Two putatively novel loci associated with spike length and their breeding potential in Chinese endemic wheat

Spike length (SL) is a key determinant of wheat spike architecture and yield potential. In this study, SL was evaluated across multiple environments in a panel of 182 Chinese endemic wheat accessions. Substantial phenotypic variation and high broad-sense heritability were observed, indicating strong genetic control. Genome-wide association study (GWAS) was performed using 38,490 high-quality SNPs under a mixed linear model incorporating population structure and kinship (Q + K). Four loci significantly associated with SL were identified on chromosomes 2B, 3B, 4A, and 7A, explaining 2.53-8.06% of the phenotypic variation. Two loci on chromosomes 4A and 7A co-localized with previously reported SL QTL within the linkage disequilibrium decay distance, confirming their genetic stability. In contrast, loci on chromosomes 2B (QSL.sau.2B) and 3B (QSL.sau.3B) reside in genomic regions not previously associated with SL, suggesting potentially novel genetic factors. Allelic effect analysis based on BLUP values revealed pleiotropic effects of SL-associated loci on spike density, spikelet number, plant height, and anthesis date. Notably, QSL.sau.3B was consistently associated with SL across environments and further supported through effect analysis in an additional wheat population of 220 accessions, confirming its stability and breeding relevance. These results advance understanding of the genetic architecture of SL and provide valuable resources for wheat improvement.