Genome‐Wide Identification of SNP Markers and Favourable Allelic Combinations Associated With Panicle Architecture Traits in a Subset of the 3K Rice Genome Panel ( Oryza sativa L.)

ABSTRACT Rice ( Oryza sativa L.) is one of the most widely consumed cereal crops, serving as a staple food for billions of people worldwide. However, unpredictable climatic fluctuations and the continuous decline in cultivable land pose significant challenges to sustaining stable grain yields. As grain yield is a complex trait with low heritability, indirect selection through highly heritable yield‐component traits, particularly panicle architecture, offers a promising strategy to enhance rice productivity and contribute to global food security. In this study, 300 germplasm accessions selected from the 3K Rice Genome Panel were evaluated during Kharif 2023 for panicle length, panicle weight and number of grains per panicle using an alpha‐lattice design at Mandya and Gangavathi, Karnataka, India. Analysis of variance revealed substantial phenotypic variability for all evaluated traits. Phenotypic data integrated with genotypic information were subjected to genome‐wide association studies to identify genomic regions associated with panicle architecture traits. A total of 41 and 39 marker‐trait associations (MTAs) were identified using the FarmCPU and BLINK models, respectively. Nine MTAs were consistently detected across both models, three of which co‐localised with previously reported genes or QTL regions. Notably, 38 and 36 MTAs identified through FarmCPU and BLINK, respectively, represent potentially novel associations, highlighting key genomic regions for future validation and candidate‐gene discovery. Haplotype analysis of candidate genes revealed favourable allelic combinations associated with increased panicle length ( OsLP1 and OsGRRP ) and higher grain number per panicle ( Gn1a ). Furthermore, the significant SNPs identified in this study can be converted into breeder‐friendly KASP or CAPS markers following validation to facilitate marker‐assisted selection. Among the evaluated accessions, IRGC 647 (6.23 t/ha), IRGC 993 (6.13 t/ha) and IRGC 952 (6.02 t/ha) possessed putative favourable haplotypes across candidate genes for panicle architecture, representing valuable candidate donor lines for future functional validation and climate‐resilient rice breeding programmes.