Bay-0 x Shahdara
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NEW GENETIC MAP !!! see below... 'Map2'
Contact : Olivier Loudet (loudet@versailles.inra.fr) or Christine Camilleri (camiller@versailles.inra.fr)
- Introduction
The Bay-0 x Shahdara population has been created by Olivier Loudet and Sylvain Chaillou between 1997 and 2000 at INRA Versailles. Complete description of the population can be found in Loudet et al., 2002 (Theoretical and Applied Genetics, vol 104, pp 1173-1184). The original 420 recombinant inbred lines were derived from a cross between Bay-0 and Shahdara accessions; where Bay-0 is a line derived from accession N954 and Shahdara is a line derived from accession N929, from the Nottingham Arabidopsis Stock Center. Bay-0 and Shahdara were chosen because of their known geographical, ecological and genetic distances (Note: Shahdara, 'Shakdara' and 'Shokhdara' -among others!- are different spelling of the same accession). Lines were conducted through Single Seed Descent until F6 generation without selection. Then one plant per line was used for genotyping (F6) and selfed to obtain F7 seeds. Today, F8 seeds from bulk multiplication of F7 plants are available for distribution.
The Bay-0 x Shahdara Population was the 6th RIL set deposited in Arabidopsis Stock Centers (it was given to NASC in 2002), after Ler x Col (Lister and Dean), W100 x WS (Scolnik), Ler x Cvi (Koornneef), Col x Nd-1 (Holub) and Col x Kas-1 (Somerville).
When you use the Bay-0 x Shahdara population, thank you to cite this article:
Loudet, Chaillou, Camilleri, Bouchez and Daniel-Vedele, 2002. Bay-0 x Shahdara recombinant inbred lines population: a powerful tool for the genetic dissection of complex traits in Arabidopsis. Theoretical and Applied Genetics, vol 104 (6-7), pp 1173-1184
-> 
PDF File
- The Bay-0 x Shahdara Resource
Today, available seeds are from a bulk multiplication of F7 plants (= F8 seeds). All the lines have been multiplied at the same time in a greenhouse at INRA - Versailles (France) between October 2001 and March 2002. These seeds can be used directly for phenotyping tasks. At least 12-15 plants should be bulked for multiplication purpose. To avoid any problems of identification, lines SHOULD NOT be renamed. Stock Numbers provided (from 1 to 432) correspond to a unique number for each line. Due essentially to sterility, some numbers do not exist anymore in the population (they were lost at intermediate generations). The 420 remaining lines (F6) were used for genotyping (Original Map and Map2). During F7 and F8 multiplication, 9 lines were lost because of sterility or other line-specific problems (108, 238, 247, 317, 322, 333, 347, 405, 414), these are NOT distributed in the stock centers.
The 411 remaining lines from the Bay-0 x Shahdara population (complete RIL set) are distributed by INRA Versailles and both stock centers: they represent F8 seeds from the last and unique bulk-multiplication performed at INRA Versailles.
Two sub-sets of lines were designed using T. Vision / D. Brown tool 'Mappop' (Vision TJ, Brown DG, Shmoys DB, Durrett RT and Tanskley SD, 2000. Selective mapping: A strategy for optimizing the construction of high-density linkage maps. Genetics 155: 407-420). These sub-sets gather the lines with the most interesting (recombined) genotypes.
With 165 lines, the Core-Pop165 is intended for optimised QTL mapping when using all 411 lines is impractical.
With only 18 lines, the 18 RILs - Minimal set is of course NOT intended for any markers or QTL mapping, but rather to give an idea of the variation and transgression of any specific trait in the Bay-0 x Shahdara population using a small number of lines (together with the parents). The 18-Minimal set is fully included in the Core-Pop165 set.
Lists of the different sets of lines (Genotyped RILs, Complete RIL set, Core-Pop165, Not Core-Pop165, 18-Minimal set) are included in this Excel file -> BayxSha_RILLists.xls
- The Bay-0 x Shahdara Marker Data
The Bay-0 x Shahdara RILs population (420 F6 plants) had been originally used to build a genetic map with 38 microsatellite markers, mostly new markers defined from the genomic sequence (cf Loudet et al., 2002. Theoretical and Applied Genetics, vol 104, pp 1173-1184). You will find the original 38-map data below. We have now extended this full-RIL set genetic map to 69 markers, with the same quality as in the original map (in terms of missing data rate and number of RILs genotyped = 420). Other systematic efforts to improve genotyping in subsets of this RIL population include for example (1) Affy-array SFPs from St Clair / Kliebenstein' groups at UC Davis (2) Indel-array genotyping from Queitsch' lab at U. Washington.
On the upper arm of chromosome 3, no recombination events occur between about 3 Mb and 5 Mb. This is also observed in the Sha x Col-0 RIL set and is likely due to a structural chromosomal change in the accession Shahdara compared to Bay-0 and Col-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 Bay-0 x Sha (and the Sha x Col-0) RIL populations unsuitable for map-based cloning in that specific region.
Map2 Data:
Genetic map parameters:
Average distance between markers: 6.1 cM (on average equivalent to ~2 Mb)
Missing-data rate: 0.63 %
Whole-population residual heterozygosity (F6): 3.18 %
Global allelic equilibrium: Bay 51% / Sha 49 %
% of genome free of distortion (5%) : 80 %
Maximum allelic distortion rate: 64 % / 36 % (Chromosome 4 - MSAT4.18)
The genotype data is included in the following files:
The raw data classified marker by marker is included in the text file -> BayxSha_2_Genotypes.raw, with the following code: "B"=Bay; "S"=Sha; "-"=NA. In this file, heterozygotes are considered (and coded) as missing data. This file is to be used as input file for example in Mapmaker or QTLCartographer analysis.
The full genotype data (transposed) is also included in the Excel file with the following code : "A"=Sha; "B"=Bay; "C"=Het; "D"=NA-> BayxSha_2_Genotypes.xls
The genetic map results are included in the text file -> BayxSha_2_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 genetic map are indicated in the Excel file -> BayxSha_2_MapCoord.xls
The genetic map is drawn as an image in -> BayxSha_2_GeneticMap.pdf
Information on the 69 PCR-markers used in this map are included in the Excel file -> BayxSha_2_Markers.xls
The genotype data is 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"=Sha; "B"=Bay; "C"=Het; "D"=NA):
BayxSha_2_forGGT32.ggt is a text file containing the genotype data, map data and RIL number aliases for direct opening in GGT32.
BayxSha_2_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).
Original Map Data:
Genetic map parameters:
Average distance between markers: 10.8 cM (on average equivalent to 3.4 Mb)
Missing-data rate: 0.23 %
Whole-population residual heterozygosity (F6): 3.05 %
Global allelic equilibrium: Bay 51% / Sha 49 %
% of genome free of distortion (5%) : 80 %
Maximum allelic distortion rate: 64 % / 36 % (Chromosome 4 - MSAT4.18)
The genotype data is included in the following files:
The raw data classified marker by marker is included in the text file -> BayxSha_Genotypes.raw, with the following code: "B"=Bay; "S"=Sha; "-"=NA. In this file, heterozygotes are considered (and coded) as missing data. This file is to be used as input file for example in Mapmaker or QTLCartographer analysis.
The same data (transposed) is included in the Excel file -> BayxSha_Genotypes.xls
The genetic map results are included in the text file -> BayxSha_Genotypes.maps. This is the ".maps" output file from Mapmaker analysis to be used as a ".mps" input file in QTLCartographer work.
Genetic positions of the markers on the genetic map are indicated in the text file -> BayxSha_MapCoord.txt
The genetic map is drawn as an image in -> BayxSha_GeneticMap.tif
The genotype data is 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"=Sha; "B"=Bay; "C"=Het; "D"=NA):
BayxSha_forGGT32.ggt is a text file containing the genotype data, map data and RIL number aliases for direct opening in GGT32.
BayxSha_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 Bay-0 x Shahdara Phenotypic Data
The following Excel file contains all published phenotypic description of the RILs (either Core-Pop165 or complete set) :
-> BayxSha_PublishedPheno.xls
- The Bay-0 x Shahdara 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 loudet@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 Bay-0 x Shahdara RIL population (either Core-Pop165 or complete set):