Bay-0 × Shahdara recombinant inbred line population: a powerful tool for the genetic dissection of complex traits in Arabidopsis

Abstract

Natural genetic variation in Arabidopsis is considerable, but has not yet been used extensively as a source of variants to identify new genes of interest. From the cross between two genetically distant ecotypes, Bay-0 and Shahdara, we generated a Recombinant Inbred Line (RIL) population dedicated to Quantitative Trait Locus (QTL) mapping. A set of 38 physically anchored microsatellite markers was created to construct a robust genetic map from the 420 F6 lines. These markers, evenly distributed throughout the five chromosomes, revealed a remarkable equilibrium in the segregation of parental alleles in the genome. As a model character, we have analysed the genetic basis of variation in flowering time in two different environments. The simultaneous mapping of both large- and small-effect QTLs responsible for this variation explained 90% of the total genotypic variance. Two of the detected QTLs colocalize very precisely with FRIGIDA and FLOWERING LOCUS C genes; we provide information on the polymorphism of genes confirming this hypothesis. Another QTL maps in a region where no QTL had been found previously for this trait. This confirms the accuracy of QTL detection using the Bay-0 x Shahdara RIL population, which constitutes the largest in size available so far in Arabidopsis. As an alternative to mutant analysis, this population represents a powerful tool which is currently being used to undertake the genetic dissection of complex metabolic pathways.

Functional genetics of intraspecific ecological interactions in Arabidopsis thaliana

“…The locus on which we have focused explains a large proportion of variation in the focal plant traits (an average of 12% of the variance per trait, with a maximum of 20% in silique number; table 1). This locus was previously identified by Loudet et al [34] in a study of flowering time and maps to a region of the genome that encompasses the FRI gene. FRI has previously been shown to have pleiotropic effects on fitness-related traits [42,43], and our analysis shows that it appears to also have relatively strong indirect effects on partners (the indirect effects alone are significant at the genome level).…”

“…Genotypes were assigned the index values of þ1 and 21 for the Bay-0 and Shahdara homozygotes at a locus, respectively, Therefore positive allelic effects can be interpreted as the effect of replacing the Shahdara allele with the Bay-0 allele [34]. Because of deviations from normality, we natural log-transformed BOLT and square root-transformed WT, BUD, FLWR, SILIQ and BRANCH for both the focal and partner traits.…”

High-density haplotyping with microarray-based expression and single feature polymorphism markers in Arabidopsis

“…Sequencing studies have demonstrated the existence of hundreds of SNPs between accessions Bayreuth (Bay-0) and Shahdara (Sha), but these polymorphisms had not been developed into tractable genetic markers (Nordborg et al 2005). To add markers to the existing genotypic data for the Bay-0 ‫ן‬ Sha RIL population (Loudet et al 2002), we used gene expression microarray data that had been generated as part of a larger experiment to measure transcriptional variation in these RILs to assess genotypes and produce detailed haplotypes. The SFP markers and GEMs we identified were used to construct a detailed genetic linkage map that was consistent with the gene order predicted by the genomic sequence of the Col-0 accession (The Arabidopsis Genome Initiative 2000) with minimal missing data.…”

SEG-Map: A Novel Software for Genotype Calling and Genetic Map Construction from Next-generation Sequencing

“…Nevertheless, the resulting maps were still at relatively low resolution (Eshed and Zamir 1995;Loudet et al 2002;Simon et al 2008). Recently, the emergence of next-generation sequencing technology greatly augmented the sequencing throughputs and reduced both time and cost simultaneously, and might make population-scale QTL studies feasible (Charlesworth and Willis 2009).…”