A consensus framework map of durum wheat (Triticum durum Desf.) suitable for linkage disequilibrium analysis and genome-wide association mapping

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.

Maximizing the identification of QTL for pre-harvest sprouting resistance using seed dormancy measures in a white-grained hexaploid wheat population

“…The QPhs.spa-6A QTL mapped on chromosome 6A was revealed by PG from field environments and appears to map at least 30 cM from the QPhs.ccsu-6A.1 reported by Kumar et al (2009) based on the markers position on the consensus map of wheat by Maccaferri et al (2014). Thus, QPhs.spa-6A may be a novel QTL.…”

Dissecting the old Mediterranean durum wheat genetic architecture for phenology, biomass and yield formation by association mapping and QTL meta-analysis

“…Only MQTLs flanked by common markers among the original maps and [36] were projected (S4 File). Based on overlapping MQTL SIs, three MQTLs were found in common locations with those reported by [25] on chromosomes 2B, 5B and 7B, and 12 were in common with those reported by [24] located on chromosomes 1A, 2A, 3A, 4A, 4B, 5A, 6A and 7A (Fig 1, S3 and S4 Files).…”

“…More recently, the same authors, using more SSR markers (179) in a collection of elite durum wheat accessions from the Mediterranean countries, South-Western USA and Mexico, found 27.8% of the loci in LD at P <0.01 and 15.1% at P <0.001, with a decay of the LD up to 10 cM, suggesting that for an adequate genome coverage, thousands of markers would be needed [6]. In a further study, [36] using the same panel of durum wheat genotypes but including a total of 2575 markers (SSR and DArT), reduced the extent of LD to 0 to 5 cM. In particular, the elite Mediterranean cultivars showed a LD decay within 2.20 cM.…”

A high‐density, SNP‐based consensus map of tetraploid wheat as a bridge to integrate durum and bread wheat genomics and breeding

“…Marker density in the consensus map varied widely along chromosomes, even within intervals of 20 cM or less, likely due to both variation in recombination frequency Saintenac et al, 2011) and/or in genetic diversity (ancient genetic drift and selection sweep effects and/or more recent breederdriven selection). As compared to the hexaploid wheat consensus map and the maps derived from either wild or cultivated emmer (Marone et al, 2012;Maccaferri et al, 2014), at least three large chromosome regions with reduced marker density have been consistently found in chromosomal arms 1AS, 2AS and 3AS of durum wheat across mapping populations and germplasm diversity studies.…”