Genomewide Association Study (GWAS) for agronomic traits in Pakistani rice germplasm using 10K SNP data

Abstract

Muhammad Jamil, Muhammad. Ashfaq*, Qurban Ali, Muhammad Ali, Adnan Shakir

Rice (Oryza sativa L.) is a critical global staple, essential for food security, especially in Asia. With increasing population pressure and environmental constraints, enhancing yield and agronomic performance through advanced breeding strategies is imperative. This study aimed to assess genetic diversity, identify genomic regions associated with yield-related traits in rice germplasm to facilitate marker-assisted selection and hybrid breeding. A panel of 101 diverse rice genotypes was evaluated over two growing seasons for 11 morphological and yield-related traits, including Association mapping using 10K SNP array identified 129 Marker-Trait Associations (MTAs) across the rice genome, with Phenotypic Variance Explained (PVE) ranging from 6.08% to 27.15%. Several pleiotropic loci influencing multiple traits were detected, such as RM5951 on chromosome 4 linked to plant height, 1000-grain weight, tillers per plant, yield per hectare, and seed setting percentage. These findings provide a foundation for developing high-yielding, climate-resilient rice varieties to meet future food demands. Future work should expand the germplasm base, integrate multi-omics approaches, and promote collaborative efforts for the rapid development and dissemination of improved rice cultivars.