Abstract
BackgroundDurum wheat (Triticum durum Desf.) is a tetraploid cereal grown in the medium to low-precipitation areas of the Mediterranean Basin, North America and South-West Asia. Genomics applications in durum wheat have the potential to boost exploitation of genetic resources and to advance understanding of the genetics of important complex traits (e.g. resilience to environmental and biotic stresses). A dense and accurate consensus map specific for T. durum will greatly facilitate genetic mapping, functional genomics and marker-assisted improvement.ResultsHigh quality genotypic data from six core recombinant inbred line populations were used to obtain a consensus framework map of 598 simple sequence repeats (SSR) and Diversity Array Technology® (DArT) anchor markers (common across populations). Interpolation of unique markers from 14 maps allowed us to position a total of 2,575 markers in a consensus map of 2,463 cM. The T. durum A and B genomes were covered in their near totality based on the reference SSR hexaploid wheat map. The consensus locus order compared to those of the single component maps showed good correspondence, (average Spearman’s rank correlation rho ρ value of 0.96). Differences in marker order and local recombination rate were observed between the durum and hexaploid wheat consensus maps. The consensus map was used to carry out a whole-genome search for genetic differentiation signatures and association to heading date in a panel of 183 accessions adapted to the Mediterranean areas. Linkage disequilibrium was found to decay below the r2 threshold = 0.3 within 2.20 cM, on average. Strong molecular differentiations among sub-populations were mapped to 87 chromosome regions. A genome-wide association scan for heading date from 27 field trials in the Mediterranean Basin and in Mexico yielded 50 chromosome regions with evidences of association in multiple environments.ConclusionsThe consensus map presented here was used as a reference for genetic diversity and mapping analyses in T. durum, providing nearly complete genome coverage and even marker density. Markers previously mapped in hexaploid wheat constitute a strong link between the two species. The consensus map provides the basis for high-density single nucleotide polymorphic (SNP) marker implementation in durum wheat.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-873) contains supplementary material, which is available to authorized users.
Highlights
Durum wheat (Triticum durum Desf.) is a tetraploid cereal grown in the medium to low-precipitation areas of the Mediterranean Basin, North America and South-West Asia
A core-set of six recombinant inbred lines (RILs)-based component maps was selected to obtain a robust framework map subsequently used for interpolation of unique markers
Overall, results from this study provide an exhaustive consensus framework map of simple sequence repeats (SSR) and Diversity Array Technology® (DArT) markers for the durum wheat genome that was used to assess the genetic structure of cultivated durum wheat germplasm at the level of single chromosome regions and to assess the potential of genome-wide association scan (GWAS) to dissect the genetic basis of heading date
Summary
Durum wheat (Triticum durum Desf.) is a tetraploid cereal grown in the medium to low-precipitation areas of the Mediterranean Basin, North America and South-West Asia. A dense and accurate consensus map specific for T. durum will greatly facilitate genetic mapping, functional genomics and marker-assisted improvement. Cultivated tetraploid wheat (durum wheat, Triticum durum Desf.) is genetically differentiated from hexaploid wheat (Triticum aestivum L.) by as little as ca. Both species derived from domesticated emmer (Triticum dicoccum Schrank) through a rather long human-driven selection process, including distinct and sequential domestication bottlenecks and continuous gene flow from wild emmer In the past two decades, molecular genetics and genomics of durum wheat, including breeding applications such as marker-assisted selection (MAS), have largely relied on the molecular tools developed for hexaploid wheat [2,3,4,5]. Marker’s polymorphism information content had to be reassessed directly in the durum wheat germplasm [9,10]
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