Genome-wide association mapping reveals SNP–trait associations for agronomic traits in advanced rice breeding lines

Abstract

Rice is an important staple crop, yet increasing climatic variability and abiotic stresses threaten yield stability and food security. Accelerating the genetic dissection of yield-related traits is therefore critical for developing climate-resilient rice cultivars. In this study, we characterized the genetic diversity and genomic architecture of agronomically important traits in 188 advanced breeding lines (ABLs) developed at IGKV, India. We genotyped the ABLs using genotyping-bysequencing, and identified 87 high-quality, trait-informative single-nucleotide polymorphism markers distributed across all 12 rice chromosomes. STRUCTURE analysis revealed five genetically differentiated subgroups (SG1–SG5), comprising 59, 31, 36, 44, and 18 accessions, respectively, indicating substantial genetic stratification. Eight yield-associated agronomic traits were phenotypically evaluated and subjected them to genome-wide association analysis. In total, 34 marker– trait associations (MTAs) were detected, each explaining 2.00%–11.05% of phenotypic variance, consistent with a polygenic architecture. A notable QTL hotspot on chromosome 6 was identified, representing a promising genomic region for simultaneous improvement of multiple traits. Integrating population structure, genome-wide markers, and phenotypic data provides a robust framework for exploiting favorable alleles in Central Indian rice germplasm. These MTAs and the chromosome 6 hotspot warrant validation and may support marker-assisted, genomic selection, and genomics-assisted breeding for high-yielding, climate resilient rice cultivars.