Genetic Mapping and QTL Analysis for End-use quality in Hard Red Winter Wheat

Molecular tagging of end-use quality traits including rheological properties of wheat is an essential component of wheat breeding and genetic pipeline.  End-use quality of wheat defines the price as well as acceptability of wheat and wheat products. We used 90K SNP array to fingerprint 217 wheat recombinant inbred lines (RILs) from an elite by elite cross, CO960293-2 × TAM 111. The population was evaluated for flour protein content using Near Infrared (NIR) spectroscopy, kernel diameter, kernel weight, test weight, and flour rheology. A linear mixed model for multi-trait quantitative trait loci (QTL) analysis revealed significant QTL on chromosome 1D, 1B, 2B and 5A and 5B, associated with mid-line peak integral (MLPI), mid-line peak time (MLPT), mid-line peak width (MLPW),  hardness index (HI) and protein content (PC). Most traits showed significant QTL × trait and QTL × environment interactions. The maximal R² for MLPW and MLPT in individual environment ranged from 12.6% to 32.8%. Co-localization of MLPI, MLPW and MLPT was observed in all the environments suggesting possible linkage or pleiotropic effects. Markers linked to QTL for end-use quality are potential tools for marker-assisted selection in wheat.