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.
Highlights
Wheat (Triticum spp.) is one of the most widely grown food grain crops in the world and provides about a fifth of the calories consumed by humans (FAO, http://faostat3.fao.org/home/E)
It is closely related to bread wheat (Triticum aestivum L.), which arose via spontaneous interspecific hybridization between a domesticated T
On average, 86% of the reads were mapped on Durum Wheat reference transcriptome (DWr), which denoted a low degree of hybridization between baits and off-target DNA
Summary
Wheat (Triticum spp.) is one of the most widely grown food grain crops in the world and provides about a fifth of the calories consumed by humans (FAO, http://faostat3.fao.org/home/E). Durum (Desf.)] accounts for about 10% of the total global wheat production (World Grain Statistic, www.igc.int). It is a minor crop compared to bread wheat, which is the focus of considerable efforts with regard to breeding new high performance cultivars, genomic investigations and resource developments. In this respect, new omics resources developed under the umbrella of the International Wheat Genome Sequencing Initiative (IWGSC) represents a major input for all Triticeae genomic approaches [1]. Durum) is a modern representative of a group of allotetraploid subspecies (Triticum turgidum subsp.) that were domesticated from the wild T. turgidum dicoccoides [2,3]. It is closely related to bread wheat (Triticum aestivum L.), which arose via spontaneous interspecific hybridization between a domesticated T
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