A dense durum wheat x T-dicoccum linkage map based on SNP markers for the study of seed morphology

Durum wheat (Triticum turgidum L. var. durum) is a very important crop in the Mediterranean basin. Intense breeding activities are carried out to improve its productivity, quality, and resistance, and new genomic tools are essential to speed up the breeding progress. A segregating population of 136 recombinant inbred lines derived from a cross between the durum wheat cv. Simeto and the T. dicoccum accession Molise Colli was genotyped with the wheat 90k iSelect Infinium SNP assay. A linkage map was developed with 9,040 markers. Forty-five linkage groups were obtained, which covered all of the chromosomes. The map covered 2,879.3 cM, with a mean length of 205.6 cM per chromosome. The number of markers for each chromosome was from 418 (4B) to 978 (2B), with an average of 645.7. The parents of the genetic map differ according to several features, from traits linked to spike and kernel morphology to grain yield. Quantitative trait loci (QTL) analysis was performed for traits related to kernel morphology and thousand-kernel weight: six QTL were identified on chromosomes 1B, 2B, 3A, 3B, 4B and 7A, and 2 QTL on chromosomes 3B and 4B. Bioinformatic and synteny analyses with rice and Brachypodium genomes were performed based on the SNP sequences, with the identification of a candidate gene corresponding to a kinesin under the QTL located on chromosome 1B. The SNP-based Simeto x Molise Colli linkage map represents a useful tool to dissect out the genetic basis of traits of agronomic relevance for the genetic improvement of durum wheat.