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Arabidopsis thaliana Resource Centre
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Keywords : Arabidopsis thaliana - biological resources - insertion mutants - natural variants - recombinant lines - core-collection - phenotype - genotype - QTL

 

Contacts :

Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech
Bâtiment 7
INRA Centre de Versailles-Grignon
Route de St-Cyr
78026 Versailles Cedex France

tel : +33 (0)1 30 83 30 00 - fax : +33 (0)1 30 83 33 19
Publiclines@versailles.inra.fr


Group leader
Christine Camilleri
Engineer

Bernadette Trouve
Technician

Deputy group leader
Stéphanie Durand
Technician

 

 

Summary :

The Arabidopsis thaliana Stock Centre makes available to the scientific community:

 
  1. 55.000 T-DNA insertion mutants
  2. more than 600 natural variants (natural accessions)
  3. 16 recombinant inbred line (RIL) populations
  4. a panel of epigenetic recombinant inbred lines (epiRIL)
  5. more than 100 F2 mapping populations
  6. populations of nearly isogenic lines (Heterogeneous Inbred Family, HIF).

These biological resources can be ordered here

In addition, the Resource Centre exploits this material in research projects, particularly the study of genetic incompatibilities and, with the group Organelles and reproduction (F. Budar), the study of nucleo-cytoplasmic interactions.

.


Main Results :

Resources

- A set of 55,000 T-DNA insertion lines was built in the Ws (Wassilewskija) background via Agrobacterium tumefaciens in planta transformation with the binary vector pGKB5. Flanking sequences tags (FST) have been identified for each mutant in the collection: 46,236 FSTs are available in the database Flagdb++, as well as SIGnAL and TAIR. Information about FSTs and how to genotype the insertion lines can be found here.

- More than 600 natural variants from different geographical origins were collected in order to exploit the natural diversity of the species. Nested core-collections of 8, 16, … to 48 accessions have been determined which maximize the species diversity with a limited number of accessions (McKhann et al. 2004). Every seed batch was genotyped with 384 SNP markers in order to check the conformity of all reference and distribution batches, to detect misidentified accessions and to suggest likely identities for accessions whose lineage had been lost (Simon et al. 2012). The genotyping data, as well as tools that we have developed to verify or determine the identity of accessions, are available on the dedicated web interface ANATool.

- More than 100 F2 mapping populations are available. They result from crosses between natural accessions, in particular between the 8 accessions of the most reduced core-collection.

- Recombinant Inbred Line (RIL) populations dedicated to QTL mapping have been generated to study the genetic bases of quantitative traits (Simon et al. 2008). These sets, of 350 lines each on average, originate from crosses between a common parent (Columbia) and different genetically distant accessions. They have been genotyped with a hundred of consensus SNP markers. Core-populations comprising the 164 most informative lines have been generated.

- A panel of epigenetic recombinant inbred lines (epiRILs) was generated with the aim of studying the impact of epigenetic changes such as DNA methylation on phenotypic variation. These epiRILs derive from two parents with little DNA sequence differences, but contrasting DNA methylation profiles. They can be used to identify epiallelic variants that contribute to heritable variation in complex traits.

- HIF (Heterogeneous Inbred Family) nearly-isogenic line populations have been generated to validate and clone QTLs identified with the RILs. Complete sets of HIFs have been created from three RIL populations (Bay-0 x Shahdara, Cvi-0 x Col-0 and Bur-0 x Col-0). Each population is made up of about a hundred families covering the totality of the genome. Each family comprises plants from the progeny of a line heterozygous for one genomic region; these plants have the genotype of each of the parents for this region and are identical for the rest of their genomes.

 

Genetic incompatibility studies

Within several RIL populations, different pairs of physically unlinked loci do not segregate independently: one parental allele at one locus is never associated with the other parental allele at the other locus. The mechanisms involved in two different incompatibilities were discovered. They rely on the ectopic duplication of an essential (or very important for fitness) gene, followed by the inactivation of one of the two paralogues (Bikard et al. 2009, Durand et al. 2012). In the second case, an epigenetic variation is responsible for the silencing of the gene. These mechanisms may explain lethality observed in hybridizations between varieties or species and contribute to the understanding of the speciation.

 


Selected Publications :

T-DNA mutants:
Bechtold N et al. (1993). In planta Agrobacterium mediated gene transfer by infiltration of adult Arabidopsis thaliana plants. C.R. Acad. Sci. Paris, Sciences de la vie; 316: 1194-9 (link)

Bouchez D et al. (1993). A binary vector based on Basta resistance for in planta transformation of Arabidopsis thaliana. C.R. Acad. Sci. Paris, Sciences de la vie; 316: 1188-1193 (link)

Nacry P, Camilleri C, Courtial B, Caboche M, Bouchez D (1998). Major chromosomal rearrangements induced by T-DNA transformation in Arabidopsis. Genetics 149 : 641-650. (pdf)

Brunaud V, Balzergue S, Dubreucq B, Aubourg S, Samson F, Chauvin S, Bechtold N, Cruaud C, DeRose R, Pelletier G, Lepiniec L, Caboche M, Lecharny A. (2002) T-DNA integration into the Arabidopsis genome depends on sequences of pre-insertion sites. EMBO Rep. 3(12):1152-7. (pdf)

Samson F et al. (2002) FLAGdb/FST : a database for mapped flanking insertion sites (FSTs) of Arabidopsis thaliana T-DNA transformants. Nucleic Acids Res. 30 (1):94-7. (pdf)

Natural variants:
McKhann H I, Camilleri C, Bérard A, Bataillon T, David J L, Reboud X, Le Corre V, Caloustian C, Gut I G, Brunel D.(2004). Nested core collections maximizing genetic diversity in Arabidopsis thaliana. Plant J 38 : 193-202. (pdf)

Reboud X, Le Corre V, Scarcelli N, Roux F, David J L, Bataillon T, Camilleri C, Brunel D, and McKhann H (2004). Natural variation among accessions of Arabidopsis thaliana: Beyond the flowering date, what morphological traits are relevant to study adaptation. In Plant Adaptation: Molecular Genetics and Ecology, Q.C.B. Cronk, J. Whitton, R.H. Ree, and I.E.P. Taylor, eds (Ottawa, Canada: NRC Research Press), pp. 135-142. (pdf)

Ostrowski MF, David J, Santoni S, McKhann H, Reboud X, Le Corre V, Camilleri C, Brunel D, Bouchez D, Faure B and Bataillon T (2006). Evidence for a large-scale population structure among accessions of Arabidopsis thaliana : possible causes and consequences for the distribution of linkage disequilibrium. Molecular Ecology 15(6) ; 1507-17. (pdf)

Bouchabke.O, Chang.F, Simon.M, Voisin.R, Pelletier.G, Durand-Tardif.M. (2008) Natural variation in Arabidopsis thaliana as a tool for highlighting differential drought responses. PLoS ONE 3(2) e1705. (pdf)

Simon M, Simon A, Martins F, Botran L, Tisné S, Granier F, Loudet O and Camilleri C (2012). DNA fingerprinting and new tools for fine-scale discrimination of Arabidopsis thaliana accessions. The Plant Journal 69: 1094-1101. (pdf)

Recombinant inbred lines:
Loudet O, Chaillou S, Camilleri C, Bouchez D, Daniel-Vedele F (2002). Bay-0 x Shahdara recombinant inbred line population : a powerful tool for the genetic dissection of complex traits. Theor Appl Genet 104 : 1173-1184. (pdf)

Barriere, Y., Denoue, D., Briand, M., Simon, M., Jouanin, L. and Durand-Tardif, M. (2006) Genetic variations of cell wall digestibility related traits in floral stems of Arabidopsis thaliana accessions as a basis for the improvement of the feeding value in maize and forage plants. Theor Appl Genet. (pdf)

Simon, M., Loudet, O., Durand, S., Bérard, A., Brunel, D., Sennesal, F-X, Durand-Tardif, M., Pelletier, G. and Camilleri, C. (2008). QTL mapping in five new large RIL populations of Arabidopsis thaliana genotyped with consensus SNP markers. Genetics 178: 2253-2264. (pdf)

Jubault M, Lariagon C, Simon M, Delourme R, Manzanares-Dauleux MJ. (2008) Identification of quantitative trait loci controlling partial clubroot resistance in new mapping populations of Arabidopsis thaliana.Theor Appl Genet 117(2) 191-202. (pdf)

Vlad, D., Rappoport, F., Simon, M. and Loudet, O. (2010) Gene Transposition Causing Natural Variation for Growth in Arabidopsis thaliana. PLoS Genetics 6(5): e1000945. (pdf)

Cubillos F.A., Yansouni J., Khalili H., Balzergue S., Elftieh S., Martin-Magniette M.L., Serrand Y., Lepiniec L., Baud S., Dubreucq B., Renou J.P., Camilleri C., Loudet O. (2012). Expression variation in connected recombinant populations of Arabidopsis thaliana highlights distinct transcriptome architectures. BMC Genomics 13: 117.  (pdf)

EpiRILs:
Johannes F., Porcher E., Teixeira F., Saliba-Colombani V., Simon M., Agier N., Bulski A., Albuisson J., Heredia F. AudigierP., Bouchez D., Dillmann C., Guerche P., Hospital F., Colot V.(2009). Assessing the impact of transgenerational epigenetic variation on complex traits. PLoS Genet 5(6): e1000530. (pdf)

Genetic incompatibilities:
Bikard D., Patel D., Le Metté C., Giorgi V., Camilleri C., Bennett M.J., Loudet O. (2009) Divergent evolution of duplicate genes leads to genetic incompatibilities within A. thaliana. Science 323: 623-626. (pdf)

Durand S, Bouché N, Perez Strand E, Loudet O and Camilleri C. (2012) Rapid establishment of genetic incompatibility through natural epigenetic variation. Current Biology 22: 326-331. (pdf)

 

 

 

  

 


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