Genomic Reources on Insertional Mutants-5015

8/4/2019 Genomic Reources on Insertional Mutants-5015

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Indian Agricultural Research Institute

New Delhi 110012

National Research Centre on Plant Biotechnology

Course: MOLECULAR GENETICS (MBB-505)

ASSIGNMENT

Genomic Resources for Insertional Mutagenesis in

Few Plants.

Submitted by

Donald James

MBB

Roll No: 20078


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INTRODUCTION

Insertional mutagenesis is the use of DNA sequences as mutagens. A number of

different insertional mutagenesis systems have been developed for plants, but all are basedeither on transposons or the integration of T-DNA.

A number of transposons have been used for mutagenesis programs, includingActivator (Ac), Suppressor-mutator (Spm) and Mutator (Mu) from corn (Zea mays; maize),Tam3 from Antirrhinum majus, and Tos17 from rice (Oryza sativa). Some of thesetransposons function only in their natural host plant, while others are promiscuous and canbe used in a variety of heterologous species. The corn Ac element, for example, has beenshown to function in Arabidopsis, tobacco, rice, potato (Solanum tuberosum), petunia(Petunia hybrida), tomato (Lycopersicon esculentum), and many other plants.T-DNA is nota transposon but is a short segment of DNA that is transferred from a bacterial plasmid to

the plant genome when plants are infected by the soil pathogen Agrobacteriumtumefaciens. T-DNA transfer by A. tumefaciens has been used extensively to generatetransgenic plants and more recently, for insertional mutagenesis.

The most direct way to establish the function of a plant gene is by mutation.Traditionally, genefunction relationships have been studied in a phenotype drivenapproach, sometimes described as forward genetics. Mutagenesis has been achieved byirradiating seeds or treating them with chemical mutagens, and then searching forinteresting mutant phenotypes in subsequent generations. If a large enough population ofseeds is mutagenized, it should be possible to recover mutants affecting any gene in thegenome

The disadvantage of radiation and chemical mutagens is that they tend to generatepoint mutations, which are difficult to map and make the process of gene isolationlaborious and time consuming. Insertional mutagenesis is advantageous because genestend to be completely disrupted, which favors the recovery of null mutants. Furthermore,the interrupted gene becomes tagged with the insertion, which can be used to cloneflanking sequences, either by traditional means or strategies based on the polymerasechain reaction (PCR). The approach is generally known as gene tagging or signature taggedmutagenesis (STM).

Reverse genetics is a gene-driven approach, in which a sequence with no known

function is deliberately mutated allowing the resulting mutant phenotype to be studiedInsertional mutagenesis has recently become established as an alternative reverse geneticsstrategy in plants. Although it is not possible to systematically target specific genes fordisruption, it is possible to saturate the genome with mutations and maintain a resource ofseeds representing interruptions in every single gene. A researcher discovering a particulargene and wanting to know its function can then search for insertional mutants affecting thegene of interest, either by screening the mutant seed bank or by searching databases offlanking sequences.


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Thus of late the importance of Genomic resources such as databases on mutant seed stocksof various crops and plant species have become an important part of the functionalgenomics and molecular genetic studies of plants. This assignment provides a glimpse intothe various genomic resources for insertional mutagenesis available for a few major plant

species viz. Arabidopsis, Maize, Rice and Tomato .The World Genetic Resource site underthe Shared information on Genetics resources(SHIGEN) maintained by the SHIGEN projectcarried out at theCenter for Genetic Resource Information, National Institute of Genetics,Mishima, Japan gives a glimpse of all such resources and their corresponding links. http://www.shigen.nig.ac.jp/wgr/quickSearchAction.do

Genomic resources for insertional mutagenesis inArabidopsis.

Insertional mutagenesis techniques, including transposon and TDNAmediated

mutagenesis, are key resources for systematic identification of gene function in the modelplant speciesArabidopsis thaliana. Researchers at The Cold Spring Harbor Lab, NY, USA

along with the John Innes Centre, Norwich, UK have developed a database called theATIDB:Arabidopsis thaliana insertion database (http://atidb.cshl.org/) for archiving,searching and analyzing insertional mutagenesis lines. Flanking sequences fromapproximately 10 500 insertion lines (including transposon and TDNA insertions) fromseveral tagging programs inArabidopsis were mapped to the genome sequence through ourannotation system before being entered into the database. (Xiaokang Pan et al Nucl. AcidsRes. (2003) 31 (4):12451251.doi: 10.1093/nar/gkg222)

Some important links which give access to all genomic resources of Arabidopsis are

TAIR, The Arabidopsis Information Resourcehttp://www.arabidopsis.org/

GARNet . An Arabidopsis thaliana Genomic Reource collaboration for UK basedscientists.Its resources for Mutants collections in Arabidopsis can be found athttp://www.garnetcommunity.org.uk/resources/mutant-collections

ATIDB : The Arabidopsis thaliana Integrated Database available athttp://atidb.org/Some important Stock centers and mutant lines have been listed below with references.

Worldwide Forward and Reverse Genetics Resources for Arabidopsis. (Insertional

lines

Resource

name Type

Back-

groun

d

Line

Vector Info View Mutation on Genome

Availab

le From

Alonso, Crosby

and Ecker

Simple insert (sets

of pools and

individual lines)

Col-0 pROK2 n/a ABRC

NASC
http://www.shigen.nig.ac.jp/wgr/quickSearchAction.dohttp://www.shigen.nig.ac.jp/wgr/quickSearchAction.dohttp://www.nig.ac.jp/http://www.nig.ac.jp/http://www.nig.ac.jp/http://www.shigen.nig.ac.jp/wgr/quickSearchAction.dohttp://www.shigen.nig.ac.jp/wgr/quickSearchAction.dohttp://atidb.cshl.org/http://atidb.cshl.org/http://atidb.cshl.org/http://www.arabidopsis.org/http://www.arabidopsis.org/http://www.arabidopsis.org/http://www.garnetcommunity.org.uk/resources/mutant-collectionshttp://www.garnetcommunity.org.uk/resources/mutant-collectionshttp://atidb.org/http://atidb.org/http://atidb.org/http://arabidopsis.org/abrc/alonso.jsphttp://arabidopsis.org/abrc/alonso.jsphttp://signal.salk.edu/tdna_protocols.htmlhttp://signal.salk.edu/tdna_protocols.htmlhttp://arabidopsis.org/abrc/alonso.jsphttp://arabidopsis.org/abrc/alonso.jsphttp://atidb.org/http://www.garnetcommunity.org.uk/resources/mutant-collectionshttp://www.arabidopsis.org/http://atidb.cshl.org/http://www.shigen.nig.ac.jp/wgr/quickSearchAction.dohttp://www.nig.ac.jp/http://www.shigen.nig.ac.jp/wgr/quickSearchAction.do


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Biological

Research

Center(Hungar

y)*

Promoter trap and

activation tag

(individual lines)

Col multiple T-

DNA vectors

locus mapping available on

project website

contact

authors

CSHL Gene trap andenhancer trap

(individual lines)

Ler Ac, DsG andDsE T-DNAs

AtEnsemblAtIDBSeqViewerSIGnAL

ABRCNASC

EXOTIC/ JIC

Gene Trap

Gene trap

transposon

(individual lines)

Ler Ds-GT and

Tpase

AtEnsemblAtIDBSIGnAL ABRC

NASC

Feldmann Simple insert (sets

of pools and

individual lines)

Ws-2 3850:1003 Ti n/a ABRC

NASC

GABI-Kat* T-DNA insertion

(individual lines)

Col pAC161 AtEnsemblAtIDBSeqViewerS

IGnAL

ABRC

NASC

GARNet - JIC

SM

Single insert Ds-

Spm (insertion

lines)

Col-0 SLJ8313

SLJ8337

SLJ8353

AtEnsemblAtIDBSIGnAL ABRC

NASC

IMA * Ds insertion

(individual lines)

Ler Ds element

(kanamycin

resistance, GUS

reporter)

SeqViewerSIGnAL ABRC

NASC

JIC Activate Activation trap

(individual lines)

Ler Tn113 (Ds

starter line) X

Tn25 (Ac

transposase

lines)

AtEnsemblAtIDB ABRC

NASC

Misc. Insertion

Collections

Misc. Misc. n/a n/a ABRC

NASC

Misc. T-DNA

pools for

forward

screening

Misc. Misc. n/a n/a ABRC

NASC
http://www.szbk.u-szeged.hu/~arabidop/mappingoftdnalines.htmhttp://www.szbk.u-szeged.hu/~arabidop/mappingoftdnalines.htmhttp://www.szbk.u-szeged.hu/~arabidop/mappingoftdnalines.htmhttp://www.szbk.u-szeged.hu/~arabidop/mappingoftdnalines.htmhttp://www.szbk.u-szeged.hu/~arabidop/mappingoftdnalines.htmhttp://www.szbk.u-szeged.hu/~arabidop/mappingoftdnalines.htm#vectormapshttp://www.szbk.u-szeged.hu/~arabidop/mappingoftdnalines.htm#vectormapshttp://genetrap.cshl.org/http://genetrap.cshl.org/traps.htmlhttp://genetrap.cshl.org/traps.htmlhttp://atensembl.arabidopsis.info/http://www.arabidopsis.org/servlets/svhttp://signal.salk.edu/cgi-bin/tdnaexpresshttp://www.jic.bbsrc.ac.uk/science/cdb/exotic/index.htmhttp://www.jic.bbsrc.ac.uk/science/cdb/exotic/index.htmhttp://www.jic.bbsrc.ac.uk/science/cdb/exotic/index.htmhttp://www.jic.bbsrc.ac.uk/science/cdb/exotic/index.htmhttp://atensembl.arabidopsis.info/http://signal.salk.edu/cgi-bin/tdnaexpresshttp://arabidopsis.org/abrc/feldmann.jsphttp://www.arabidopsis.org/servlets/TairObject?type=vector&id=500300068http://www.gabi-kat.de/http://www.gabi-kat.de/General_Information/GABI-Kat-pAC161T-DNAmapPr.htmlhttp://atensembl.arabidopsis.info/http://www.arabidopsis.org/servlets/svhttp://signal.salk.edu/cgi-bin/tdnaexpresshttp://garnet.arabidopsis.org.uk/transposons_for_functional_genomics.htmhttp://garnet.arabidopsis.org.uk/transposons_for_functional_genomics.htmhttp://jicgenomelab.co.uk/fileadmin/Download/Documents/pdf/Tissier_PC_1999.pdfhttp://jicgenomelab.co.uk/fileadmin/Download/Documents/pdf/Tissier_PC_1999.pdfhttp://jicgenomelab.co.uk/fileadmin/Download/Documents/pdf/Tissier_PC_1999.pdfhttp://atensembl.arabidopsis.info/http://signal.salk.edu/cgi-bin/tdnaexpresshttp://www.arabidopsis.org/abrc/ima.jsphttp://www.plantcell.org/cgi/content/full/11/12/2263http://www.plantcell.org/cgi/content/full/11/12/2263http://www.plantcell.org/cgi/content/full/11/12/2263http://www.plantcell.org/cgi/content/full/11/12/2263http://www.arabidopsis.org/servlets/svhttp://arabidopsis.info/CollectionInfo?id=29http://atensembl.arabidopsis.info/http://atensembl.arabidopsis.info/http://atensembl.arabidopsis.info/http://arabidopsis.info/CollectionInfo?id=29http://www.arabidopsis.org/servlets/svhttp://www.arabidopsis.org/servlets/svhttp://www.plantcell.org/cgi/content/full/11/12/2263http://www.plantcell.org/cgi/content/full/11/12/2263http://www.plantcell.org/cgi/content/full/11/12/2263http://www.plantcell.org/cgi/content/full/11/12/2263http://www.arabidopsis.org/abrc/ima.jsphttp://signal.salk.edu/cgi-bin/tdnaexpresshttp://atensembl.arabidopsis.info/http://atensembl.arabidopsis.info/http://jicgenomelab.co.uk/fileadmin/Download/Documents/pdf/Tissier_PC_1999.pdfhttp://jicgenomelab.co.uk/fileadmin/Download/Documents/pdf/Tissier_PC_1999.pdfhttp://jicgenomelab.co.uk/fileadmin/Download/Documents/pdf/Tissier_PC_1999.pdfhttp://garnet.arabidopsis.org.uk/transposons_for_functional_genomics.htmhttp://garnet.arabidopsis.org.uk/transposons_for_functional_genomics.htmhttp://signal.salk.edu/cgi-bin/tdnaexpresshttp://www.arabidopsis.org/servlets/svhttp://www.arabidopsis.org/servlets/svhttp://atensembl.arabidopsis.info/http://atensembl.arabidopsis.info/http://www.gabi-kat.de/General_Information/GABI-Kat-pAC161T-DNAmapPr.htmlhttp://www.gabi-kat.de/http://www.arabidopsis.org/servlets/TairObject?type=vector&id=500300068http://arabidopsis.org/abrc/feldmann.jsphttp://signal.salk.edu/cgi-bin/tdnaexpresshttp://atensembl.arabidopsis.info/http://atensembl.arabidopsis.info/http://www.jic.bbsrc.ac.uk/science/cdb/exotic/index.htmhttp://www.jic.bbsrc.ac.uk/science/cdb/exotic/index.htmhttp://www.jic.bbsrc.ac.uk/science/cdb/exotic/index.htmhttp://www.jic.bbsrc.ac.uk/science/cdb/exotic/index.htmhttp://signal.salk.edu/cgi-bin/tdnaexpresshttp://www.arabidopsis.org/servlets/svhttp://www.arabidopsis.org/servlets/svhttp://atensembl.arabidopsis.info/http://atensembl.arabidopsis.info/http://genetrap.cshl.org/traps.htmlhttp://genetrap.cshl.org/traps.htmlhttp://genetrap.cshl.org/http://www.szbk.u-szeged.hu/~arabidop/mappingoftdnalines.htm#vectormapshttp://www.szbk.u-szeged.hu/~arabidop/mappingoftdnalines.htm#vectormapshttp://www.szbk.u-szeged.hu/~arabidop/mappingoftdnalines.htmhttp://www.szbk.u-szeged.hu/~arabidop/mappingoftdnalines.htmhttp://www.szbk.u-szeged.hu/~arabidop/mappingoftdnalines.htmhttp://www.szbk.u-szeged.hu/~arabidop/mappingoftdnalines.htm


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RIKEN * Ds transposon

insertion

(individual lines))

No-O series of Ds

constructs

AtEnsemblRARGESIGnAL RIKEN

BRC

SAIL (formerly

GARLIC/TMRI)

T-DNA insertion

(individual lines)

Col pCSA110pDAP

101

AtEnsemblAtIDBSeqViewerS

IGnAL

ABRC

NASC

SALK T-DNA insertion

(individual lines)

Col pROK2 AtEnsemblAtIDBSeqViewerS

IGnAL

ABRC

NASC

Confirmed

SALK insertion

lines

T-DNA insertion

(PCR-

validatedhomozygo

usor heterozygous

individual lines)

Col pROK2 SeqViewerSIGnAL ABRC

NASC

Sussman and

Amasino

Simple insert (set of

pools)

Ws-2 pD991-AP3 n/a ABRC

NASC

TAMARA Tn mediated

activation tag

(individual lines)

Col-0 TAMARA contact authors NASC

Wisconsin Ds-

Lox

Ds-Lox insertion

(individual lines)

Col pDS-Lox AtEnsemblAtIDBSeqViewerS

IGnAL

ABRC

NASC

Wisconsin KO T-DNA insertion

(set of pools)

Ws pD991-AP3 n/a ABRC

NASC
http://rarge.gsc.riken.jp/dsmutant/index.plhttp://rarge.gsc.riken.jp/dsmutant/index.plhttp://rarge.gsc.riken.jp/dsmutant/index.plhttp://rarge.gsc.riken.jp/dsmutant/index.plhttp://atensembl.arabidopsis.info/http://signal.salk.edu/cgi-bin/tdnaexpresshttp://www.arabidopsis.org/abrc/sail.jsphttp://www.arabidopsis.org/abrc/sail.jsphttp://www.arabidopsis.org/abrc/sail.jsphttp://www.arabidopsis.org/abrc/pCSA110.pdfhttp://www.arabidopsis.org/abrc/pDAP101.pdfhttp://atensembl.arabidopsis.info/http://www.arabidopsis.org/servlets/svhttp://signal.salk.edu/cgi-bin/tdnaexpresshttp://signal.salk.edu/tabout.htmlhttp://signal.salk.edu/tdna_protocols.htmlhttp://atensembl.arabidopsis.info/http://www.arabidopsis.org/servlets/svhttp://signal.salk.edu/cgi-bin/tdnaexpresshttp://signal.salk.edu/gabout.htmlhttp://signal.salk.edu/gabout.htmlhttp://signal.salk.edu/gabout.htmlhttp://signal.salk.edu/geno/sum.txthttp://signal.salk.edu/geno/sum.txthttp://signal.salk.edu/geno/sum.txthttp://signal.salk.edu/tdna_protocols.htmlhttp://www.arabidopsis.org/servlets/svhttp://arabidopsis.org/abrc/sussman_fwd.jsphttp://arabidopsis.org/abrc/sussman_fwd.jsphttp://www.biotech.wisc.edu/NewServicesAndResearch/Arabidopsis/pD991-AP3_finalseq.htmlhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16087178http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16087178http://www.hort.wisc.edu/krysan/Ds-Lox/http://www.hort.wisc.edu/krysan/Ds-Lox/http://www.hort.wisc.edu/krysan/Ds-Lox/http://atensembl.arabidopsis.info/http://www.arabidopsis.org/servlets/svhttp://signal.salk.edu/cgi-bin/tdnaexpresshttp://www.arabidopsis.org/abrc/akf.jsphttp://www.biotech.wisc.edu/NewServicesAndResearch/Arabidopsis/pD991-AP3_finalseq.htmlhttp://www.biotech.wisc.edu/NewServicesAndResearch/Arabidopsis/pD991-AP3_finalseq.htmlhttp://www.arabidopsis.org/abrc/akf.jsphttp://signal.salk.edu/cgi-bin/tdnaexpresshttp://www.arabidopsis.org/servlets/svhttp://www.arabidopsis.org/servlets/svhttp://atensembl.arabidopsis.info/http://atensembl.arabidopsis.info/http://www.hort.wisc.edu/krysan/Ds-Lox/http://www.hort.wisc.edu/krysan/Ds-Lox/http://www.hort.wisc.edu/krysan/Ds-Lox/http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16087178http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16087178http://www.biotech.wisc.edu/NewServicesAndResearch/Arabidopsis/pD991-AP3_finalseq.htmlhttp://arabidopsis.org/abrc/sussman_fwd.jsphttp://arabidopsis.org/abrc/sussman_fwd.jsphttp://www.arabidopsis.org/servlets/svhttp://www.arabidopsis.org/servlets/svhttp://signal.salk.edu/tdna_protocols.htmlhttp://signal.salk.edu/geno/sum.txthttp://signal.salk.edu/geno/sum.txthttp://signal.salk.edu/gabout.htmlhttp://signal.salk.edu/gabout.htmlhttp://signal.salk.edu/gabout.htmlhttp://signal.salk.edu/cgi-bin/tdnaexpresshttp://www.arabidopsis.org/servlets/svhttp://www.arabidopsis.org/servlets/svhttp://atensembl.arabidopsis.info/http://atensembl.arabidopsis.info/http://signal.salk.edu/tdna_protocols.htmlhttp://signal.salk.edu/tabout.htmlhttp://signal.salk.edu/cgi-bin/tdnaexpresshttp://www.arabidopsis.org/servlets/svhttp://www.arabidopsis.org/servlets/svhttp://atensembl.arabidopsis.info/http://atensembl.arabidopsis.info/http://www.arabidopsis.org/abrc/pDAP101.pdfhttp://www.arabidopsis.org/abrc/pCSA110.pdfhttp://www.arabidopsis.org/abrc/pCSA110.pdfhttp://www.arabidopsis.org/abrc/sail.jsphttp://www.arabidopsis.org/abrc/sail.jsphttp://www.arabidopsis.org/abrc/sail.jsphttp://signal.salk.edu/cgi-bin/tdnaexpresshttp://atensembl.arabidopsis.info/http://atensembl.arabidopsis.info/http://rarge.gsc.riken.jp/dsmutant/index.plhttp://rarge.gsc.riken.jp/dsmutant/index.plhttp://rarge.gsc.riken.jp/dsmutant/index.pl


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The above mentioned stock centers are

1) The Arabidopsis Biological Resource Center (ABRC) maintained by the Ohio StateUniversity, USA. Details of all mutant and mapping populations can be seen bysearching the Arabidopsis Information Resource

2) The Nottingham Arabidopsis Stock Centre (NASC) also known as The EuropeanArabidopsis Stock Centre provides seed and information resources totheInternational Arabidopsis Genome Programmeand the wider researchcommunity and is maintained at the University of Nottingham, Sutton BoningtonCampus, and UK.Details on various lines of mutants at the NASC can be seen byfollowing the linkhttp://arabidopsis.info/BrowsePage

3) Another database and stock centre is the RIKEN Plant Science centre of theYokohama Institute, Japan (RIKEN Bioresource Center (BRC)/ SENDAI ArabidopsisSeed Stock Center (SASSC) )The details can be found at RARGE-Riken ArabidopsisGenomic Encyclopedia http://rarge.psc.riken.jp/dsmutant/index.pl orhttp://www.brc.riken.jp/lab/epd/Eng/catalog/seed.shtml

4) INRA-Versailles Genomic Resource Center located at IJPB Versailles, France has alsoa collection of Arabidopsis T-DNA insertional mutant lines called AGROBACT + .Details can be availed athttp://www-ijpb.versailles.inra.fr/en/cra/cra_accueil.htmorhttp://dbsgap.versailles.inra.fr/agrobactplus/English/Accueil_eng.jsp

5) GABI - Genome Analysis of the Plant Biological System from the Max-Planck-Institutefor Molecular Plant Physiology,Germany.
http://arabidopsis.info/InfoPages?template=progreports;web_section=germplasmhttp://arabidopsis.info/InfoPages?template=progreports;web_section=germplasmhttp://arabidopsis.info/InfoPages?template=progreports;web_section=germplasmhttp://arabidopsis.info/BrowsePagehttp://arabidopsis.info/BrowsePagehttp://arabidopsis.info/BrowsePagehttp://rarge.psc.riken.jp/dsmutant/index.plhttp://rarge.psc.riken.jp/dsmutant/index.plhttp://www.brc.riken.jp/lab/epd/Eng/catalog/seed.shtmlhttp://www.brc.riken.jp/lab/epd/Eng/catalog/seed.shtmlhttp://www-ijpb.versailles.inra.fr/en/cra/cra_accueil.htmhttp://www-ijpb.versailles.inra.fr/en/cra/cra_accueil.htmhttp://www-ijpb.versailles.inra.fr/en/cra/cra_accueil.htmhttp://dbsgap.versailles.inra.fr/agrobactplus/English/Accueil_eng.jsphttp://dbsgap.versailles.inra.fr/agrobactplus/English/Accueil_eng.jsphttp://dbsgap.versailles.inra.fr/agrobactplus/English/Accueil_eng.jsphttp://www-ijpb.versailles.inra.fr/en/cra/cra_accueil.htmhttp://www.brc.riken.jp/lab/epd/Eng/catalog/seed.shtmlhttp://rarge.psc.riken.jp/dsmutant/index.plhttp://arabidopsis.info/BrowsePagehttp://arabidopsis.info/InfoPages?template=progreports;web_section=germplasm


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The important Insertional mutant lines include

1. Salk T-DNA lines provided by the SALK Institute, La Jolla, CA USA. [About Salk T-DNA]

2. SAIL T-DNA lines.Syngenta Arabidopsis Insertion Library (SAIL) collection [About

the SAIL lines][Order from ABRC].

3.GABI-Kat linesGABI - Genome Analysis of the Plant Biological System from the Max-Planck-Institute for Molecular Plant Physiology ,Germany.

4.FLAGdb/FSTof the Institute of Agronomic Research, Versailles, France ( INRAVersailles Stock )

5.Wisconsin T-DNA linesprovided by the University of Wisconsin ,Madison USA.

6.CSHL genetrap linesprovided by the Cold Spring Harbor Lab ,NY,USA.

7.RIKEN T-DNA & Dslines. [Order from RIKEN BRC]( RIKEN / SENDAI SASSC stock)

8.JIC SM lines.[About the SM lines][NASC] from the Sainsbury Laboratory, John InnesCentre, Colney Lane, Norwich NR4 7UH, United Kingdom,

9.IMA Dslines from Institute of Molecular Agrobiology, National University ofSingapore.

10.Saskatoon SK Linesprovided by the Agriculture and Agri Food Department ofCanadian Govt.

Details of Accessions

Salk T-DNA

Columbia

137,259 lines 166,127 mapped 10/28/20

Salk T-DNA Homozygous 33,744 lines 40,652 mapped 05/18/20

SAIL FST 62,041 mapped 10/28/200

SAIL T-DNA Homozygous 4,522 lines 4,828 mapped 05/18/20

Wisc FST 32,607 21,406 mapped 09/30/20
http://signal.salk.edu/tabout.htmlhttp://signal.salk.edu/tabout.htmlhttp://signal.salk.edu/tabout.htmlhttp://www.arabidopsis.org/abrc/sail.jsphttp://www.arabidopsis.org/abrc/sail.jsphttp://www.arabidopsis.org/abrc/sail.jsphttp://www.arabidopsis.org/abrc/sail.jspmailto:[email protected]:[email protected]:[email protected]://www.mpiz-koeln.mpg.de/GABI-Kat/http://www.mpiz-koeln.mpg.de/GABI-Kat/http://www.mpiz-koeln.mpg.de/GABI-Kat/http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11752264http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11752264http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11752264https://mywebspace.wisc.edu/groups/Krysan/Web/2010/default.htmhttps://mywebspace.wisc.edu/groups/Krysan/Web/2010/default.htmhttps://mywebspace.wisc.edu/groups/Krysan/Web/2010/default.htmhttp://genetrap.cshl.org/http://genetrap.cshl.org/http://genetrap.cshl.org/http://rarge.gsc.riken.go.jp/dsmutant/index.plhttp://rarge.gsc.riken.go.jp/dsmutant/index.plhttp://rarge.gsc.riken.go.jp/dsmutant/index.plhttp://www.brc.riken.jp/lab/epd/Eng/catalog/seed.shtmlhttp://www.brc.riken.jp/lab/epd/Eng/catalog/seed.shtmlhttp://www.brc.riken.jp/lab/epd/Eng/catalog/seed.shtmlhttp://www.jic.bbsrc.ac.uk/science/cdb/exotic/index.htmhttp://www.jic.bbsrc.ac.uk/science/cdb/exotic/index.htmhttp://www.jic.bbsrc.ac.uk/science/cdb/exotic/index.htmhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10521516http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10521516http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10521516http://seeds.nottingham.ac.uk/Nasc/action.lasso?&-response=browse/sm/smlist.lassohttp://seeds.nottingham.ac.uk/Nasc/action.lasso?&-response=browse/sm/smlist.lassohttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10590156&dopt=Abstracthttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10590156&dopt=Abstracthttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10590156&dopt=Abstracthttp://aafc-aac.usask.ca/FST/http://aafc-aac.usask.ca/FST/http://aafc-aac.usask.ca/FST/http://signal.salk.edu/gabout.htmlhttp://signal.salk.edu/gabout.htmlhttp://signal.salk.edu/gabout.htmlhttp://aafc-aac.usask.ca/FST/http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10590156&dopt=Abstracthttp://seeds.nottingham.ac.uk/Nasc/action.lasso?&-response=browse/sm/smlist.lassohttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10521516http://www.jic.bbsrc.ac.uk/science/cdb/exotic/index.htmhttp://www.brc.riken.jp/lab/epd/Eng/catalog/seed.shtmlhttp://rarge.gsc.riken.go.jp/dsmutant/index.plhttp://genetrap.cshl.org/https://mywebspace.wisc.edu/groups/Krysan/Web/2010/default.htmhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11752264http://www.mpiz-koeln.mpg.de/GABI-Kat/mailto:[email protected]://www.arabidopsis.org/abrc/sail.jsphttp://www.arabidopsis.org/abrc/sail.jsphttp://signal.salk.edu/tabout.html


9/13

(22,089)

Wisc Homozygous by Salk 1,981 lines 1,981 mapped 05/18/20

FLAGdb FST Wassilevskija 41,369 37,142 mapped 06/23/20

GABI-Kat FST

Columbia

130,65498,559 mapped (70,578

lines)06/29/20

GABI-Kat Confirmed 7,656 lines 11,030 mapped 04/12/20

GABI-Kat Homozygous by

Salk1,040 lines 1,373 mapped 05/18/20

RIKEN FST N^ssen 18,622 mapped 06/23/200

JIC SM FST

Landsberg

22,664 w

seeds24,206 mapped 10/28/200

CSHL FST24,444

(17,689 lines)23,998 mapped 10/25/20

IMA FST 488 lines 808 mapped 10/28/200

Saskatoon FST Col-4 15,507 lines 14,941 mapped 08/17/200

Other FST 175 mapped 06/23/200

Total 452,065 mapped 12/01/20

References

1.)T-DNA insertional mutagenesis in Arabidopsis: a tool for functional genomicsRadhamony R.N,Ramamurthy Srinivasan et al, Electronic Journal of Biotechnology ISSN:0717-3458 Vol.8 No.1, Issue of April 15, 2005


10/13

Genomic resources for insertional mutagenesis in Rice.

Various international groups are working to produce and characterize diverse rice mutant

stocks. The table below provides links to such resources:

Hirohiko HirochikaNIAS, National Institute of AgrobiologicalSciences, Japan.

Tos17 InsertionMutant Database

Gyn AnPostech Plant Functional Genomics LaboratoryKorea

T-DNA InsertionMutants

NarayanaUpadhyaya

CSIRO Plant IndustryRice Functional Genomics Group

Australia

T-DNA and DsInsertion Mutants

EmmanuelGuiderdoni

OrygenesDb, OryzaTagLines Insertional mutant

Group AliasPublicatio

nContact Vector

Number

of FST

CSIRO CSIRO [View]narayana.upadhyaya(@)csi

ro.auT-DNA 611

National Institute of

Agrobiological Sciences NIAS [View] hirohiko(@)nias.affrc.go.jp Tos17 18,024

CerealGene Tags,

European UnionOSTID [View] andy.pereira(@)wur.nl Ds 1,380

CIRAD-INRA-IRD-

CNRS,Genoplante

OTL T-

DNA[View]

emmanuel.guiderdoni(@)ci

rad.frT-DNA 27,555

CIRAD-Genoscope OTLTos17

emmanuel.guiderdoni(@)cirad.fr

Tos17 14,355

Gyeongsang National

UniversityPMBBRC [View]

cdhan(@)nongae.gsnu.ac.k

rDs 1,072
http://pc7080.abr.affrc.go.jp/~miyao/pub/tos17/http://pc7080.abr.affrc.go.jp/~miyao/pub/tos17/http://www.postech.ac.kr/life/pfg/http://www.postech.ac.kr/life/pfg/http://www.pi.csiro.au/fgrttpub/home.htmhttp://www.pi.csiro.au/fgrttpub/home.htmhttp://orygenesdb.cirad.fr/http://orygenesdb.cirad.fr/http://urgi.versailles.inra.fr/OryzaTagLine/about.htmhttp://urgi.versailles.inra.fr/OryzaTagLine/about.htmhttp://urgi.versailles.inra.fr/OryzaTagLine/about.htmhttp://www.pi.csiro.au/fgrttpub/http://www.pi.csiro.au/fgrttpub/http://dx.doi.org/10.1111/j.1467-7652.2004.00081.xhttp://dx.doi.org/10.1111/j.1467-7652.2004.00081.xhttp://tos.nias.affrc.go.jp/http://tos.nias.affrc.go.jp/http://tos.nias.affrc.go.jp/http://dx.doi.org/10.1105/tpc.012559http://dx.doi.org/10.1105/tpc.012559http://orygenesdb.cirad.fr/http://orygenesdb.cirad.fr/http://dx.doi.org/10.1007/s11103-005-8532-6http://dx.doi.org/10.1007/s11103-005-8532-6http://urgi.infobiogen.fr/OryzaTagLine/http://urgi.infobiogen.fr/OryzaTagLine/http://dx.doi.org/10.1111/j.1365-313X.2004.02145.xhttp://dx.doi.org/10.1111/j.1365-313X.2004.02145.xhttp://urgi.infobiogen.fr/OryzaTagLine/http://urgi.infobiogen.fr/OryzaTagLine/http://dx.doi.org/10.1111/j.1365-313X.2004.02116.xhttp://dx.doi.org/10.1111/j.1365-313X.2004.02116.xhttp://dx.doi.org/10.1111/j.1365-313X.2004.02116.xhttp://urgi.infobiogen.fr/OryzaTagLine/http://dx.doi.org/10.1111/j.1365-313X.2004.02145.xhttp://urgi.infobiogen.fr/OryzaTagLine/http://urgi.infobiogen.fr/OryzaTagLine/http://dx.doi.org/10.1007/s11103-005-8532-6http://orygenesdb.cirad.fr/http://orygenesdb.cirad.fr/http://dx.doi.org/10.1105/tpc.012559http://tos.nias.affrc.go.jp/http://tos.nias.affrc.go.jp/http://dx.doi.org/10.1111/j.1467-7652.2004.00081.xhttp://www.pi.csiro.au/fgrttpub/http://urgi.versailles.inra.fr/OryzaTagLine/about.htmhttp://orygenesdb.cirad.fr/http://www.pi.csiro.au/fgrttpub/home.htmhttp://www.postech.ac.kr/life/pfg/http://pc7080.abr.affrc.go.jp/~miyao/pub/tos17/http://pc7080.abr.affrc.go.jp/~miyao/pub/tos17/


11/13

Plant Functional

Genomics LaboratoryPostech [View] genean(@)postech.ac.kr T-DNA 107,171

National Center of Plant

Gene Research (Wuhan)RMD [View] swang(@)mail.hzau.edu.cn T-DNA 33,197

Shanghai T-DNA

Insertion PopulationSHIP ship(@)sibs.ac.cn T-DNA 12,614

Taiwan Rice Insertional

Mutant ProgramTRIM [View]

bohsing(@)gate.sinica.edu.t

wT-DNA 11,799

University of California at

DavisUCD [View] sundar(@)ucdavis.edu Ds 17,730

Total 245,508

References

1.)OrygenesDB website

2.)Oryzabase website
http://www.postech.ac.kr/life/pfg/risd/index.htmlhttp://www.postech.ac.kr/life/pfg/risd/index.htmlhttp://dx.doi.org/10.1046/j.1365-313x.2000.00767.xhttp://dx.doi.org/10.1046/j.1365-313x.2000.00767.xhttp://rmd.ncpgr.cn/http://rmd.ncpgr.cn/http://rmd.ncpgr.cn/http://dx.doi.org/10.1093/nar/gkj016http://dx.doi.org/10.1093/nar/gkj016http://ship.plantsignal.cn/home.dohttp://ship.plantsignal.cn/home.dohttp://trim.sinica.edu.tw/http://trim.sinica.edu.tw/http://trim.sinica.edu.tw/http://dx.doi.org/10.1007/s11103-006-9093-zhttp://dx.doi.org/10.1007/s11103-006-9093-zhttp://www-plb.ucdavis.edu/labs/sundar/Rice_Genomics.htmhttp://www-plb.ucdavis.edu/labs/sundar/Rice_Genomics.htmhttp://www-plb.ucdavis.edu/labs/sundar/Rice_Genomics.htmhttp://dx.doi.org/10.1111/j.1365-313X.2005.02570.xhttp://dx.doi.org/10.1111/j.1365-313X.2005.02570.xhttp://dx.doi.org/10.1111/j.1365-313X.2005.02570.xhttp://www-plb.ucdavis.edu/labs/sundar/Rice_Genomics.htmhttp://www-plb.ucdavis.edu/labs/sundar/Rice_Genomics.htmhttp://dx.doi.org/10.1007/s11103-006-9093-zhttp://trim.sinica.edu.tw/http://trim.sinica.edu.tw/http://ship.plantsignal.cn/home.dohttp://ship.plantsignal.cn/home.dohttp://dx.doi.org/10.1093/nar/gkj016http://rmd.ncpgr.cn/http://rmd.ncpgr.cn/http://dx.doi.org/10.1046/j.1365-313x.2000.00767.xhttp://www.postech.ac.kr/life/pfg/risd/index.htmlhttp://www.postech.ac.kr/life/pfg/risd/index.html


12/13

Genomic resources for insertional mutagenesis in Maize.

The RescueMu Maize Mutant Phenotype Databaseavailable at the MaizeGDB (Maize

Genetics and Genomics Database ).This phenotype database is part of the NSFproject"Maize Gene Discovery, DNA Sequencing, and Phenotypic Analysis." A largepopulation of maize plants was generated aiming to contain RescueMu transposoninsertions in every maize gene. These plants were screened for morphologicalabnormalities and the phenotype observations were recorded in this database.Corresponding seeds can be obtained from theMaize Genetics Cooperation - StockCenter. The Maize Gene Discovery Project is sequencing maize DNA flanking RescueMutransposons, and provides this information and plants (identified by a PCR-based assay)that contain the mutant allele of interest to users for a fee of $150.

UniformMu is a unique maize population developed for maize genetics research

(McCarty et al., 2005). This material is widely used for experimental analysis of maize genefunction, because 1) the uniform plants and seeds provide an excellent basis for comparingunaltered, wild-type controls to detectable changes in new plant phenotypes, 2) theUniformMu transposable elements actively generate new mutations when they insert intoindividual genes, and 3) a searchable database (at MaizeGDB.org) matches gene sequencesto specific mutants with Mu insertions in genes of interest (with seed stocks immediatelyavailable from the Maize Genetics Cooperation Stock Center via MaizeGDB.org)Linkshttp://endosperm.info/, http://uniformmu.org)

The Maize Targeted Mutagenesis population is publically available(http://mtm.cshl.edu/)with a service charge of $1400 per PCR screen. TUSC (Trait Utility

System for Corn) populations are available at no cost from Pioneer Hi-Bred upon signing acollaborative agreement.

References

1.)Maize Gene Discovery Project ( MaizeGDB)
http://www.maizegdb.org/rescuemu-phenotype-background.phphttp://www.maizegdb.org/rescuemu-phenotype-background.phphttp://www.maizegdb.org/rescuemu-phenotype-background.phphttp://www.maizegdb.org/documentation/mgdp/index.phphttp://www.maizegdb.org/documentation/mgdp/index.phphttp://www.maizegdb.org/documentation/mgdp/index.phphttp://www.maizegdb.org/rescuemu-phenotype-how-to-order-seed.phphttp://www.maizegdb.org/rescuemu-phenotype-how-to-order-seed.phphttp://www.maizegdb.org/rescuemu-phenotype-how-to-order-seed.phphttp://www.maizegdb.org/documentation/uniformmu/http://www.maizegdb.org/documentation/uniformmu/http://endosperm.info/http://endosperm.info/http://mtm.cshl.edu/http://mtm.cshl.edu/http://mtm.cshl.edu/http://mtm.cshl.edu/http://endosperm.info/http://www.maizegdb.org/documentation/uniformmu/http://www.maizegdb.org/rescuemu-phenotype-how-to-order-seed.phphttp://www.maizegdb.org/rescuemu-phenotype-how-to-order-seed.phphttp://www.maizegdb.org/documentation/mgdp/index.phphttp://www.maizegdb.org/rescuemu-phenotype-background.php


13/13

Insertional mutagenesis in tomato.

Insertion Mutant databases in tomato are comparatively less .Only a few mutant stockdatabases have data though none pertains to Insertional mutants until now.

TheTomato Genetics Resource Centreof Dr CM Ricks at UC Davis, USA The SOL Genomics Network (SGN);Genes that make Tomato. TOMATOMA- A Tomato mutant archive of the University of Tsukuba,Japan

Insertional mutagenesis in tomato has been carried out mostly withthe maizeAc/Ds transposable elements. Following the first report showingthatAc/Ds elements are active in tomato, patterns ofAc/Ds transposition in this specieshave been described. A number of tomato genes have been isolated by transposon taggingwithAc/Ds. These include the Cf-9 and Cf-4 loci , which control resistance to various races

ofCladosporium fluvum; Dwarf, a gene encoding a cytochrome p450 homologue defectivechloroplasts and leaves (DCL), which controls chloroplast development ; and FEEBLY, a geneinvolved in metabolism and development .In most cases, these genes were tagged bytargeted tagging, that is, by taking advantage of the preferential transposition ofAc/Ds tonearby sites and and of the linkage between the target and previouslymapped Ds elements . There has been a concerted effort by European groups to map alarge number ofDs elements in the tomato genome to facilitate targeted tagging. Using asystem similar to that described previously, the European Union-funded TAGAMAP projecthas recently completed the mapping of 141 Ds-containing T-DNA inserts spreadthroughout the 12 chromosomes of tomato (D Gidoni, personal communication). TheDefective embryo and meristems (Dem) tomato gene was found in a non-targeted screen for

mutant phenotypes inAc/Ds-tagged plants

Despite these successes in transposon tagging in tomato, efficient reverse genetics tools arestill needed, especially in light of the continuing release of tomato ESTs into publicsequence databases, such as GenBank, and the subsequent assembly of ESTs into tentativegenes

In tomato, no transposon-tagged population is available yet, although a pilot population ofabout 3000 lines containing 60009000 insertions has been produced by Emmanuel et alIt is estimated that 200 000300 000 insertion lines, each containing two or three copies ofthe Ds transposon that inserts preferentially into genes, would be required for near-

saturated mutagenesis in tomato In tomato, the sequencing of insertion sites has beeninitiated on a small scale using Ds-tagged insertion lines . To date, there are no reports ofactivation tagging in tomato.

References

1.)Emmanuel et al ,Current Opinion in Plant Biology ,Volume 5, Issue 2, 1 April 2002,Pages 112-117.)
http://tgrc.ucdavis.edu/index.aspxhttp://tgrc.ucdavis.edu/index.aspxhttp://tgrc.ucdavis.edu/index.aspxhttp://zamir.sgn.cornell.edu/mutants/index.htmlhttp://zamir.sgn.cornell.edu/mutants/index.htmlhttp://zamir.sgn.cornell.edu/mutants/index.htmlhttp://tomatoma.nbrp.jp/about/aboutEn.jsphttp://tomatoma.nbrp.jp/about/aboutEn.jsphttp://www.sciencedirect.com/science/article/pii/S1369526602002376#ref_BIB17http://www.sciencedirect.com/science/article/pii/S1369526602002376#ref_BIB18http://www.sciencedirect.com/science/article/pii/S1369526602002376#ref_BIB19http://www.sciencedirect.com/science/article/pii/S1369526602002376#ref_BIB19http://www.sciencedirect.com/science/article/pii/S1369526602002376#ref_BIB18http://www.sciencedirect.com/science/article/pii/S1369526602002376#ref_BIB17http://tomatoma.nbrp.jp/about/aboutEn.jsphttp://zamir.sgn.cornell.edu/mutants/index.htmlhttp://tgrc.ucdavis.edu/index.aspx