DOI: 10.5061/dryad.v655ns36
title: Data from: The recombination landscape in Arabidopsis thaliana F2 populations

description: Recombination during meiosis shapes the complement of alleles segregating
 in the progeny of hybrids, and has important consequences for phenotypic
 variation. We examined allele frequencies as well as crossover locations
 and frequencies in over 7000 plants from 17 F2 populations derived from
 crosses between 18 Arabidopsis thaliana accessions. We observe segregation
 distortion between parental alleles in over half of our populations. The
 potential causes of distortion include variation in seed dormancy and
 lethal epistatic interactions. Such a high occurrence of distortion was
 only detected here because of the large sample size of each population,
 and the number of populations characterized. Most plants carry only one or
 two crossovers per chromosome pair, and therefore inherit very large,
 non-recombined genomic fragments from each parent. Recombination
 frequencies vary between populations but consistently increase adjacent to
 the centromeres. Importantly, recombination rates do not correlate with
 whole-genome sequence differences between parental accessions, suggesting
 that sequence diversity within A. thaliana does not normally reach levels
 that are high enough to exert a major influence on the formation of
 crossovers. A global knowledge of the patterns of recombination in F2
 populations is crucial to better understand the segregation of phenotypic
 traits in hybrids, in the laboratory or in the wild.
description: allele
 frequenciesGenotype frequencies for
 all 17 F2 populations. AA: plants homozygous for grandparent A; BB: plants
 homozygous for grandparent B; AB: heterozygous plants. NA: plants with no
 genotype information. For all SNP positions the associated p-value is
 given, for the Chi square test for deviation from a mendelian 1:2:1
 segregation ratio.discriminating
 SNPslist of SNPs from the
 initial set of 402 that were used to differentiate between parental
 accessions. The number of populations discriminated by each SNP is
 indicated (from 1 to 16, out of 17.genetic
 distancesmatrix of pair-wise
 genetic distances between the 17 parental accessions. Also includes
 genetic distances of all 17 F2 populations calculated from 149 and 402 SNP
 sets. Parental accession genotypes used for calculation of genetic
 distances with our set of 402 SNPs is also given.maps K H
 CFgenetic maps measured
 with the Haldane (H), Kosambi (K) and Carter-Falconer (CF) map functions
 in R/qtl. Note that the Kosambi and Carter-Falconer genetic maps for the
 P8 population failed to compute.XO counts per
 plantNumber of crossovers per
 chromosome pair and per plant. Each spreadsheet corresponds to a given
 chromosome.XO counts per
 positionNumber of crossovers per
 F2 population and per position. The position of each crossover was
 approximated to the mid-point of the interval containing the crossover.
 SNP: indicates the SNP located to the right-side of the interval
 containing the crossover; mid-point: position (in bp) of the mid-point of
 the interval.XO
 interferenceList of positions of
 first (XO1) and second (XO2) crossovers of the crossover pairs. XO
 positions and inter-XO distances are given in bp, cM and normalized cM
 positions.all
 XOsPositions of all
 crossover events (single and double) per plant and chromosome. zip file
 containing data for all 17 F2 populations.