Genotyping by Sequencing Using Specific Allelic Capture to Build a High-Density Genetic Map of Durum Wheat

Abstract

Targeted sequence capture is a promising technology which helps reduce costs for sequencing and genotyping numerous genomic regions in large sets of individuals. Bait sequences are designed to capture specific alleles previously discovered in parents or reference populations. We studied a set of 135 RILs originating from a cross between an emmer cultivar (Dic2) and a recent durum elite cultivar (Silur). Six thousand sequence baits were designed to target Dic2 vs. Silur polymorphisms discovered in a previous RNAseq study. These baits were exposed to genomic DNA of the RIL population. Eighty percent of the targeted SNPs were recovered, 65% of which were of high quality and coverage. The final high density genetic map consisted of more than 3,000 markers, whose genetic and physical mapping were consistent with those obtained with large arrays.

Fig 1. Description of the bait design.

Orange lines represent the durum wheat genome, with the targeted SNP in brackets. Bait sequences are represented in grey. The number of SNPs targeted by each type of bait is specified.

Fig 2. Detection of a bonus SNP on the homeolog of a targeted contig.

A portion of A and B genomes were represented, with an SNP on the A genome (in red) and an SNP on the B genome (in blue). Divergences between both genomes are represented in green. The bait shown in grey was designed initially to capture a portion of the A genome, but captured also the homeologous portion of the B genome, with the related bonus SNP.

Fig 3. Correlations between putative physical and genetic positions.

The 14 durum wheat chromosomes are shown separately, with the putative physical position on the X-axis (bp) and the genetic position on the Y-axis (cM). The chromosome name is given at the top left of each plot. The number of markers is given in brackets. A red line represents the fitted polynomial model and a grey area represents the 95% confidence interval. The two vertical grey lines are maximum and minimum values of the physical positions.