High-Density SNP Mapping and Quantitative Trait Locus Analysis of Agronomic Traits in Common Wheat

High density maps are useful for thorough identification of quantitative trait loci (QTL). The 90,000 single nucleotide polymorphism (SNP) Infinium II iSelect whole-genome array was used to genotype a doubled haploid population of 324 lines derived from a hexaploid wheat (Triticum aestivum L. em Thell.) cross between ‘Carberry’ and ‘AC Cadillac’. After filtering in GenomeStudio, a total of 6,578 high-quality SNPs were identified.  In addition, 567 polymorphic DArT markers were identified, and a genetic map of all markers covering 4,366 cM was generated using MSTMap and JoinMap v4.1.  One hundred lines of the population and parents were phenotyped for seven agronomic traits at two locations near Swift Current and at Saskatoon, Canada over four years 2011 to 2014. Composite interval mapping analysis using QTL Cartographer revealed 10 significant (LOD≥3) QTL for each of test weight, thousand kernel weight, heading date and maturity, 9 QTL for plant height, 8 QTL for shattering, and 5 QTL for lodging tolerance. The QTL individually accounted for 4 to 61% of the phenotypic variation. No QTL were detected on chromosomes 1D, 3B, 4D, and 7B. Chromosomes 2B, 3A, 4A, 4B, 5A, and 7D had several QTL identified in different combinations for heading, maturity, height, shattering, test weight, and thousand kernel weight.