A high density GBS map of bread wheat and its application for dissecting complex disease resistance traits

Abstract

BackgroundGenotyping-by-sequencing (GBS) is a high-throughput genotyping approach that is starting to be used in several crop species, including bread wheat. Anchoring GBS tags on chromosomes is an important step towards utilizing them for wheat genetic improvement. Here we use genetic linkage mapping to construct a consensus map containing 28644 GBS markers.ResultsThree RIL populations, PBW343 × Kingbird, PBW343 × Kenya Swara and PBW343 × Muu, which share a common parent, were used to minimize the impact of potential structural genomic variation on consensus-map quality. The consensus map comprised 3757 unique positions, and the average marker distance was 0.88 cM, obtained by calculating the average distance between two adjacent unique positions. Significant variation of segregation distortion was observed across the three populations. The consensus map was validated by comparing positions of known rust resistance genes, and comparing them to wheat reference genome sequences recently published by the International Wheat Genome Sequencing Consortium, Rye and Ae. tauschii genomes. Three well-characterized rust resistance genes (Sr58/Lr46/Yr29, Sr2/Yr30/Lr27, and Sr57/Lr34/Yr18) and 15 published QTLs for wheat rusts were validated with high resolution. Fifty-two per cent of GBS tags on the consensus map were successfully aligned through BLAST to the right chromosomes on the wheat reference genome sequence.ConclusionThe consensus map should provide a useful basis for analyzing genome-wide variation of complex traits. The identified genes can then be explored as genetic markers to be used in genomic applications in wheat breeding.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1424-5) contains supplementary material, which is available to authorized users.

Genome diversity in Triticum aestivum

“…This platform adopted a combination of complexity reduction methods developed initially for array-based DArT and sequencing of resulting representations on next-generation sequencing platforms. DArTseq is essentially the same method as Cornell-style reduced representation sequence-based genotyping by sequencing (GBS) (Li et al, 2015). It supersedes hybridization-based DArT recently because the cost and throughput of sequencers reached a point where any GBS-type approach can compete effectively with hybridisation-based DArT (Li et al, 2015).…”

Opportunities for unlocking the potential of genomics for African trees

“…Among the common methods for collecting genomic data in nonmodel African tree species without prior molecular resources include amplified fragment length polymorphisms (AFLPs), GBS, diversity arrays technology (DArT), DArTseq, restriction site associated DNA sequencing (RADseq), and de novo transcriptome assembly (Fry et al, 2009;Elshire et al, 2011;De Wit et al, 2012;Van Schalkwyk et al, 2012;Li et al, 2015). These methods offer a moderately cheap means of collecting thousands of genomic DNA data points on multiple samples from nonmodel species without reference genomes (Hohenlohe et al, 2010;Elshire et al, 2011;Yeaman et al, 2014).…”

The wheat pangenome: assembly and analysis

“…The framework genetic map produced for that study contained 112 thousand SNPs and had a total length of 2,826cM in 1,335 recombination bins. That is smaller than the genetic map constructed in this chapter and also smaller than many other genetic maps produced for several wheat mapping populations , Quarrie et al, 2005, Semagn et al, 2006, Poland et al, 2012b, Torada et al, 2006, Li et al, 2015c, Li et al, 2015b. Overall, these maps had a length ranging from 3,000cM to 4,500cM in 1,500 to 2,500 recombination bins.…”

“…Genetic mapping assays have shown that the D genome consistently has fewer markers and recombination bins , Li et al, 2015c, Sorrells et al, 2011, Semagn et al, 2006, Gupta et al, 2005, KamMorgan, 1988. It has been suggested that the little diversity found in the D genome is due to the little gene flow between the wild relative Ae.…”