Genome-wide Association Study on Cadmium Contents of Temperate Japonica Varieties
2016
Lee, S.B., National Institute of Agriculture Science (NAIS), Wanju, Republic of Korea | Kim, K.W., Kongju National University, Yesan, Republic of Korea | Yoon, M.Y., Kongju National University, Yesan, Republic of Korea | Kim, G.J., National Institute of Agriculture Science (NAIS), Wanju, Republic of Korea | Yoo, J.H., National Institute of Agriculture Science (NAIS), Wanju, Republic of Korea | Kim, W.I., National Institute of Agriculture Science (NAIS), Wanju, Republic of Korea | Moon, B.C., National Institute of Agriculture Science (NAIS), Wanju, Republic of Korea | Park, S.W., National Institute of Agriculture Science (NAIS), Wanju, Republic of Korea | Park, Y.J., Kongju National University, Yesan, Republic of Korea
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 ㎍/㎏ and Cd levels ranged from 0.050 to 5.699 ㎍/㎏. 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.
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