Sha x Col-0

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Contact : Christine Camilleri (camiller@versailles.inra.fr) or Matthieu Simon ( msimon@versailles.inra.fr)

• Introduction

The Sha x Col-0 RIL population has been generated at INRA Versailles between 2001 and 2005. Complete description of the population can be found in Simon et al. (in preparation). The recombinant inbred lines were derived from a cross between Col-0 and Sha accessions, where Col-0 (=186AV in Versailles) and Sha (=236AV in Versailles) are lines derived respectively from accessions N1092 and N929 from the Nottingham Arabidopsis Stock Center. Lines were conducted through Single Seed Descent until F6 generation without selection. Then one plant per line was chosen again for selfing to obtain F7 seeds, which were used as a bulk for genotyping (equivalent to genotyping THE F6 plant). Today, F7 seeds are available for distribution.

When you use the Sha x Col-0 population, thank you to cite this article:
*** Simon et al., in preparation
-> PDF File (not yet available)

• The Sha x Col-0 Resource

All the lines have been produced at the same time in a greenhouse at INRA Versailles (France). 349 RILs were successfully genotyped, among which 346 (Complete RIL set) are available for distribution (three lines: 26, 233 and 483, were genotyped but are NOT distributed due to problems of multiplication). Today, F7 seeds from these 346 RILs are distributed; they can be used directly for phenotyping tasks. At least 12-15 plants should be bulked for multiplication purposes to avoid segregation bias. To avoid any problem of identification, lines SHOULD NOT be renamed. Stock Numbers provided (from 1 to 512) correspond to a unique number for each line. Some numbers do not exist anymore in the population: plants were lost at intermediate generations, essentially because of sterility, or lines were removed because genotyping data were missing.

Two sub-sets of lines were designed following goals close to the 'selective mapping' strategy. These sub-sets gather the lines with the most interesting (recombined) genotypes, removing lines with missing data points and globally ensuring a better allelic equilibrium.

With 164 lines, the Core-Pop164 is intended for optimised QTL mapping when using all 346 lines is impractical.

With only 20 lines, the 20 RIL-Minimal set is of course NOT intended for mapping, but rather to give an idea of the variation and transgression of any specific trait in the Sha x Col-0 population using a small number of lines (together with the parents). The 20-Minimal set is fully included in the Core-Pop164 set.

Lists of the different sets of lines (Complete RIL set, Core-Pop164, Not Core-Pop164, 20-Minimal set) are included in this Excel file -> ShaxCol_RILLists.xls

• The Sha x Col-0 Marker Data

The Sha x Col-0 RILs (349 F6 plants) have been used to build a genetic map with 86 markers (of which 82 SNP markers: Single Nucleotide Polymorphism).
On the upper arm of chromosome 3, no recombination events occur in a region of nearly 2.2 Mb, between markers c3_02968, c3_04141 and c3_05141. This is also observed in the Bay-0 x Sha RIL set created by LOUDET et al. (2002) and is likely due to a structural chromosomal change in the accession Shahdara compared to Col-0 and Bay-0 such as a large inversion of this region, an event known to strongly suppress recombination in the concerned interval. This suppression of recombination obviously makes the Sha x Col-0 (and the Bay-0 x Sha) RIL populations unsuitable for map-based cloning in that specific region.

BEWARE: genotyping data are from 349 RILs, of which only 346 (Complete RIL set) are distributed. The three lines genotyped but not available are lines 26, 233 and 483; they are present in the genotype tables and they should appear in your phenotype tables as missing data.

Genetic map parameters:
Average distance between markers: 4.7 cM (on average equivalent to 1.4 Mb)
Missing-data rate: 0.4 %
Whole-population residual heterozygosity (F6): 3.3 %
Global allelic equilibrium: Col-0 50.8 % / Sha 49.2 %
% of genome free of distortion (at 1%) : 55 %
Maximum allelic distortion rate: Col-0 66.9 % / Sha 33.1 % (Chromosome 5 - around 22.4 Mb)

The genotype data is included in the following files:
The complete genotype data (349 RILs, each row from row#8 is a RIL) is included in the Excel file -> ShaxCol_Genotypes.xls, where "A"=Col; "B"=Sha; "C"=Het; "D"=NA (missing)

The raw data ordered marker by marker is included in the text file -> ShaxCol_Genotypes.raw, with the following code: "A"=Col; "B"=Sha; "U"=NA. In this file, heterozygotes are considered (and coded) as missing data ("U"). This file is to be used as input file for example in Mapmaker or QTLCartographer analysis.

The genetic map results are included in the text file -> ShaxCol_Genotypes.maps. This is the ".maps" output file from Mapmaker analysis to be used as a ".mps" input file in QTLCartographer work.

Genetic and physical positions of the markers on the maps are indicated in the Excel file -> ShaxCol_MapCoord.xls.

The genetic map is drawn as an image in -> ShaxCol_GeneticMap.pdf

The genotype data are also presented in the following files to be used with "GGT32", a very nice tool made to graphically represent the genotypes of individual RILs including Het and missing data genotypes (code for GGT32: "A"=Col; "B"=Sha; "C"=Het; "D"=NA):
ShaxCol_forGGT32.ggt is a text file containing the genotype data, map data and RIL number aliases for direct opening in GGT32.
ShaxCol_forGGT32.gst is a text file containing nice settings (color, spacings...) to be used in GGT32 (automatically recognized if named accordingly and placed under the same folder as the .ggt file).

• The Sha x Col-0 Phenotypic Data

The following Excel file contains all published phenotypic description of the RILs (either Core-Pop164 or complete set) :
-> ShaxCol_PublishedPheno.xls [No published data yet]

• The Sha x Col-0 Declared Projects

We request that you tell us what you plan to do with this RIL material as you order it, so that we can update the following table, which is very useful to avoid duplication of effort in QTL mapping. Please email to msimon@versailles.inra.fr or camiller@versailles.inra.fr

As far as we are aware of, these are the different projects and quantitative traits that different labs are conducting in the Sha x Col-0 RIL population (either Core-Pop164 or complete set):