Genome wide dissection and haplotype analysis to identify candidate loci for harvest index under spot blotch in bread wheat

Harvest index (HI), a key yield-related trait in wheat, is influenced by genetic, phenological, environmental, and stress factors. In the Indo-Gangetic Plains (IGP) of India, spot blotch (SB) poses a major biotic stress, reducing grain yield by affecting photosynthesis and HI. Identifying stable wheat genotypes and genomic regions controlling these traits are essential for developing resilient wheat for the IGP. We evaluated 1500 elite wheat lines in four environments at IGP, including SB and disease-free (DF) conditions. On average, in the SB condition HI (%) reduced by 4.3% compared to its DF environment. Genome-wide association studies identified important SNPs:1A_494392059, 1A_495192503, 2A_32931719, 3B_10249157, 3B_10644041, 3B_6127880, 5B_538548049, 6A_96651968, 7A_49592941 and 7D_326728664, and a favourable haplotype TTGTCG (n = 303), which showed higher average HI (39.75%) under SB conditions. Additionally, most of candidate genes associated with the identified SNPs were involved in senescence and disease resistance. Stability analysis using AMMI and genotype selection index identified a set of genotypes with consistently high and stable HI under both SB and DF conditions. Further, genotypes with favourable alleles at all these identified significant MTAs, and stable genotypes identified for HI shared common genetic contributors, including the SR50 gene and prominent wheat varieties such as KACHU, PASTOR, and PRL. These genetic backgrounds play a pivotal role in conferring both disease resistance and yield stability, highlighting their importance in wheat breeding programs for IGP. Further, Genomic predictions using genome-wide markers demonstrated moderate predictive accuracy, ranging from 0.22 to 0.39, with higher accuracy observed under SB conditions. The stable genotypes and genomic regions identified in this study could serve as important resources and knowledge for developing resilient genotypes adapted to the IGP.