GWAS analysis for mapping of genomic regions associated with higher grain zinc with higher yield in rice

Rice, being a major staple crop globally, holds significant potential in addressing the malnutrition challenge by sustainably increasing the Zn content in its grains through biofortification. To achieve this, it is essential to comprehend the genetic basis of Zn accumulation in rice grains. This study conducted Genome-Wide Association Studies (GWAS) analysis on a subset of 340 lines from the 3K Rice Genome panel (3K RG). The subset was evaluated at two locations, IRRI South Asia hub, Hyderabad and Banaras Hindu University, Varanasi and were analysed with 0.5 million single nucleotide polymorphisms (SNPs). The findings of the study revealed the identification of 11 MTAs that span across chromosomes 2, 3, 4, 5, 11, and 12. These MTAs showed a wide range of PVE values, ranging from 0.55 to 10.9. These MTAs covered a total of 18 candidate genes that are potentially involved in Zn accumulation in grain Zn. Haplo-pheno analysis of the 18 genes identified superior haplotypes for three specific genes, namely LOC_Os03g63500, LOC_Os05g04150, and LOC_Os03g63510 found in four accessions in 3K subset, IRGC 16273-2, IRGC 29089-1, IRGC 34831-1 and, IRGC 66518-1. These accessions were chosen as potential donors with high grain Zn content with higher yield that could prove to be valuable resources in rice breeding programs aimed at enhancing Zn content in grains. Overall, this study significantly contributes to our understanding of superior haplotypes associated with higher grain Zn content in rice. By improving the nutritional quality of rice, this research contributes to the broader goal of combating malnutrition and promoting food security worldwide.