Development of High Density Linkage Map and Genome-Wide QTL Mapping for Grain Yield in Wheat Cross Under Multiple Rainfed Environments.

High density linkage maps may be useful to genetically dissect and find the key genes underlying complex traits like grain yield in wheat. The present study was undertaken to (i) develop high density linkage map in 204 recombinant inbred lines (RILs) of wheat derived from contrasting parents Harry and Wesley, (ii) determine the accuracy and reliability of the newly constructed map with known genes of chaff color and leaf wax/ glaucousness, and (iii) identify QTLs, digenetic interactions and QTL x environment interaction for grain yield under multiple rainfed environments. After imputations and stringent filtering, a high-density linkage map was constructed that contained 2923 markers distributed on 36 linkage groups and spanned 5269.34 cM with an average distance of 1.79 cM between adjacent markers. The high accuracy and reliability of this map was illustrated by finding and co-localizing the genes for chaff color and leaf wax/glaucousness to previously mapped genomic regions. QTL mapping for grain yield revealed in total 14 QTLs across all locations on linkage groups 2D, 3A, 4A, 4B, 5B, 6B, 6D and 7A. The phenotypic variance explained by these QTLs ranged from 3.9 to 19.47 %. QTL qyld.hw.6B.2 was stable and detected in 3 locations followed QTL qyld.hw.6B.1 detected in two locations. Favorable alleles for grain yield were contributed by both the parents. Digenetic interactions between QTLs was evident, however, none of the interactions were stable across locations. Six QTLs revealed significant interactions with environment and accounted 1.94 to 18.46 % of total phenotypic variation.