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8/4/2019 Genomic Reources on Insertional Mutants-5015
1/13
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.do8/4/2019 Genomic Reources on Insertional Mutants-5015
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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.htm8/4/2019 Genomic Reources on Insertional Mutants-5015
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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.pl8/4/2019 Genomic Reources on Insertional Mutants-5015
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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=germplasm8/4/2019 Genomic Reources on Insertional Mutants-5015
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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.html8/4/2019 Genomic Reources on Insertional Mutants-5015
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(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
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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/tos17/8/4/2019 Genomic Reources on Insertional Mutants-5015
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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.html8/4/2019 Genomic Reources on Insertional Mutants-5015
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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.php8/4/2019 Genomic Reources on Insertional Mutants-5015
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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