Genome-wide association study of stable loci for grain yield and related traits across contrasting drought- and heat-prone environments in spring bread wheat (Triticum aestivum L.)

Abstract

Drought and heat stress constrain bread wheat (Triticum aestivum L.) production in West Asia, North Africa, and sub-Saharan Africa. Identifying stable genetic loci across contrasting environments is essential for improving wheat adaptation to stress-prone conditions. Here, a genome-wide association study was conducted using 196 elite ICARDA spring bread wheat genotypes evaluated for days to heading, days to maturity, plant height, thousand-kernel weight, and grain yield across six environments in Morocco, Sudan, Egypt, and Lebanon during 2019–2020. Genotyping with the Illumina iSelect 25 K wheat single-nucleotide polymorphism array yielded 14,999 high-quality markers. Associations were analyzed using BLINK, FarmCPU, MLMM, and mixed linear models, accounting for population structure and genetic relatedness. Grain yield varied substantially among environments (2.16–6.45 t ha−1) and showed comparatively low heritability, whereas phenological traits, plant height, and thousand-kernel weight generally showed moderate to high heritability. Across environments and models, 220 significant marker–trait associations were identified, including 74 loci associated with multiple traits. Several loci were consistently detected across environments and/or models, including Excalibur_c30151_528 (7D), BS00094057_51 (3 A), GENE-1785_118 (3B), and wsnp_Ra_c14920_23225219 (4D). Several stable associations co-localized with putative candidate genes with annotated functions related to calcium signaling, protein kinase-mediated signaling, redox regulation, and the shikimate pathway. These findings identify genomic regions for further validation and breeding evaluation and highlight the importance of multi-environment testing for identifying loci relevant to stress-prone conditions.