Main content area

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

Maccaferri, Marco, Cane, Maria Angela, Sanguineti, Maria C., Salvi, Silvio, Colalongo, Maria C., Massi, Andrea, Clarke, Fran, Knox, Ron, Pozniak, Curtis J., Clarke, John M., Fahima, Tzion, Dubcovsky, Jorge, Xu, Steven, Ammar, Karim, Karsai, Ildiko, Vida, Gyula, Tuberosa, Roberto
BMC Genomics 2014 v.15 no.873 pp. 1-21
Triticum turgidum subsp. durum, biotic stress, chromosome mapping, durum wheat, genetic markers, genetic variation, genome, genomics, heading, hexaploidy, linkage disequilibrium, loci, microsatellite repeats, single nucleotide polymorphism, tetraploidy, Mediterranean region
Genomics applications in durum (Triticum durum Desf.) 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. Here, we reported the construction of a consensus framework map of durum wheat using the genotypic data from 14 mapping populations of tetraploid wheat. In this study, high quality genotypic data from six core recombinant inbred populations were used to obtain a consensus framework map of 598 simple sequence repeats (SSR) and Diversity Array Technology(R) (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' rank correlation r 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. Strong molecular differentiations among sub-populations were mapped to 87 chromosome regions. The 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. The consensus map also provides the basis for high-density single nucleotide polymorphic (SNP) marker implementation in durum wheat.