Development of High-Density Linkage Map and QTL Mapping For Agronomic Traits in Bread Wheat Evaluated Across Multiple Rainfed Environments

The SNPs generated through genotyping-by-sequencing (GBS) can be used to develop high-density linkage maps for precision QTL mapping. The present study was undertaken to (1) determine the genetic variability in recombinant inbred line (RIL) population derived from the cross between ‘Harry’ (drought tolerant) and ‘Wesley’ (drought susceptible) winter wheat (Triticum aestivum L.), (2) develop high-density linkage map based on GBS derived SNPs, (3) validate the quality of linkage map, (4) and perform the genome-wide QTL mapping of agronomic traits evaluated across multiple rainfed environments. High levels of variation and transgressive segregants were observed among RILs. A high-density linkage map was constructed containing 3,641 markers distributed on 21 chromosomes and spanned 1,959 cM. The map showed strong co-linearity with POPSEQ-based on the high-density linkage map. The accuracy of the linkage map for QTL mapping was confirmed by co-localizing the genomic regions for two highly heritable traits: chaff color and leaf cuticular wax. Genome-wide mapping identified 89 additive effect QTL for all the traits across all environments. Major effect and stable QTL were identified for a flowering date, flag leaf length, flag leaf width, grain yield and plant height. Co-located QTLs were evident for all traits, and one region on chromosome 6B harbored QTL for grain yield and yield component traits. QTL expression was highly variable across the environments, and strong QTL x environment interaction was observed for grain yield, flag leaf area and less so for plant height and thousand kernel weight. Digenetic interactions were notable but highly variable across the environments and explained less phenotypic variance than main effect QTLs. The major QTLs identified may provide a foundation for future studies to fine map and identify key genes underlying these QTLs and to introgress these QTLs to fine tune plant height, adaptation and grain yield under rainfed environments in Great Plains.