Multi-Environment GWAS Identifies Germplasm and Genomic Resources for Breeding Pre-Harvest Sprouting-Resistant Spring Wheat in Kazakhstan

Breeding spring wheat for stable pre-harvest sprouting (PHS) resistance is constrained by the environmental sensitivity of seed dormancy and the need to maintain agronomic performance. This study integrated multi-environment phenotyping and multi-model GWAS to identify breeding resources in Kazakh spring wheat. A panel of 270 accessions was evaluated during the 2024 and 2025 seasons, representing southeastern and northern Kazakhstan. Twelve traits for adaptation and yield, including PHS resistance and germination index (GI), were assessed. Genotyping with the Axiom® Wheat Breeder’s Genotyping Array yielded 9212 polymorphic SNPs after quality filtering. Best linear unbiased predictions (BLUPs) and five GWAS models were used to improve association reliability. Region and year significantly affected PHS resistance and the GI, emphasizing the need for multi-environment selection. Weak phenotypic correlations between PHS resistance and yield-related traits suggest that improving PHS resistance may be possible without substantial adverse effects on productivity; however, this relationship requires further validation across additional environments and genetic backgrounds. Seven accessions that combine PHS resistance with moderate seed dormancy were identified as promising pre-breeding material. In total, 5256 significant quantitative trait nucleotides (QTNs) were identified and grouped into 2297 QTL regions, of which 102 were considered higher-confidence loci supported by at least two GWAS models and Bonferroni correction. QPHS.ta.ipbb-2B.1 was supported by all five models, but was specific to the Almaty region, whereas QGI.ta.ipbb-4B.2 was supported by all models and across-environment BLUPs. Putative positional candidate genes had predicted functions in gibberellin signaling, sugar transport, carbohydrate metabolism, and cell wall remodeling. These germplasm and genomic resources provide priorities for marker validation and breeding spring wheat cultivars adapted to variable environments with improved PHS resistance.