereal Yellow Dwarf viruses, leaf rust and Fusarium head blight. Molecular markers derived from wheat have been used to identify and characterize wheatgrass-wheat translocations. However, most wheat-derived PCR markers do not identify wheatgrass specific polymorphisms and consequently typically are used as negative (wheat DNA fragment missing) markers. In order to identify single feature polymorphisms (SFPs) that are either codominant for wheatgrass and wheat or are dominant for wheatgrass, wheat oligonucleotide arrays were hybridized with labeled cRNA isolated from five wheat-wheatgrass substitution or addition lines. Each line contained one of two wheatgrass 7E chromosomes and the reference wheat line, Chinese Spring. SFPs can be single nucleotide polymorphisms (SNPs), insertion/deletions (InDels) or explained by alternative splicing. The oligonucleotide arrays were analyzed for SFPs using a robustified projection pursuit (RPP) algorithm (Cui et al, 2005). Comparisons of the translocation perfect match (PM) probes and probe sets yielded approximately 200 putative 7E SFPs with about 150 already noted as SNPs from the wheat SNP database (http://wheat.pw.usda.gov/GG2/blast.shtml). Currently, 50 probe and probe set fragments have been cloned from the starting wheat-wheatgrass substitution and addition lines. About 30 have been sequenced with 4 SNPs identified and one InDel. Future endeavors are to finish sequencing and analyzing the remaining fragments and design markers for the specific SFPs. Finally, using already developed translocation lines, SFP locations will be determined.
Contact information: Elizabeth Buescher, Department of Agronomy, Purdue University, 915 W. State Street, West Lafayette, IN 47907 USA; Phone: 765-494-6759; E-mail: [email protected]
Elizabeth Buescher1, Xinping Cui2, Joseph M. Anderson3
ABSTRACT: detecting Single-Feature Polymorphisms on the 7E Thinopyrum Chromosome Using the Wheat Oligonucleotide Array
1Agronomy Department, Purdue University, West Lafayette, IN USA2Department of Statistics, University of California Riverside, Riverside, CA USA3USDA-ARS, Purdue University, West Lafayette, IN USA
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The Nationally-funded Wheat Coordinated Agricultural Project involves collaborations among 25 wheat breeding/genetics programs at public institutions, and four USDA-ARS genotyping laboratories throughout the USA. The goal of the project is to apply Marker-Assisted Selection (MAS) and other genomics technologies for the improvement of wheat for crop production, resistance to biotic and abiotic stresses, and grain quality traits. Important components include research, as well as education and extension activities with students and farmers. Objectives are: 1) establish MAS in public wheat breeding programs and produce improved germplasm lines and cultivars, 2) map new genes that improve wheat yield, quality, pest resistance, and abiotic stress tolerance, 3) develop SNP markers in 12 selected wheat populations, 4) attract students to agriculture, and 5) inform growers and the public about the impact of biotechnology.
Contact Information: Herbert Ohm, Department of Agronomy, 915 W. State Street, West Lafayette, IN 47907 USA; Phone: 765-494-8072; Fax: 765-496-2926; Email: [email protected]
M. Soria1, J. Anderson2, P. Baenziger3, B. Berzonsky4, G. Brown-Guedira5, K. Campbell6, B. Carver7, S. Chao8, J. Dubcovsky1, A. Fritz9, C. Griffey10, G. Bai11, S. Haley12, J. Johnson13, S. Kianian4, K. Kidwell14, M. Mergoum4, H. Ohm15, J. Peterson16, O. Riera Lizarazu16, J. Rudd17, L. Talbert18, J. Sherman18, M. Sorrells19, E. Souza20, L. Yan7, R. Zemetra21
Project Coordinator: J. Dubcovsky
ABSTRACT: Wheat Coordinated Agricultural Project: Applying Genomic Technologies to Wheat Improvement
1Plant Sciences Dept., University of California, Davis, CA 95616-87802Agronomy and Plant Genetics Dept., University of Minnesota, St. Paul, MN 551083Agronomy and Horticulture Dept., University of Nebraska, Lincoln, NE 68583-09154Plant Sciences Dept., North Dakota State University, Fargo, ND 581025USDA-ARS, North Carolina State University, Raleigh, NC 276066USDA-ARS Wheat Genetics, Washington State Univ., Pullman WA 99164-64207Plant and Soil Sciences Dept., Oklahoma State University, Stillwater, OK 740788USDA-ARS,Biosciences Research Lab, Fargo, ND 58105.9Agronomy Dept., Kansas State University, Manhattan KS 6650610Crop & Soil Environmental Sciences Dept., Virginia Tech, Blacksburg, VA 2406111USDA-ARS Plant Science and Entomology Research Unit, 4008 Throckmorton Hall, Kansas State University, Manhattan KS 6650612Soil and Crop Sciences Dept., Colorado State University, Ft Collins CO 8052113Crop and Soil Science Dept., University of Georgia, Griffin, GA 30223-119714Crop and Soil Sciences Dept., Washington State University, Pullman, WA 99164-642015Agronomy Dept., Purdue University, West Lafayette, IN 47907 16Crop and Soil Science Dept., Oregon State University, Corvallis, OR 9733317Texas A&M Agricultural Research Center, Amarillo, Texas 7910618Plant Science Dept., Montana State University, Bozeman, MT 5971719Plant Breeding & Genetics Dept., Cornell University, Ithaca, NY 14853-190220USDA-ARS Soft Wheat Quality Lab, Wooster, OH 4469121Plant, Soil and Entomological Sciences Dept., University of Idaho, Moscow, ID 83844 #127
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Previous work from our laboratory demonstrated prepartum energy intake impacted mRNA expression profiles in liver tissue from periparturient cows. In adipose tissue, however, large scale mRNA transcript profiling has not been performed in periparturient cows, nor from cows consuming different amounts of energy prepartum. Fourteen Holstein cows were randomly assigned to diets designed to allow overconsumption of energy with regard to their requirements (OVER) or to control intake to approximately 100% of their requirements (CON) during the non-lactating period. At parturition, one lactation diet was fed to all cows. Subcutaneous adipose biopsies were performed before dietary treatments began (baseline), then on d -14, 1, and 14 relative to parturition. A 13,257 bovine oligonucleotide microarray was used for mRNA expression profiling. Annotation of the array was based on similarity searches using BLASTN and TBLASTX genes against human, mouse, and bovine UniGene databases, the human genome, and bos taurus TIGR data base. Preliminary analysis using GeneSpring software indicated that 215 transcripts were differentially expressed (FDR < 0.05) over all timepoints. Compared to baseline, largest changes in expression patterns were observed on d 1 (300 upregulated; 331 downregulated). Between treatments, 56 transcripts were upregulated and 77 downregulated by ≥ 1.5 fold in OVER vs CON. Similarly, 297 and 149 transcripts were up- or downregulated, by ≥ 2.0 fold on d -14 in OVER vs CON. Preliminary results suggest that overfeeding energy prepartum altered adipose mRNA profiles, especially for genes related to fatty acid synthesis and energy storage.
Contact Information: Nicole A. Janovick-Guretzky, Department of Animal Science, University of Illinois, 1207 W. Gregory Dr., Urbana, IL 61801 USA; Phone: 217-333-0466; Fax: 217-333-7088; Email: [email protected]
J. J. Loor1, N. A. Janovick-Guretzky1, R. E. Everts1, H. A. Lewin1,2, J. K. Drackley1
ABSTRACT: Prepartum Plane of Energy Intake Alters Pre- and Postpartum mRNA Expression Profiles in Subcutaneous Adipose Tissue from Periparturient Holstein Cows
1Department of Animal Science, University of Illinois, Urbana, IL, USA2Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
The primary sequence of the genome at endogenous loci can be altered with high efficiency in mammalian cells using designed zinc finger nucleases (ZFNs; Urnov et al. Nature 435: 646). Ongoing studies indicate that a precisely-placed double-strand break (DSB) induced by engineered ZFNs can stimulate integration of long DNA stretches into a predetermined genomic location in human cells, resulting in site-specific gene addition. Zinc finger protein technology represents a significant breakthrough relative to the ability to edit and engineer genomes in a precise manner.
In this presentation, results from a collaboration between Dow AgroSciences LLC and Sangamo Biosciences that is focused on applications of designed zinc-finger protein technology in plant species will be described. Multiple zinc-finger proteins, including zinc-finger nucleases and zinc-finger transcription factors, have been designed to target specific genes in model and agriculturally important plant species. Validation of this technology and examples of its utility for plant biotechnology will be discussed.
Contact Information: Stephen Novak, Trait Genetics and Technologies, Dow AgroSciences LLC., 9330 Zionsville Road, Indianapolis, IN 46268 USA; Phone: 317-337-3897; Fax: 317-337-5989; Email: [email protected]
Vipula Shukla¹, Teresa Bauer¹, Nicole Arnold¹, Zhifang Gao¹, Dave McCaskill¹, Jon Mitchell¹, Lynn Rowland¹, Matt Simpson¹, Sarah Worden¹, Kerrm Yau¹, Stephen Novak¹, Fyodor Urnov², Jeffrey Miller², Jeremy Rock², Erica Moehle², Russell DeKelver², Yannick Doyon², Ed Rebar², Trevor Collingwood², Lei Zhang²
ABSTRACT: Application of designed zinc-Finger Protein Technology in Plants
1Dow AgroSciences, LLC., Indianapolis, IN 462682Sangamo Biosciences, Inc., Richmond, CA 94804
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Elucidating genes controlling growth, development, and metabolism of swine mammary glands can reveal potential metabolic or signaling pathways that might help improve efficiency of milk synthesis. A swine microarray consisting of 13,263 oligonucleotides (70 mer) was used for transcript proling of mammary tissue from 4-5 sows at -34, -14, -4, 0, 7, 14, 21, and 28 d relative to parturition. ANOVA (FDR ≤ 0.10) identied 2,664 differentially expressed genes (DEG) due to physiological state. Ingenuity Pathway Analysis® (IPA) revealed that cell growth and proliferation (n = 548) and cell signaling (n = 612) were among the most affected molecular functions due to physiological state in DEG. A clear switch in metabolic state of mammary gland from pregnancy to lactation was apparent, with up-regulation of genes involved in milk component synthesis (e.g., LALBA, CSN3, BTN1A1) and concomitant down-regulation of genes involved in catabolism and energy production (e.g., ACOX1, NDUFA4). Peak of lactation (21 d) was characterized by the largest number of DEG with ≥1.5-fold expression (714 ↑, 791 ↓) relative to late pregnancy (-34 d ). IPA also identified 110 transcription regulators with ≥1.5-fold in at the least one time point relative to -34 d. Among these, 14 (e.g., RARB, TP53BP1) had ≥3 fold up-regulation during lactation relative to pregnancy.
The imminent onset of lactation elicited tremendous adaptations in mammary gene expression. Analysis uncovered many novel molecular functions affected during pregnancy and lactation. Among these were novel transcription regulators which might help explain long-term adaptations in mammary gland development and function.
Contact Information: Simona Tramontana, Animal Science Laboratory, University of Illinois, 1207 W. Gregory Dr., Urbana, IL 61801 USA; Phone: 217-265-8497; Fax: 217-333-8286; Email: [email protected]
Juan J. Loor1, Simona Tramontana1, Arjava Sharma1, Massimo Bionaz1, Daniel Graugnard1, Elisabeth A. Cutler1, Robin E. Everts1, Sandra L. Rodriguez-Zas1, Walter L. Hurley1
ABSTRACT: MammOmicsTM in Sus scrofa: Uncovering Genomic Adaptations Underlying Mammary development during Pregnancy and Lactation
1Department of Animal Sciences, University of Illinois, Urbana, IL, USA
The molecular networks controlling skeletal muscle growth in rapidly-growing steer calves remain to be fully elucidated. Objectives were to uncover and evaluate temporal expression of gene networks in longissimus muscle (LM) of early-weaned (~140 d age) Angus steers (n = 7/diet) fed a high-energy (HiE, NEG = 1.43 Mcal/kg) or high-fiber (HiF, NEG = 1.19 Mcal/kg) diet during the growing phase (120 d after weaning). LM biopsies for transcript profiling were collected at 0, 60, and 120 d of feeding. A 13,257 bovine oligonucleotide (70-mers) array was used for transcript profiling. Annotation was based on similarity searches using BLASTN and TBLASTX against human, mouse, and bovine UniGene databases, the human genome, and the cattle TIGR database.
Feeding HiE vs. HiF during the growing phase enhanced animal performance (3.0 vs 2.4 lbs/d ) primarily during the first 60 d of feeding. Transcript profiling showed that a considerable number of genes (5,000; FDR ≤ 0.05) were differentially expressed (DEG) by time alone during the growing phase. Analysis also uncovered DEG due to time × diet interaction (500, FDR ≤ 0.30). Among DEG due to time, Ingenuity Pathway Analysis® (IPA) identified lipid metabolism and protein synthesis as key molecular functions, as well as 69 transcription factors (e.g., EGR1, SREBF1, PPARA, PPARG) with crucial functions in growth and metabolism. Overall, results suggest that gene networks uncovered in LM were closely associated with cell growth and proliferation as well as metabolism, which might in part account for differences in animal performance during the growing phase.
Contact Information: Daniel Graugnard, Department of Animal Sciences, University of Illinois, 1207 W. Gregory Dr., Urbana, IL 61801 USA; Phone: 217-265-8497; Fax: 217-333-8286; Email: [email protected]
J.J. Loor1, d. E. Graugnard1, S. L. Rodriguez-Zas1, D. B. Faulkner1, L. L. Berger, R. E. Everts1, H. A. Lewin1,2
ABSTRACT: defining Gene Networks Controlling Longissimus Dorsi Growth in Beef Cattle
1Department of Animal Sciences, University of Illinois, Urbana, IL, USA2Institute for Genomic Biology, University of Illinois, Urbana, USA
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Exposure of early life-stages of fish to endocrine disrupting compounds can result in a variety of negative effects, including abnormal growth, development, and altered sex differentiation. These effects can be traced to changes in gene expression. However, little is known about the baseline changes in gene expression of reproductive and developmental genes in early life-stages of fish and on the relationship between gene expression and physiological changes. The objective of this study was to describe ontogenetic changes in gene expression in a commonly used ecotoxicological model, the fathead minnow (Pimephales promelas). At weekly intervals from day 0 to 28 post-fertilization in whole embryos, we measured expression of 10 genes important for growth and sex differentiation, including growth hormone (GH), insulin growth factor (IGF), thyroid and sex steroid hormone receptors, steroidogenic acute regulatory protein (StAR), vitellogenin, and aromatase (CYP19 ovary isoform). Gene expression was quantified using quantitative polymerase chain reaction (q-PCR). Our results indicate gene-specific ontogenic changes. As expected, the expression of GH and IGF increased significantly over time. However, only one of the two thyroid hormone receptors (ß) increased during development. Vitellogenin increased up to day 10 and decreased thereafter, whereas the expression of CYP19 and StAR peaked at days 15 and 21, respectively. Knowledge of the normal changes in gene expression during development will allow for better experimental design and selection of suitable biomarkers when testing for the toxicological effects of endocrine disrupting compounds in this model species.
Contact Information: Sonia Mae Johns, Department of Forestry and Natural Resources, Purdue University, 195 Marstellar Road, West Lafayette, IN 47906 USA; Phone: 315-212-1631; Email: [email protected]
Johns S. M1, M. D. Kane2, N. D. Denslow3, K. H. Watanabe4, E. F. Orlando5, M. S. Sepúlveda1
ABSTRACT: Characterization of Ontogenic Changes in Gene Expression in the Fathead Minnow (Pimephales promelas)
1Department of Forestry & Natural Resources, Purdue University, West Lafayette, IN2Department of Computer and Information Technology, Purdue University, West Lafayette, IN3Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 4Oregon Health & Science University, Beaverton, OR5Florida Atlantic University, Boca Raton, FL
Proteomics research plays a key role in supporting gene discovery, product development and product registration studies in Dow AgroSciences. In the past five years we have developed protocols that allow us to 1) monitor protein profiles throughout plant cell fermentation 2) identify key enzymes involved in the alteration of structure and synthesis of a natural product insecticide 3) discover new insecticidal toxins 4) characterize target transgenic proteins in crop systems, and 5) Working with Monarch (known as INCAPS, an Indianapolis-based proteomics company). We have applied a label-free LC-MS/MS approach to quantify protein expression in a number of stress resistant maize lines. Key aspects of these proteomic applications will be presented.
Contact information: Weiting Ni, Dow AgroSciences, 9330 Zionsville Rd, Indianapolis, IN 46268 USA; Phone: 317 337 5219; Fax: 317 337 3228; Email: [email protected]
Weiting Ni1
ABSTRACT: Proteomics Applications in Agriculture Research
1Discovery R&D, Dow AgroSciences, Indianapolis, IN, USA
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Alternative splicing (AS) of mRNA transcripts is increasingly recognized as a common source of diversity in the eukaryotic transcriptome. To date, most AS studies have focused on intergenomic comparisons across taxa or on intragenomic comparisons across genes. We have generated a novel data set that represents one of the first population genetic comparisons of AS across individuals. In Ambystomatid salamanders, AS of the MHC class IIß chain gene produces two transcripts, one full-length and one truncated. The truncated transcript is missing exon 2, which encodes a major portion of the peptide binding region in the intact class II molecule. We captured wild tiger salamander larvae (Ambystoma tigrinum tigrinum; n = 34) and extracted RNA from both gill and spleen tissue. These larvae were all genotyped at the Amti-DAB gene via DNA sequencing of exon 2, and the relative expression level of each transcript was evaluated using RT-PCR and melting curve analyses. The mean proportion of truncated transcript was 0.29 across individuals and was generally consistent across both gill and spleen (although the absolute level of alternative transcript expression was higher in gill). The high level of nucleotide variation among the 7 Amti-DAB alleles detected in our survey means that we had substantial power to detect not only nucleotide substitutions within exon 2 that influenced the relative level of AS, but also DNA polymorphisms tightly linked to exon 2 (e.g., in adjacent introns). The data reveal no correlation between zygosity and AS, or between a given allele and AS. However, several lines of indirect evidence suggest that the truncated Amti-DAB transcript is functional and actively maintained by natural selection.
Contact information: Andrew DeWoody, Department of Forestry & Natural Resources, Purdue University, West Lafayette, IN, USA; Phone: 765-496-6109, Fax: 765-496-2422; Email: [email protected]
zafer Bulut1*, David H. Bos1*, Cory R. McCormick1*, J. Andrew DeWoody1**these authors all contributed equally to this work
ABSTRACT: Alternative Splicing of Major Histocompatibility Complex (MHC) Transcripts in a Wild Population of Salamanders
1The Bindley Bioscience Center and the Department of Forestry & Natural Resources, Purdue University,West Lafayette, IN 47907-1159 #135
Knowledge of temporal adaptations in mRNA expression of transcription factors (TF) and related networks in liver can help to better understand the tissue’s long-term adjustments to diet and physiological state. ANOVA using MIXED was conducted on liver microarray data (174 arrays) from 2 of our published studies (Physiol. Genomics 23:217-226, 27:29-41) using a platform with 7,872 bovine cDNA inserts. Data were generated from Holstein cows fed control (100% of requirements, CT), ad-libitum (ca. 150% of requirements; AA), or restricted (ca. 80% of requirements; RR) energy pre-partum, and biopsied at -65, -30, -14, 1, 14, 28, and 49 d relative to parturition. A total of 4,790 genes had a time × diet interaction (FDR < 0.05). Among these, 3,254 with ≥1.5-fold expression in at least one time point vs -65 d were used for further analysis. Ingenuity Pathway Analysis® uncovered 317 TF. Seventy-eight of these differed by ≥1.5-fold in both AA and RR vs CT. In AA vs. RR, 24 of the 78 had expression levels ≥2-fold in at least 1 time point. Temporal expression of 9 of the 24 TF was affected by AA (6 ↑ e.g., SRA1, STAT1; 3 ↓ e.g., XBP1, KLF15), and 19 of the 24 was affected by RR (8 ↑ e.g., XBP1, STAT3; 11 ↓ e.g., ELF2, BRDW1). Ten of these TF generated networks incorporating 98 differentially expressed genes, with cell death and cell signaling as top molecular functions. This study uncovered novel hepatic TF and related networks affected by prepartum level of energy intake.
Contact information: Massimo Bionaz, Animal Science Laboratory, University of Illinois, 1207 West Gregory Dr., Urbana, 61801 IL, USA; Phone: 217-265-8497, Fax: 217-333-8286; Email: [email protected]
Juan J. Loor1, Massimo Bionaz1, Sandra L., Rodriguez-Zas1, Heather M. Dann1, Nicole A. Janovick Guretzky1, Robin E. Everts1, Rosane Oliveira1, Harris A. Lewin1,2, James K. Drackley1
ABSTRACT: Liver Transcription Factor Networks Affected by Prepartum Plane of dietary Energy and Physiological State in Periparturient Holstein Cows
1Department of Animal Sciences, University of Illinois, Urbana, USA2Institute for Genomic Biology, University of Illinois, Urbana, USA #134
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PPAR gamma gene expression can be used as a marker of adipogenic differentiation in mesenchymal stem cells (MSCs). Real-time RT-PCR (qPCR) requires data normalization to account for analytical errors. Evaluation of internal controls is crucial for reliability of data. The aims of the present work were: (1) to evaluate several genes as internal controls for adipogenic differentiation of porcine mesenchymal stem cells (MSCs); and (2) to study PPAR gamma gene expression in the same experiment. Adult stem cells from subcutaneous adipose tissue and bone marrow of adult pigs were isolated and differentiated along the adipogenic lineage. The adipogenic differentiation of the MSCs was assessed by their morphological and phenotypic properties. RNA at 0, 2, 4, 7, 14, 21, 28 days of differentiation (dd) was extracted and qPCR was performed. Ingenuity Pathway Analysis® (IPA) and GeNorm software were used to evaluate the reliability of 4 genes as internal control (GAPDH, GTF2H, NUBP, PPP2C). The absence of co-regulation among the internal control genes was assessed by IPA. GeNorm uncovered GTF2H, NUBP, and PPP2C as the most reliable internal controls. PPARG showed in both tissues a rapid and large increase (> 20 fold vs 0 dd; P < 0.01) during the first dd and reached a peak at 5 dd, afterward it exhibited a gradual decrease until 20 dd. GTF2H, NUBP, and PPP2C can be used as internal control for qPCR analysis of MSCs. PPARG was shown to be essential for the adipogenic differentiation during the first dd.
Contact Information: Elisa Monaco, Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1207 West Gregory Drive, Urbana, IL, 61801, USA; Phone: 217-244-3150; Fax: 217-333-8286; Email: [email protected]
Matthew B. Wheeler1, Elisa Monaco1, Alecsandra Lima1, Shanna Wilson1, Dongshin Kim1, Massimo Bionaz1
ABSTRACT: Identification of Reference Genes for qPCR and PPARG Gene Expression during Adipogenic differentiation of Porcine Adult Mesenchymal Stem Cells
1Department of Animal Sciences, University of Illinois, Urbana, IL, USA
The major histocompatibility complex (MHC) is a large multigene family that plays a central role in the vertebrate immune response. The maintenance of high allelic diversity in the MHC is generally thought to be the result of natural selection pressure from pathogens and sexual selection to produce offspring with heterozygous MHC types. However, the relative contribution that either selective force has made in shaping the evolution of MHC remains unclear. Therefore, we propose to isolate an MHC locus in order to study two intensively monitored populations of the banner-tailed kangaroo rat (Dipodomys spectabilis) to 1) look for evidence of MHC-based sexual selection and 2) determine whether MHC loci display a signature of natural selection. We will use a class II-ß locus to compare MHC variation against an existing framework of ecological data (parentage, proximity of relatives, survivorship, etc.). This combination of data will allow us to test for MHC-based associations such as mate choice, survivorship, and longevity, providing a rare opportunity to assess the selective forces acting on the MHC of natural populations.
Contact Information: Joseph D. Busch, Department of Forestry & Natural Resources, Purdue University, 715 W. State St., West Lafayette, IN 47907 USA; Phone: 765-496-6868; Fax 765-494-9461; Email: [email protected]
Joseph d. Busch1, Peter M. Waser2, J. Andrew DeWoody1
ABSTRACT: Sexual and Natural Selection on MHC Genes of the Banner-Tailed Kangaroo Rat
1Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, USA2Department of Biology, Purdue University, West Lafayette, IN, USA
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Ogura Cytoplasmic male sterility CMS and its corresponding nuclear fertility restorer gene, Rfo, have been introduced from radish to Brassica species by interspecific crosses. Rfo restores male fertility by altering the translational expression of Orf138, a mitochondrial gene, whose expression results in the male sterile phenotype. This system has been extensively investigated and breeding restorer lines for the Ogura CMS has become a major objective for hybrid seed production in many canola breeding programs. In this study, we have sequenced genomic clones of Rfo amplified from a canola restorer line R2000, licensed from INRA, France, and a Dow AgroSciences proprietary non-restorer line Nexera 705 using primers designed from the radish Rfo sequence (GenBank accession AJ550021). Sequence alignment revealed three paralogs of Rfo. Two of the paralogs were present in both R2000 and Nexera 705 but the third one was present only in R2000. These results suggested that the first two sequences could be the orthologs of Rfo already existing in the canola genome and the third one could be the radish Rfo introduced into canola. Based on the sequence differences between the restorer and non-restorer lines, Rfo allele-specific PCR markers were developed. We also developed a high throughput, Rfo allele-specific Invader assay through Third Wave Technologies. Linkage analysis revealed a co-segregation between the markers and the phenotypes for fertility restoration. These markers have been proved to be very useful for direct selection of Rfo alleles for fertility restoration during marker-assisted introgression of the Ogura restorer for hybrid development in canola.
Contact Information: Xueyi Hu, Dow AgroSciences, LLC, 9330 Zionsville Road, Indianapolis, IN 46268 USA; Phone: 317-337-3460; Fax: 317-337-5989; Email: [email protected]
Xueyi Hu1, Mandy Sullivan-Gilbert1, Tom Kubik2, Jason Danielson2, Nathan Hnatiuk2, Wesley Marchione1, Manju Gupta1, Katherine Armstrong1, Steven Thompson1
ABSTRACT: development of Molecular Markers Specific to the Ogura Fertility Restorer Gene Rfo in Canola (Brassica napus L.)
1Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN 46268, USA2Dow AgroSciences LLC, 101-421 Downey Road, Saskatoon, SK S7N-4L8, Canada
This project is a documentation of significant genetic research funded by the Minnesota Agricultural Experiment Station since 1888. The result is a book that chronicles the contributions of University of Minnesota research projects and their world-wide impact. All the examples are related to genetic discoveries and other “firsts” of Minnesota scientists. The stories are told in words, photos, and watercolor illustrations, plus a timeline, all of which makes for easy digestion of often technical topics. They cover fields as varied as fisheries, food and fruit, with additional chapters on livestock reproduction, soil microbes and plant breeding. The history was developed from archives, annual reports, journals, and interviews with current and retired scientists. The goal of the project is to show to the general public, and groups interested in – or concerned about – current research, how research has evolved from “Genetics to Genomics” over the last century-plus. Copies of the book will be distributed free to those attending the conference.
Contact Information: David Hansen, Minnesota Agricultural Experiment Station, University of Minnesota, 405 Coffey Hall, 1420 Eckles Ave, St. Paul, MN 55108. Phone: 612-625-7290; Fax: 612-624-7724; Email: [email protected]
Leland Hardman1, David Hansen2
ABSTRACT: Genetics to Genomics; Landmark discoveries from the Minnesota Agricultural Experiment Station
1Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA 2Minnesota Agricultural Experiment Station, University of Minnesota, St. Paul, MN, USA
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Analysis of transgenic plants involves the ability to track the gene-of-interest at the DNA level and to quantitate expression at the protein level. The ability to detect and quantitate transgenic protein expression is a critical metric required to characterize events in any transgenic program and is also required for regulatory submission. ELISA is the traditional method for protein detection/quantitation and works well when there is sufficient divergence between expressed and native proteins that allows for the development of antibodies that can differentially recognize these proteins. Unfortunately, when the difference between the native and transgenic proteins is small, for example, a 1 or 2 amino acid insertion, or a single amino acid substitution, it is not always possible to develop an antibody capable of differentiating these proteins. LC/MS/MS provides the ability to individually detect and quantitate proteins of this type of homology, allowing the transgenic protein expression in corn to be monitored.
This assay measures the amount of the targeted protein expressed in plant tissue, by analyzing for diagnostic tryptic peptide fragments of the protein variants. We have shown that crude plant extract can be enzymatically digested, resulting in the formation of diagnostic peptide fragments. The diagnostic fragments contain the amino acid insertion or mutation of interest, and LC/MS/MS analysis is used for detection of these fragments. This LC-MS/MS based assay has the sensitivity and selectivity to differentiate seed expressed transgenic from native protein, and the capacity to rapidly screen transgenic lines for the selection of the highest expressing lead events.
Contact Information: Debbie Schwedler, Dow AgroSciences, 306/B2, 9330 Zionsville Road, Indianapolis, IN 46268 USA; Phone: 317-337-3540; Fax: 317-337-3255; Email: [email protected]
debbie Schwedler1, Ted E. Weglarz1, Andrew W. Carr1, Thomas W. Greene1, John R. Lawry1, Lizhen Wang1, Jill R. Bryan1, Jeffrey R. Gilbert1
ABSTRACT: Plant Protein Expression Analysis by LC/MS/MS Monitoring of Tryptic Peptides
1Dow AgroSciences, Indianapolis, IN, USA #140
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Baker, R. J. ........................................... 10Beachy, Roger N. .................................. 12Beavis, William ..................................... 14Beeman, Dick ....................................... 16Bennetzen, Jeffrey ................................ 18Buckler, Edward .................................... 20Cheng, Hans .......................................... 22Collins, Frank H. .................................. 24Collmer, Alan ........................................ 26Ecker, Joseph ........................................ 28Fields, Nathan ...................................... 30Goddard, M. E. ..................................... 32Goldman, Irwin..................................... 34Hoekstra, Hopi ...................................... 36Liu, Zhanjiang (John) ........................... 38McDonald, John F. ................................ 40McLean, John ....................................... 42O’Brien, Stephen J. .............................. 44Phillips, Ronald .................................... 46Rokhsar, Daniel .................................... 48Sanderson, Michael J. .......................... 50Schnable, Patrick .................................. 52Schook, Lawrence ................................. 54Sussman, Michael ................................. 56Thompson, Steve .................................. 58Womack, James E. ............................... 60
Aggarwal, Rajat ................................... 64, 65Akers, R. M. ......................................... 71Ammons, Andrew ................................. 63Anderson, D. ........................................ 64Anderson, J. ......................................... 75Anderson, Joseph M. ............................ 66, 70, 74Armstrong, Katherine ........................... 81Arnold, Nicole ....................................... 76Baenziger, P. ........................................ 75Bai, G. .................................................. 75Bai, Hua ................................................ 66Baker, Lisa ............................................ 73Barkley, Noelle ..................................... 72Bauer, Teresa ........................................ 73, 76Benatti, Thiago ..................................... 64, 65Bentur, Jagadish ................................... 69Berenbaum, May R. ............................. 63Berger, L. L. ......................................... 77Berzonsky, B. ....................................... 75Bionaz, M. ............................................ 71Bionaz, Massimo ................................... 77, 79, 80Birren, Bruce ......................................... 67Blue, Ryan ............................................ 73Bos, David H. ....................................... 79Boucias, Grion G. ................................. 68Broman, Karl W. .................................. 74Brown-Guedira, G. .............................. 75Bryan, Jill R. ........................................ 84Buescher, Elizabeth ............................... 74Bulut, Zafer ........................................... 79Cai, Charles ........................................... 73Campbell, K. ........................................ 75Carr, Andrew W. ................................... 84Carver, B. ............................................. 75Casteel, Clare L. ................................... 63Chen, M-S. ........................................... 65Chen, Ming-Shun .................................. 69Collingwood, Trevor .............................. 73, 76Collins, Frank H. .................................. 67Cui, Xinping .......................................... 74Cutler, Elisabeth A. .............................. 77Daniels, K. M. ...................................... 71Danielson, Jason .................................. 81Dann, Heather M. ................................ 79
AUTHOR INDEX SPEAKER INDEX
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IndexDe Lucia, Evan H. ................................ 63Dean, Rob ............................................. 72DeKelver, Russell .................................. 73, 76Denton, Anne M. .................................. 72Denslow, N. D. ..................................... 78DeWoody, J. Andrew ............................. 79Doyon, Yannick ..................................... 76Drackley, J. K. ...................................... 71, 76Drackley, James K. ............................... 79Dubcovsky, J. ........................................ 75Duge, Megan ........................................ 74Emore, Christine ................................... 63Everts, R. E. .......................................... 71, 76, 77Everts, Robin E. .................................... 77, 79Farmerie, William G. ........................... 68Faulkner, D. B. ..................................... 77Fellers, J. P. .......................................... 65Fritz, A. ................................................ 75Gahr, Scott A. ....................................... 74Gao, Zhifang ......................................... 76Geraci, Nicholas S. ............................... 67Gilbert, Jeffrey R. ................................ 84Gillaspie, Graves................................... 72Graugnard, D. ...................................... 71Graugnard, D. E. .................................. 77Graugnard, Daniel ............................... 77Gray, Benjamin ..................................... 62Greene, Thomas W. ............................. 84Gregory, Philip ..................................... 73Griffey, C. ............................................. 75Guerrero, Felix D. ................................ 67Gupta, Manju ........................................ 81Haley, S. ............................................... 75Hansen, David ...................................... 81Hardman, Leland ................................. 81Hill, Catherine A. ................................. 67, 68, 73Hnatiuk, Nathan ................................... 81Housley, Thomas L. .............................. 66Hu, Xueyi .............................................. 81Hubert, S. ............................................. 65Hunt, Greg ............................................ 63Hurley, Walter L. .................................. 77Janovick-Guretzky, N. A. ..................... 76Janovick-Guretzky, Nicole A. ............... 79
Jenkins, Tracie ...................................... 72Johns, S. M. .......................................... 78Johnson, J. ........................................... 75Kane, M. D. .......................................... 78Kianian, S. ........................................... 75Kidwell, K. ........................................... 75Kim, Dongshin ...................................... 80Knolhoff, Lisa M. .................................. 67Kong, Lingrang ..................................... 70Kongsila, Pasajee ................................. 66Kraus, Emily C. ..................................... 73Kubik, Tom ............................................ 81Kumpatla, S. ........................................ 64Kumpatla, Siva P. ................................. 65Lawry, John R. ..................................... 84Lewin, H. A. ......................................... 71, 76, 77Lewin, Harris A. ................................... 79Li, Hong-Mei ......................................... 70Lima, Alecsandra .................................. 80Lizarazu, O. Riera ................................. 75Loor, J. J. .............................................. 71, 76, 77Loor, Juan J. ........................................ 77, 79Marchione, Wesley ................................ 81McCaskill, Dave ..................................... 76McCormick, Cory R. .............................. 79McDowell, Donald ................................. 62McPherson, M. ..................................... 64Mergoum, M. ....................................... 75Meyer, Jason M. ................................... 67Miller, Jeffrey ........................................ 73, 76Mitchell, Jon.......................................... 76Mittapalli, Omprakash .......................... 69Moehle, Erica ........................................ 76Monaco, Elisa ........................................ 80Morin, D. E. .......................................... 71Moyes, K. M. ........................................ 71Muir, William ........................................ 70Murdock, Larry L. ................................ 70Novak, Stephen .................................... 76Neal, Jonathan ..................................... 69Nene, Vish M. ....................................... 67Ni, Weiting ............................................ 78Nichols, Krista M. ................................. 74Ohm, H. ............................................... 75
AUTHOR INDEX (cont.)
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Ohm, Herbert W. .................................. 70Oi, Faith M. .......................................... 68Oliveira, Rosane ................................... 79Onstad, David W. ................................. 67Orlando, E. F. ....................................... 78Palli, Subba Reddy ............................... 66Pederson, Gary ..................................... 72Peterson, J. .......................................... 75Pellow, J. .............................................. 64Petolino, Joseph F. ............................... 73Phillips, Ruth B. ................................... 74Piantoni, P. ........................................... 71Pittendrigh, Barry R. ........................... 70Prüß, Birgit ........................................... 69, 72Ramaseshadri, Parthasarathy .............. 66Ratcliffe, Susan T. ................................. 67Rebar, Ed .............................................. 76Rexroad, III, Caird E. ........................... 74Robertson, Hugh M. ............................. 67Rock, Jeremy ......................................... 76Rodriguez-Zas, S. L. ............................ 71, 77Rodriguez-Zas, Sandra L. .................... 77, 79Rowland, Lynn ...................................... 76Rudd, J. ................................................ 75Scharf, Michael E. ................................ 68Schemerhorn, B. J. ............................... 65, 70Schlueter, Jessica .................................. 68Sepúlveda, M. S. .................................. 78Shah, Manali R. ................................... 65Sharma, Arjava .................................... 77Sherman, J. .......................................... 75Shukle, Richard .................................... 69Shukla, Vipula ...................................... 76Simpson, Matt ....................................... 76Singh, Harvinder .................................. 62Singh, N. K. ......................................... 62Soria, M. .............................................. 75Sorrells, M. .......................................... 75Souza, E. .............................................. 75Stuart, Jeffrey ....................................... 64, 65, 67, 69Sule, Preeti ........................................... 69Sullivan-Gilbert, Mandy ....................... 81Sun, Lijie .............................................. 70Sundin, Kyle .......................................... 74
Talbert, L. ............................................ 75Tartar, Aurélien ..................................... 68Thompson, A. ...................................... 65Thompson, Steven ................................ 81Thorgaard, Gary H. ............................. 74Townsend, Megan K. ............................ 72 Tramontana, Simona ............................ 77Urnov, Fyodor ....................................... 73, 76Van Zee, Janice P. ................................. 67, 68, 73Walden, Kim K. O. ............................... 67Wang, Lizhen ........................................ 84Wang, Ming Li ...................................... 72Watanabe, K. H. .................................. 78Weglarz, Ted E. .................................... 84Wheeler, Matthew B. ............................ 80Wheeler, Paul A. .................................. 74Wikel, Stephen K. ................................ 67Wilson, Shanna ..................................... 80 Wise, Ian ............................................... 69Worden, Andy ....................................... 73Worden, Sarah ...................................... 76Worku, Mulumebet ............................... 62Wu, Jianfei ............................................ 72Wu, Jing ................................................ 70Xie, Jun ................................................. 70Yan, L. .................................................. 75Yau, Kerrm ............................................ 76Young, Jennifer ..................................... 74Zavala, Jorge A. .................................. 63Zemetra, R. .......................................... 75Zhang, Lei ............................................. 76Zhao, C. ................................................ 64, 65Zhou, Xuguo ......................................... 68
AUTHOR INDEX (cont.)
Addendum
Employment Announcement Board North Ballroom
Conference Banquet (Monday Evening) Cash Bar Opens at 6:00 pm
Poster Session and Mixer (Tuesday Evening) Cash Bar Opens at 6:00 pm Poster Awards Announced at 8:00 pm
Agenda Overview Tuesday and Wednesday Lunch Break - Lunch on your own
Poster additions #141 - Yuejin Sun, dow AgroSciences LLC, Indianapolis, IN “Global Transcript Analysis of the Transition from Mitotic Cell Division to Endoreduplication During Maize Endosperm Development”
#142 - Todd Gaines, Colorado State University, Fort Collins, CO “Molecular Methods to Study Herbicide Resistant Weeds and Inter-Specific Gene Flow”
#143 - Giridara-Kumar Surabhi, Kansas State University, Manhattan, KS “Environmental and Ecological Controls on Gene Expression of Root Processes in Prairie Plants”
