Genome wide association study of rice agronomical traits and seed ionome with the NARO Open Rice Collection.
To meet the nutritional needs of the rising human population, genetic variants are necessary for the breeding of new cultivars. Rice (Oryza sativa L.) is a staple food for over half of the world's population. Here, we developed a new rice genetic resource, the NARO Open Rice Collection (NRC) with high-resolution genome data. NRC consists of 623 accessions, and approximately 200 accessions are categorized into three major subgroups, categorized as Indica, Japonica, and Aus. In this study, we performed genome-wide association studies (GWAS) for rice heading date, seed shape, and seed ionome using the NRC. Well-known genes related to heading date and seed shape were detected by GWAS using the NRC accessions. Therefore, we concluded that our new rice collection is suitable for GWAS. In addition, GWAS with each subgroup was advantageous for the detection of particular genes. Finally, we performed GWAS for seed ionome with the aim of improving the nutritional properties of rice, as essential minerals for humans, such as iron (Fe) and zinc (Zn), are not sufficient in rice seeds. Our study revealed that OsATL31, a likely ubiquitin E3 ligase, was involved in the control of Fe and Zn contents in seeds.