Joint linkage and association analysis identifies genomic regions and candidate genes for yield-related traits in wheat

Twenty-six QTLs associated with yield-related traits in wheat were identified through joint linkage and association analysis, with TraesCS5A03G0002500 being selected as a candidate gene for QGl.caas-5A.1. As a major staple crop worldwide, continuously increasing wheat yield is crucial for ensuring food security. Wheat yield is influenced by multiple traits, and elucidating the genetic basis of yield-related traits lays a foundation for future gene cloning and molecular mechanism studies. In this study, a recombinant inbred line (RIL) population derived from 292 lines of Hengguan 35/Zhoumai 18 was genotyped with the Affymetrix wheat 660 K SNP array. Combined with the phenotype of the RIL population in 13 environments, linkage analysis of six yield-related traits including plant height, grain number per spike, thousand-grain weight, grain length, grain width, and grain thickness was conducted. A total of 262 quantitative trait locus (QTLs) (logarithm of odds [LOD] > 3) were identified across 21 chromosomes, in which 50 QTLs were repeatedly detected in more than three environments. Numerous QTLs harbored cloned genes and overlapped with those reported in previous studies. Subsequently, joint analysis of genome-wide association study (GWAS) data from the advanced backcross-nested association mapping plus inter-crossed (AB-NAMIC) population and QTLs identified in the RIL population revealed 26 overlapping genomic regions. Notably, the QGl.caas-5A.1 associated with grain length on chromosome 5A was detected in both the RIL and AB-NAMIC populations, and TraesCS5A03G0002500 was selected as a candidate gene. A kompetitive allele-specific PCR (KASP) marker based on a variant [A/G] in TraesCS5A03G0002500 was developed and validated in a natural population containing 350 accessions. Taken together, these results provide valuable information for fine mapping and cloning of yield-related wheat genes in the future.