Genetic identification and candidate gene analysis for loci of spike density in wheat

GWAS of Chinese endemic wheat identifies two stable and potentially novel spike density loci as a resource for future breeding. Spike density (SD) is an important component of spike architecture that influences grain number per spike and ultimately wheat yield potential. Chinese endemic wheat germplasm represents a valuable but underexplored reservoir of genetic diversity for spike-related traits. In this study, a genome-wide association study (GWAS) was conducted using 182 Chinese endemic wheat accessions evaluated for SD across four environments. Substantial phenotypic variation was detected, and SD exhibited high broad-sense heritability (96.81%), indicating a strong genetic contribution to trait variation. Using 38,490 single-nucleotide polymorphisms (SNPs) from the wheat 55 K SNP array, two stable quantitative trait loci (QTL) associated with SD were identified on chromosomes 2BS and 7AL. The most prominent locus, QSD.sau.2B, was localized on chromosome 2B, with the lead marker AX-111715789 explaining up to 7.97% of the phenotypic variance. Comparative analysis with previously reported loci suggested that QSD.sau.2B and QSD.sau.7A may represent potentially novel genomic regions associated with SD. The identified QTL also exhibited pleiotropic effects on other spike-related traits, highlighting their potential importance in wheat spike architecture. These results provide new insights into the genetic architecture of SD in Chinese endemic wheat and identify loci that may be useful for further functional characterization. The detected QTL represent potential targets for marker-assisted selection aimed at improving spike architecture and yield-related traits in wheat breeding programs.