Norton Gareth J, Douglas Alex, Lahner Brett, Yakubova Elena, Guerinot Mary Lou, Pinson Shannon R M, Tarpley Lee, Eizenga Georgia C, McGrath Steve P, Zhao Fang-Jie, Islam M Rafiqul, Islam Shofiqul, Duan Guilan, Zhu Yongguan, Salt David E, Meharg Andrew A, Price Adam H
Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom.
Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, United States of America.
PLoS One. 2014 Feb 25;9(2):e89685. doi: 10.1371/journal.pone.0089685. eCollection 2014.
The mineral concentrations in cereals are important for human health, especially for individuals who consume a cereal subsistence diet. A number of elements, such as zinc, are required within the diet, while some elements are toxic to humans, for example arsenic. In this study we carry out genome-wide association (GWA) mapping of grain concentrations of arsenic, copper, molybdenum and zinc in brown rice using an established rice diversity panel of ∼ 300 accessions and 36.9 k single nucleotide polymorphisms (SNPs). The study was performed across five environments: one field site in Bangladesh, one in China and two in the US, with one of the US sites repeated over two years. GWA mapping on the whole dataset and on separate subpopulations of rice revealed a large number of loci significantly associated with variation in grain arsenic, copper, molybdenum and zinc. Seventeen of these loci were detected in data obtained from grain cultivated in more than one field location, and six co-localise with previously identified quantitative trait loci. Additionally, a number of candidate genes for the uptake or transport of these elements were located near significantly associated SNPs (within 200 kb, the estimated global linkage disequilibrium previously employed in this rice panel). This analysis highlights a number of genomic regions and candidate genes for further analysis as well as the challenges faced when mapping environmentally-variable traits in a highly genetically structured diversity panel.
谷物中的矿物质浓度对人体健康至关重要，对于以谷物为主食的人群尤为如此。饮食中需要多种元素，如锌，而有些元素对人体有毒，例如砷。在本研究中，我们利用一个由约300份材料和36900个单核苷酸多态性（SNP）组成的既定水稻多样性群体，对糙米中砷、铜、钼和锌的籽粒浓度进行全基因组关联（GWA）定位。该研究在五种环境中进行：孟加拉国的一个田间地点、中国的一个田间地点和美国的两个田间地点，其中美国的一个地点重复了两年的数据。对整个数据集以及水稻不同亚群进行的GWA定位揭示了大量与籽粒中砷、铜、钼和锌含量变异显著相关的基因座。在多个田间地点种植的籽粒数据中检测到了其中17个基因座，并且有6个与先前鉴定的数量性状基因座共定位。此外，许多负责这些元素吸收或转运的候选基因位于显著相关的SNP附近（在200 kb范围内，这是此前在该水稻群体中使用的估计全局连锁不平衡范围）。该分析突出了一些需要进一步分析的基因组区域和候选基因，以及在高度结构化的遗传多样性群体中定位环境可变性状时所面临的挑战。
