Can-0 x Col-0

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Contact : Publiclines (ijpb-publiclines@inra.fr)

 

  • Introduction

The Can-0 x Col-0 RIL population has been generated at INRA Versailles (France) between 2004 and 2008. The recombinant inbred lines were derived from a cross between Col-0 and Can-0 accessions, where Col-0 (=186AV in Versailles) and Can-0 (=163AV in Versailles) are lines derived respectively from accessions N1092 and N1064 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, F8 seeds from bulk multiplication of F7 plants are available for distribution.

When you use the Can-0 x Col-0 population, thank you to cite this article:
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 file

 

  • The Can-0 x Col-0 Resource

All the lines have been produced at the same time in a greenhouse. F8 seeds from 371 RILs successfully genotyped 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 2 to 500) 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 371 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 Can-0 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 -> CanxCol_RILLists.xls

 

  • The Can-0 x Col-0 Marker Data

The Can-0 x Col-0 RILs (371 F6 plants) have been used to build a genetic map with 84 markers (of which 81 SNP markers: Single Nucleotide Polymorphism).

Genetic map parameters:
Average distance between markers: 4.9 cM
Missing-data rate: 0.6 %
Whole-population residual heterozygosity (F6): 3.2 %
Global allelic equilibrium: Col-0 54.9 % / Can-0 45.1 %
% of genome free of distortion (at 1%) : 70 %
Maximum allelic distortion rate: Col-0 66.3 % / Can-0 33.7 % (Chromosome 4 - around 5.8 Mb)

The genotype data is included in the following files:
The complete genotype data (371 RILs, each row from row#8 is a RIL) is included in the Excel file -> CanxCol_Genotypes.xls, where "A"=Col; "B"=Can; "C"=Het; "D"=NA (missing)

The raw data ordered marker by marker is included in the text file -> CanxCol_Genotypes.raw, with the following code: "A"=Col; "B"=Can; "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 -> CanxCol_Genotypes.maps. This is the ".csv" 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 -> CanxCol_MapCoord.xls.

The genetic map is drawn as an image in -> CanxCol_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"=Can; "C"=Het; "D"=NA):
CanxCol_forGGT32.ggt is a text file containing the genotype data, map data and RIL number aliases for direct opening in GGT32.
CanxCol_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 Can-0 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.

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

Trait Author
Institute
Publication
Flowering time F. Roux
Universite des Sciences et Technologies de Lille1 Lille - France
Cold tolerance E. Teoule
INRA - Versailles - France
  A. Pecinka
Max Planck Institute for Plant Breeding Research - Köln - Germany
Sucrose-mediated shoot apical meristem activation in darkness M. Proveniers
Utrecht University - Netherlands
Nitrogen use efficiency F. Chardon
INRA - Versailles - France