Physical mapping of QTL associated with agronomic and end-use quality traits in spring wheat under conventional and organic management systems.

KEY MESSAGE Using phenotypic data of four biparental spring wheat populations evaluated at multiple environments under two management systems, we discovered 152 QTL and 22 QTL hotspots, of which two QTL accounted for up to 37% and 58% of the phenotypic variance, consistently detected in all environments, and fell within genomic regions harboring known genes. Identification of the physical positions of quantitative trait loci (QTL) would be highly useful for developing functional markers and comparing QTL results across multiple independent studies. The objectives of the present study were to map and characterize QTL associated with nine agronomic and end-use quality traits (tillering ability, plant height, lodging, grain yield, grain protein content, thousand kernel weight, test weight, sedimentation volume, and falling number) in hard red spring wheat recombinant inbred lines (RILs) using the International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v2.0 physical map. We evaluated a total of 698 RILs from four populations derived from crosses involving seven parents at 3-8 conventionally (high N) and organically (low N) managed field environments. Using the phenotypic data combined across all environments per management, and the physical map between 1058 and 6526 markers per population, we identified 152 QTL associated with the nine traits, of which 29 had moderate and 2 with major effects. Forty-nine of the 152 QTL mapped across 22 QTL hotspot regions with each region coincident to 2-6 traits. Some of the QTL hotspots were physically located close to known genes. QSv.dms-1A and QPht.dms-4B.1 individually explained up to 37% and 58% of the variation in sedimentation volume and plant height, respectively, and had very large LOD scores that varied from 19.0 to 35.7 and from 16.7 to 55.9, respectively. We consistently detected both QTL in the combined and all individual environments, laying solid ground for further characterization and possibly for cloning.