Magnesium is important not only for the growth of rice itself, but also as an essential micronutrient component of half of the world population who are supported by rice. Here, we performed genome-wide association study (GWAS) with high-resolution density SNPs to identify natural allelic variation in Mg²⁺ increase from rice set, which is derived from a total 24,368 rice germplasms. The range of the concentration and distribution of Mg²⁺ in 295 core accessions of brown rice grain were wide, from 18.17mg/L to 57.11mg/L, with mean 39.71mg/L. In particular, GWAS result shows that the high peak found on chromosomes 3 and 11. The new natural variants identified through haplotyping analysis would be useful to develop new rice varieties with improved storage ability of the valuable mineral through the future molecular breeding.

Objective
of this study was to investigate the difference of cadmium (Cd) levels in rice grains from non-polluted fields and to define the gene associated with Cd uptake for producing safety food. Cd was analyzed by Inductively Coupled Plasma Mass Spectrometer (ICP-MS). The average concentration of Cd in rice grains was 0.943 μg/kg and Cd levels ranged from 0.050 to 5.699 μg/kg. Genome-Wide Association study (GWAS) based on phenotype data for Cd levels was performed. However, results of GWAS were affected by subpopulation structure and caused false positive. Therefore, GWAS for rice ecotypes (temperate Japonica, tropical Japonica, Indica, Aus, Aromatic, and Admixture) was performed to minimize false positive. GWAS results showed that Os01g0611300, Os01g0611900, Os01g0611950, Os01g0612000, Os01g0612200, Os11g0444400, Os11g0444700, Os11g0444800, and Os11g0444900 genes have significant correlation with Cd levels in rice grains. The sequences of these genes were compared to sequence positions of each other gene (haplotype analysis). According to the results of haplotype analysis, Cd levels of non-synonymous group were higher than other groups and sequence of non-synonymous group was similar to that of Indica. These results were corresponding to the previous research result that Cd levels of Indica were higher than Japonica. Therefore, candidate genes detected through GWAS need to be examined by knock-out or cross breeding.