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Cotton Breeding for Fusarium wilt
race 4 (FOV4) Resistance in Cotton
with additional molecular approach
FOV4 Genetics and QTL Mapping
FOV4 Transcriptomics / Gene Expression
USDA-ARS, University Cooperators, CA Cotton Growers, and
Cotton Incorporated
– Cooperative Project - Prepared by Dr. Mauricio Ulloa
California FOV4 Nursery 2017
2006
2017
Breeding Efforts Supported by California Cotton
Grower’s Organizations, including CCGGA and CI
University of California,
Dr. Robert Hutmacher, Mark Keeley, Steve
Wright with many other staff and students,
and more recently Tarilee Frigulti have
performed the breeding activities since
2012 of this collaborative effort.
Continue Breeding Support
Effort 2012-Present
of Dr. Ulloa, USDA-ARS,
Lubbock, TXPrepared by Dr. Mauricio Ulloa, USDA, ARS
Cotton Germplasm Collections Evaluated by
USDA-ARS and Univ. of CA. for FOV4 Resistance
New Mexico State University – Dr. Roy Cantrell
• NM 59-851, ACALA 1517-75, ACALA 1517-88, ACALA 1517-91, ACALA
1517-95, ACALA 1517-99, etc., Dr. Ulloa/Research Associate -1996 - 1998,
Pima lines provided MS. Cindy Waddell – 2003
USDA-ARS – Maricopa AZ – Dr. Percy 2003
• Pima S-series, PS1-PS32, Pima lines from NMSU, Pima population
developed for Genetics/QTLs mapping 1999 -2000 F1 and F2. (around 186
F6 lines - collaborative project with Dr. Ulloa).
USDA-ARS Shafter, CA - & College Station, TX Collection
• Acala FBCX-2, Shorty, Acala Shafter Station, Del Cerro SS227, UCD368
Hopi M5-11, Acala 8, Acala 4-42 1958-A , Acala 4-42 1966-A, Acala SJ-2,
SJ-3SJ-5, etc., 2003 – 2006.
Regional Breeding Testing Network (RBTN) germplasm
• from more than 12 breeding cotton programs across the belt. Since 2004
- Present.
Prepared by Dr. Mauricio Ulloa, USDA, ARS
International Cotton Germplasm Programs/Collections
Evaluated for FOV4 Resistance
Australia CSIRO – Fiber Max germplasm collection2004 visited and exchanged germplasm.
• Tested germplasm for this program which also included tolerant Upland
Sicot 189 and resistance source MCU-5 germplasm lines to FOV
Australian races.
• Australian germplasm lines were susceptible to the California FOV4.
Republic of Uzbekistan germplasm collection FOV racesSince 2006 and visited several times since 2009, 2011, 2103.
Tested several germplasm lines.
• Discovered new potential source of FOV4 resistance.
Country of Peru Visited in 2009, 2016 and had the opportunity to visit cotton fields and
evaluate germplasm known as Tanguis.
2016 started new Agreement with IPA Peru to exchange and develop
germplasm. In 2017, Seven breeding lines ongoing evaluation.
Prepared by Dr. Mauricio Ulloa, USDA, ARS
FIRST TIMELY RESPONSE FROM FOV4
RESISTANCE EVALUATIONS
Identified Pima Germplasm resistant to FOV4
Some USDA-ARS Pima (e.g., Pima-S6) – Original
Pima-S6 (PS6) release was a variable/heterozygous-pool, but it is a good
source for FOV4 resistance from USDA-ARS compared to other PS1,2…
releases. PS6 resistance source has been confirmed by independent
labs (UC, Davis, UC Riverside, USDA-ARS College Station, and
Phytogen Seed Co.)
An experimental, later known as commercial cultivar
Phytogen 800
This research identified potentially new improved resistant
germplasm for release
Greenhouse EvaluationsField Evaluations
Prepared by Dr. Mauricio Ulloa, USDA, ARS
2007/2008
PUBLIC PIMA GERMPLASM LINES JONTLY RELEASED BY USDA-
ARS, UNIV. OF CALIFORNIA, & UNV. OF NEW MEXICO
SJ-07P-FR01, SJ-07P-FR02, SJ-07P-FR03, and SJ-07P-FR04
Pedigrees: 8810 (P72xP73 Pima Series AZ) and NMSI-1601 originated from a Sea Island cotton
2015/2016
PUBLIC PIMA GERMPLASM LINES JONTLY RELEASED BY USDA-
ARS & UNIV. OF CALIFORNIA
SJ-FR05, SJ-FR06, SJ--FR07, SJ-FR08, and SJ-FR09
Pedigrees: Pima S6 (Series AZ) and 89590 Line (P62 x Sea Island St. Vicent)
Projected New Pima Releases
2018 Pedigree: Pima-S6 x Pima-S7
Prepared by Dr. Mauricio Ulloa, USDA, ARS
Field Site with Fusarium wilt - FOV4
Susceptible Resistant
USDA-ARS and University of California Davis – Cooperative -
Prepared by Dr. Mauricio Ulloa
Fusarium wilt RACE 4 (FOV4)
USDA-ARS and University of California Davis – Cooperative
Project - Prepared by Dr. Mauricio Ulloa
ROOT DIP GREENHOUSE FOV4 TEST FOV race 4 Seedling
Inoculation
Vascular stem and root staining (VRS)
VRS = 0 VRS = 2 - 3 VRS =5
Susceptible CheckPima-S7 (PS7)
Resistant CheckPima-S6 (PS6)
DSI = 0 DSI = 2 - 3 DSI = 5
Disease severity index (DSI) of leaves, (scale 0 – 5)
Present Summary for FOV4 Resistance
Upland Germplasm Evaluated from the USDA-ARS
Collection, College Station, TX
More than 400 obsolete cultivars and/or SA lines Upland Lines
Identified Upland SA lines tolerant to FOV4
Developed Upland Progeny with identified
Resistant/Tolerant Sources
More than 500 crosses combinations
More than 1,500 progeny developed and so far about 400 FOV4
evaluated
Identified an Upland RBTN source Now clean of AP and tested-
Negative for AP from NMSU
Identified and Developed new progeny resistant to FOV4 from
PS6xUzbekistan germplasm
Prepared by Dr. Mauricio Ulloa, USDA, ARS
Seed Increase for Germplasm Release under Clean
or Uninfested FOV4 Field
Continue Breeding Efforts 2012-Present
of Dr. Ulloa, USDA-ARS, Lubbock, TX with the CA group -
Dr. Hutmacher. Univ. of CA.
UPLAND FOV4 TOLERANCE/RESISTANCE
UPDATE
Upland TM-1 x Pima-S6 and Upland Shorty X Pima-S6 AND
Reciprocal-Progeny
Upland SA-Lines (obsolete cultivars) X US63 (Uzbek x Pima-S6)
AND Reciprocal-Progeny
Upland SA-Lines (obsolete cultivars)
Upland SA-Lines (obsolete cultivar) X Upland SA-Lines (obsolete
cultivars) AND Reciprocal-Progeny
Upland RBTN-NMSU Line X Upland SA-Lines (obsolete cultivars)
AND Reciprocal-Progeny
DEVELOPING FOV4 TOLERANT BREEDING LINES OR PROGENY
Sources of Breeding/Selection made for FOV4 Tolerance/Resistance
Cleaning lines of AP (transgenic contamination – USDA-ARS and UC Davis)Prepared by Dr. Mauricio Ulloa, USDA, ARS
bp
527
404 F1 S R S S S S S S S S R R R R R R R R R R
1 2
SSR marker evaluated on susceptible (S) Upland Shorty [ No. 1, (Gossypium
hirsutum L.)]; resistant (R) Pima-S6 [No. 2, (G. barbadense L.)], and R F2
(Shorty x Pima-S6) single plants.
Molecular marker such as Microsatellite or SSR
Previous research identified/developed approximately 150 SSRs
published (www.cottongen.com) with Major and Minor association to
Disease Resistance which include all FOV races and root-knot nematode
(RKN)
SSR markers have been and could be used for marker assisted selection
or MAS.
Additional Research of Inheritance, Genetic and
QTL Mapping for FOV race 4 Resistance Ongoing
Prepared by Dr. Mauricio Ulloa, USDA, ARS
Different gene-specificity for FOV resistance:
Fov1 (race 1) – chromosomes 6,8,11, 12, 16 and 19
(Ulloa et al., 2011; Wang et al. 2017 submitted).
Fov3 (race 3) – Chromosomes – Ongoing (Uzbek - USDA
Collaboration)
Fov4 (race 4) – chromosomes 3,6,8,14 and 17
(Ulloa et al. 2013; Wang et al. 2014; Ulloa et al. 2016; Wang et al.
2017 submitted).
FWR (race 7) - chromosome 17
(Wang et al., 2009).
Australian race of Fov – chromosomes 6,
22, and 25 (Becerra et al., 2012).
Reported Loci/genes associated to FOV Resistance
Explaining 10% - 80% FOV4
resistance variation. Approximately – 10 SSRs with major and 55
with minor Association with FOV resistance.Prepared by Dr. Mauricio Ulloa, USDA, ARS
Information about FOV4 Research - California Selected Publications
2005 Kim, Y.f, R.B. Hutmacherd, R.M. Davisd. 2005. Characterization of California
Isolates of Fusarium oxysporum f. sp. Vasinfectum. Plant Disease 89:366-372.
2005 Hutmacher, R.B.d, R.M. Davisd, S.D. Wrightg, M. Ulloac, D.S. Munkg, B.H.
Marshg, B.A. Robertsg, R.N. Vargasg, M.P.Keeleyb. 2005. New Fusarium Issues
for California Cotton. Cotton Industry – National Cotton Council and J. Cotton
Sci.
2006 Ulloa, M.d, R.B. Hutmacherd, R. M. Davisg, S.D. Wrightg, R. Percyc, B. Marshg.
2006. Breeding for Fusarium Wilt Race 4 Resistance in Cotton Under Field and
Greenhouse Conditions. J. Cotton Sci. 10:114-127.
2006 Hutmacher, R.B.a, R.N. Vargasg, S.D. Wrightg. 2006. Methods to Enable the
Coexistence of Diverse Cotton Production Systems. Agricultural Biology In
California Series, Publication # 8191. Univ. of CA Div. Agric. Nat. Resources,
http://anrcatalog.ucdavis.edu
2006 Ulloa, M.a, R. Percyc, R.B. Hutmacherg, R.G. Cantrellh. 2006. Registration of
SJ-U86 Cotton Germplasm Line with High Yield and Excellent Fiber Quality.
Crop Sci. 46:2336-2338.
2007 Ulloa, M.a, R.G. Percyc, R.B. Hutmacherg, R.G. Cantrellh. 2007. Notice of
release of one Upland cotton germplasm line (SJ-U86) for California possessing
superior lint yield, fiber traits and heat tolerance. Germplasm Release. Crop Sci.:
47:106-107.
2007 Ulloa, M.a, Percy, R.c, R.B. Hutmacherg, J.F. Zhange 2007. The Future of cotton
breeding in the Western United States. Paper #1355. Proc. World Cotton
Research Conference IV, September 11-14, 2007, Lubbock, TX, Cotton Council
International, 15 pp. electronic:
http://www.icac.org/meetings/wcrc/wcrc4/presentations/data/html
2007 Bennett, R.S.a, R.M. Davisg, R.B. Hutmacherg. 2007. Fusarium oxsysporun f,
Sp, vasinfectum Race 4 in California: A Reemerging Threat to Cotton
Production. Paper #1383. Proc. World Cotton Research Conference IV,
September 11-14, 2007, Lubbock, TX, Cotton Council International, 9 pp.
electronic: http://www.icac.org/meetings/wcrc/wcrc4/presentations/data/html
Contributions to
2008 Bennett, Rebecca S., R.B. Hutmacher, R. Michael Davis. 2008. Seed
Transmission of Fusarium oxysporum f. sp. vasinfectum Race 4 in California. J.
Cotton Science. 12: 160-164.
2008 Ulloa, M., Percy, R.G., Hutmacher, R.B., Wright, S. and Davis, M. 2008.
Release of SJ-07P-FR01, SJ-07P-FR02, SJ-07P-FR03, and SJ-07P-FR04
‘Cotton’. USDA Germplasm Release. Pp. 79-81.
2008 Gilbert, C.A., N. Zhang, R.B. Hutmacher, R. M. Davis, C.D. Smart. 2008.
Development of a DNA-based Macroarray for the Detection and Identification of
Fusarium oxysporum f. sp. vasinfectum in cotton tissue. J. Cotton Science
12:165-170.
2009 Ulloa, M., R. Percy, R.B. Hutmacher, J. Zhang, R.M. Davis, S.D. Wright. 2009.
Registration of Four Pima Cotton Germplasm lines (SJ-07P-FR01 – FR04)
Possessing Good Levels of Resistance to Fusarium wilt race 4 With Moderate
Yields, and Good Fibers. J. Plant Registration. 3(2):198-202.
2011 Bennett, D.W. Spurgeon, W.R. DeTar, J.S. Gerik, R.B. Hutmacher, B.D. Hanson.
2011. Efficacy of four soil treatments against Fusarium oxysporum f sp.
Vasinfectum Race 4 on cotton. J. Plant Disease. 95:967-976..
2011. Ulloa, M., C. Wang, R.B. Hutmacher, S.D. Wright, R. Michael Davis, S.A. Saski,
P.A. Roberts. 20__. Mapping Fusarium Wilt Race 1 Resistance Genes in
Cotton by Inheritance, QTL, and Sequencing Composition. Molec. Genetic
Genomics. 286(1): 21-36.
2011 Bennett, R.S., W. O’Neill, L. Smith, R.B. Hutmacher. 2011. Commercial
detergents effective against conidian and chlamydospores of Fusarium
oxysporum f. sp. Vasinfectum. J. Cotton Science. 15:162-169
2013 Ulloa, M., Hutmacher, R.B., Roberts, P.A.. Wright, S.D., Nichols, R.L. and Davis,
R.M. 2013. Inheritance and QTL mapping of Fusarium wilt race 4 resistance in
cotton. Journal of Theoretical and Applied Genetics. 126:1405-1418.
2013 Hutmacher, R.B., Ulloa, M., Wright, S.D., Campbell, B.T., Percy, R.G., Wallace,
T., Myers, G., Bourland, F., Weaver, D., Chee, P., Thaxton, P., Zhang, J., Smith,
W., Dever, J., Kuraparthy, V., D. Bowman, D. Jones, J.Burke. Elite Upland
Cotton Germplasm-Pool Assessment of Fusarium wilt resistance in California.
Agronomy Journal 105:1635-1644. 2013.
2015 Cianchetta, A., T.W. Allen, R.B. Hutmacher, R.C. Kemerait, TL. Kirkpatrick, G.W.
Lawrence, K.S. Lawrence, J.D. Mueller, R.L. Nichols, M. Olsen, C. Overstreet,
J.E. Woodward, R.M. Davis. 2015. Survey of Fusarium oxysporum f. spp. Vas
infectum in the United States. J. Cotton Science. 19: 328-336.
2015 Ulloa, M., Hutmacher, R., Percy, R.G., Wright, S., Burke, J.J. Release of Pima
SJ-FR05, Pima SJ-FR06, Pima SJ-FR07, Pima SJ-FR08, and Pima SJ-FR09
Pima cotton with improved FOV4 resistance, and good lint yield and fiber quality.
Germplasm Release. p.1-2. 2015.
2016 Ulloa, M., Hutmacher, R.B., Percy, R.G., Wright, S.D., Burke, J.J. Registration of
five pima cotton germplasm lines (SJ-FR05 - FR09) with improved resistance to
fusarium wilt race 4 and good lint yield and fiber quality. Journal of Plant
Registrations. 10:154-158. 2016.
2016 Ulloa, M., Wang, C., Saha, S., Hutmacher, R.B., Stelly, D.M., Jenkins,
J.N., Roberts, P. Analysis of root-knot nematode and fusarium wilt
disease resistance in cotton (Gossypium spp.) using chromosome
substitution lines from two alien species. Genetica. 144(2):167-179.
2016
SNPi10463Gh0.0SNPi00939Gh0.5SNPi10435Gh3.3SNPi16247Gh4.4SNPi36282Gh6.1SNPi50131Gb7.2SNPi28797Gh16.3SNPi27871Gh16.9SNPi10336GhSNPi64224GmSNPi68839GlSNPi61786Gt
17.4
SNPi16965Gh21.3SNPi10321Gh23.0SNPi36890Gh29.8SNPi33150Gh30.4SNPi16938GhSNPi16939GhSNPi31262Gh
30.9
SNPi10283Gh31.5SNPi24610Gh37.7SNPi16848Gh38.0SNPi26445Gh38.3SNPi25750Gh43.9SNPi42467GhSNPi45830Gh
46.2
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51.8
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53.4
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54.5
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55.0
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55.6
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67.6
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101.6
SNPi41938Gh102.1SNPi09677Gh102.7SNPi00462GhSNPi23971Gh
110.2
SNPi48064Gh111.8SNPi09594GhSNPi46042GhSNPi09595Gh
112.4
SNPi41393Gh114.0SNPi09569Gh114.2SNPi21925Gh114.6SNPi22725Gh115.1SNPi09551Gh115.6SNPi09546GhSNPi26620Gh
116.2
SNPi09526GhSNPi09536Gh
118.4
SNPi14159Gh118.9SNPi09486Gh124.1SNPi69754Gl124.6SNPi30503Gh132.2SNPi09353Gh132.7SNPi59127Gb134.9SNPi21916GhSNPi09340Gh
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154.3
SNPi00362Gh156.0SNPi09172GhSNPi09182GhSNPi16618Gh
156.5
SNPi09181Gh156.9SNPi09180Gh157.1SNPi09169Gh157.6SNPi09163Gh158.1SNPi25035Gh159.2SNPi00269GhSNPi09121Gh
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SNPi09106Gh163.6SNPi34361Gh165.3SNPi09098Gh165.8SNPi09058GhSNPi34897Gh
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SNPi08797Gh201.0SNPi08796Gh201.6SNPi08789Gh202.7SNPi08786Gh203.2
Chr_19_ML
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SNPi16965Gh21.0SNPi10321Gh22.0
SNPi00568Gh29.0
SNPi24610Gh35.0SNPi16848Gh36.0
SNPi16824Gh40.0
SNPi10014Gh43.0SNPi43120Gh44.0
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SNPi09781Gh67.0
SNPi00997Gh83.0SNPi09680Gh84.0
SNPi00461Gh92.0SNPi48064Gh93.0SNPi09591Gh94.0SNPi09567Gh95.0SNPi09562Gh96.0SNPi22725Gh97.0SNPi09526Gh99.0
SNPi09486Gh104.0SNPi69754GI105.0
SNPi09352Gh112.0SNPi09353Gh113.0SNPi59127Gb114.0SNPi09340Gh115.0SNPi09334Gh117.0
SNPi00193Gh121.0
SNPi09290Gh124.0SNPi09287Gh125.0SNPi09227Gh127.0SNPi09210Gh130.0SNPi00362Gh131.0SNPi09169Gh132.0SNPi25035Gh133.0SNPi00269Gh136.0SNPi09106Gh138.0SNPi34361Gh139.0SNPi09098Gh140.0SNPi09058Gh141.0SNPi09051Gh142.0SNPi09053Gh143.0SNPi00328Gh144.0SNPi26444Gh145.0SNPi09032Gh146.0SNPi09004Gh148.0SNPi08958Gh149.0SNPi08914Gh153.0SNPi08908Gh154.0SNPi08906Gh155.0SNPi08887Gh158.0SNPi08878Gh159.0SNPi08860Gh162.0SNPi08855Gh163.0SNPi08852Gh165.0SNPi08828Gh167.0SNPi08825Gh168.0SNPi08802Gh170.0SNPi08789Gh172.0SNPi08797Gh174.0
Chr_19_ML63kCotton Chromosome 19
Map molecular markers such as SNPs
using the 63K Array Cotton Chip
Examples of mapping Populations or progeny-
lines from different cross-combinations
Acala Phytogen 72 x Upland Stoneville 474
Acala Phytogen 72 x NM67
TM-1 x Pima-S6
Upland TM-1 x Pima 3-79 (USDA-ARS)
Pima-S7 x Acala NemX (UC Riverside)
Cotton Accessions from the Cotton
Collection or SA-lines
Ongoing Genetic Mapping and QTL Analyses
Approach to map more than 25,000 SNPs on the 26
Cotton Chromosomes using around 1,900 lines,
progeny, and accessions
Biomarker - SNP Discovery
Prepared by Dr. Mauricio Ulloa, USDA, ARS
Discovery of genes involved in FOV race 4 (FOV4)
resistance for molecular breeding
Collection of infected roots with FOV races 1 and 4, and non-infected rootsInoculation Control Entry
Entry FOV race 1 FOV race 4 No Inoculation Total
Pima-S6 (PS6) 5 plants 5 plants 5 plants 15
Pima-S7 (PS7) 5 plants 5 plants 5 plants 15
Pima 3-79 5 plants 5 plants 5 plants 15
Upland TM-1 5 plants 5 plants 5 plants 15
Upland Shorty 5 plants 5 plants 5 plants 15
Acala FBCX-2b 5 plants 5 plants 5 plants 15
PS7 and 3-79 are susceptible to FOV4 and are tolerant to FOV race 1 (FOV1), but 3-79 is
more susceptible to race 1 than PS7.
Upland Shorty and TM-1 are very susceptible to FOV1. Shorty also is susceptible to FOV4.
FBCX-2 (tolerant to race 1) and TM-1 are moderately tolerant to FOV4. TM-1 is less
tolerant than FBCX-2 for race 4.
Next-Gen Sequencing Illumina MiSeq and HiSeq
FOV4 Gene Expression
Prepared by Dr. Mauricio Ulloa, USDA, ARS
SNP-Biomarkers target important genes
of different plant functional processes
Exploring gene diversity and discovering molecular
markes [SNP-Biomarkers] for assisting breeding
Illumina MiSeq & HiSeq Sequencers
Infected Root and Non-infected Root Genes
(Transcriptome) – Many TB of data
from FOV4 Resistant and Susceptible genotypes from
Upland and Pima Cottons
Next Generation Sequencing
SUMMARY
Investigate the Inheritance of FOV4. Different disease response between Upland vs. Pima
cottons
Improving assay & selection criteria of tolerant/resistant
Upland/Acala cottons during the breeding process
Pathogenicity evaluation of races and new FOV
biotypes
Discover candidate genes involved in FOV resistance. Validate Identified SNPs/Alleles/Genes from the
SNP63k array and Genome Reference(s) on diverse
Genotypes
Use of Next-Gen Sequencing (NGS) for gene
discovery
Develop Upland germplasm resistant to FOV. Continue searching for new sources of FOV resistance
Prepared by Dr. Mauricio Ulloa, USDA, ARS
University of California Davis
--Robert Hutmacher, Mark Keeley,Tarilee
Frigulti, and Steve Wright.
University of California Riverside
Philip Roberts, Congli Wang, and Tra Duong.
Texas A&M University
David Stelly, Amanda Hulse-Kemp, Luis De
Santiago, and Lin Yu-Ming.
USDA-ARS
Mauricio Ulloa, John Burke, Lori Hinze,
James Frelichowski, Richard Percy, John Yu,
Sukumar Saha, and many other cooperators
from different Areas.
Texas Tech University, Lubbock, TX
Rao & Pratibha Kottapalli from the Center for
Biotechnology and Genomics, and Glen
Ritchie, TTU.