A. thaliana Resource Centre for Genomics

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JP Bourgin

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genetics & plant breeding

plant nitrogen nutrition

seed biology

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biochemistry

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Arabidopsis thaliana Resource Centre for Genomics

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research groups
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Keywords : Arabidopsis thaliana - biological resources - insertion mutants - ecotypes - recombinant inbred line populations - collection - core collection

Quicklinks :

Databases:
	VNAT: a database for the study of Natural Variation in Arabidopsis thaliana
	Agrobact+: a database for the study of Versailles T-DNA insertion lines

Seed order:
T-DNA lines, accessions and RIL populations from Versailles' collection
	General information
	Ordering the biological material
	Price and payment
	Publiclines

Experimental procedures
	DNA isolation from Arabidopsis seeds

Other informations
	Information on the Versailles T-DNA collection
	Information on the FLAG_FST

Contacts :

Génétique et amélioration des plantes
INRA – Centre de Versailles – Grignon
Route de St Cyr
78 026 VERSAILLES Cedex
fax : (33) 01 30 83 33 19

Resources Production, Management and Distribution

	Matthieu SIMON (Engineer) +33 (0)1 30 83 30 15
	Christine SALLE (Technician) +33 (0)1 30 83 30 15
	LAROCHE Liliane (Technician) +33 (0)1 30 83 30 15
	Stéphanie DURAND (Technician) +33 (0)1 30 83 30 15
	Sylvie-Dominique Communal (AJT) tél : 01 30 83 33 01

	Jacqueline LEGEAY (Technician) +33 (0)1 30 83 33 01
	Bernadette TROUVE (Technician) +33 (0)1 30 83 33 01
	Jacqueline BABILLIOT (Technician) +33 (0)1 30 83 33 01
	Julie Renouf tél: 01 30 83 33 01 - (36 83 - 31 86)
	Amandine Petit (Apprentie)

Resources Characterization, Development and Use

	Georges PELLETIER (DRE) tél + 33 01 30 83 33 17
	Mylène DURAND – TARDIF (DR2) tél + 33 01 30 83 31 62
	Yansouni Jennifer (CDD) tel: + 33 01 30 83 33 15 (37 40)

	Christine CAMILLERI (IR1) tél + 33 01 30 83 33 16
	Olivier LOUDET (CR1) tél + 33 01 30 83 33 16
	Nicolas Boichard tel:+ 33 01 30 83 33 16

Background :

Arabidopsis thaliana has been adopted by the scientific community as a model species for genetic, genomic and functional studies. The complete genomic sequence of the accession Columbia was published in 2000, providing a large amount of information on the structure of the genome as well as the genes necessary for the development of a higher plant. Among the genes identified, around 30% have neither a known function nor homology with genes of known function. Biological material and analytical tools have been established at the SGAP, that are available to the scientific community, in order to contribute to the knowledge in the area of plant genomics.

Main Results :

The Resource Center for genomics has made the following three collections available to the scientific community :

A collection of 55, 000 independent insertion mutants
This mutant collection was generated by inserting a DNA cassette in the accession WS. The transformation method used depends on the capacity of DNA transfer of the soil bacterium, Agrobacterium tumefaciens. A total of 55,000 transformants were obtained with an apparently random distribution. We estimate to have potentially generated insertions in 80% of all A. thaliana genes.
Each knock-out can be observed with the phenotype giving some ideas about the potential function of the gene affected. It is also possible to look for a mutant in a gene with a known sequence but an unknown function and to observe its behavior. Each transformant is maintained in the form of a selfed line called Tn (n indicating the generation of selfing). Most mutants are available in the T3 generation, but some are distributed in T2.
The Agrobact+ database contains the phenotypic information on the lines (segregation of different phenotypes observed in vitro or in the greenhouse…). The Flagdb++ database provides diverse molecular information on the localization of the genes and on the sites of DNA cassette insertion.
A collection of more than 500 ecotypes
More than 500 populations of diverse geographic origins have been gathered. This collection allows the evaluation of the natural diversity of the species and to identify populations with a particular behavior for further in-depth study.
From each population, one plant was isolated. This plant was selfed to generate a reference line or accession for the ecotype. Each accession has been genotyped and its molecular identification card, which is currently being made, will be used for quality control.
A core collection that maximizes the genetic diversity with a reduced number of accessions has been generated (see “High-throughput genotyping”). This collection facilitates experiments that would not be possible with more than 500 accessions.
General information (passport data) is available in the Vnat database. Molecular and genotypic data are available in a database that is currently in construction.
Nearly 30 Recombinant Inbred Line (RIL) populations with approximately 450 lines each
The populations will allow the study of the genetic determinants underlying complex traits. If each mutant provides information on the function of a gene, many traits are determined by the expression of a group of genes over space (different organs) and time (different developmental stages). Following the segregation of these complex traits within a RIL population will allow the identification of the group of alleles, originating in each of the parents of the cross, that will contribute to the expression of the trait studied.
Twenty-nine accessions were crossed with the reference ecotype, Columbia. From each cross, approximately 500 F2 lines were propagated in single seed descent up to the F6 generation. Each RIL population will be mapped with molecular markers (see « High-throughput genotyping ») in order to identify and locate the contribution of each parental genome. The populations that are multiplied up to the F7 generation in priority are those that derive from the crosses with the smallest core collection (8 accessions) and Columbia.
Information on the mapping and the availability of the RIL populations will be available in the VNat database.

The different biological resources, coming from the three collections, can be ordered here.
The costs for these resources are as follows

	Academic fee, per line	Commercial fee, per line	Processing fee
Individual stock (euros)	3	12	12.5
Seed sets (per line) (euros)	1.5	6	12.5

Selected Publications :

Johannes, F., E. Porcher, Teixeira, F. K.Saliba-Colombani, V.Simon, M.Agier, N.Bulski, A.Albuisson, J.Heredia, F.Audigier,P.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

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. Bouchabke et al Bouchabke et al

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.

Ronceret A, Gadea-Vacas J, Guilleminot J, Lincker F, Delorme V, Lahmy S, Pelletier G, Chaboute M.E, Devic M. (2008) The first zygotic division in Arabidopsis requires de novo transcription of thymidylate kinase. Plant J 53(5) 776-89.

Simon M, Loudet O, Durand S, Bérard A, Brunel D, Sennesal FX, Durand-Tardif M, Pelletier G, Camilleri C. (2008) Quantitative trait loci mapping in five new large recombinant inbred line populations of Arabidopsis thaliana genotyped with consensus single-nucleotide polymorphism markers. Genetics 178(4) 2253-64.Simon et al

Giancola S, McKhann H, Bérard A, Camilleri C, Durand S, Libeau P, Roux F, Reboud X, Gut IG and Brunel D (2006) Utilization of the three high-throughput SNP genotyping methods, the GOOD assay, Amplifluor and TaqMan, in diploid and polyploid plants. Theor Appl Genet 2 ; 1-10.

Y. Barrière, D. Denoue, M. Briand, M. Simon, L. Jouanin and M. Durand-Tardif (2006),Genetic variation for cell walldigestibility related traits in floral stems of A. thaliana accessions as a basis for the improvement of the feeding value in maize and forage plants, Theor. Appl. Genet. 113:163-175.

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.

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.

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.

SGAP full publication list here

Further readings :
QTL arabidopsis et population Bay0 x Sha (Olivier Loudet)