Genetic basis of rice ionomic variation revealed by Genome-wide association studies

Rice (Oryza sativa) is an important dietary source of both the essential micronutrients and the toxic trace elements to humans. The genetic basis underlying the variations in the mineral composition, the ionome, in rice remains largely unknown. Here, we describe a comprehensive study of the genetic architecture of the variation in rice ionome by performing genome-wide association studies (GWAS) on the concentrations of 17 mineral elements in rice grain from a diverse panel of 529 accessions each genotyped at approximately 6.4 million SNP loci. We identified 72 loci associated with natural ionomic variations, 32 of which are common across locations and 40 are common within location. We have identified candidate genes for 42 loci and provide evidence for the causal nature of three genes, Os-HKT1;5 for sodium, Os-MOT1;1 for molybdenum and Ghd7 for nitrogen. Comparison of rice GWAS data with Arabidopsis thaliana also identifies the well-known as well as new candidates with potential for further characterization. Our study provides new insights into the genetic basis of ionomic variations in rice, and serves as an important foundation for further studies on the genetic and molecular mechanisms controlling the rice ionome.