Genome wide association mapping of grain arsenic, copper, molybdenum, and zinc in rice (Oryza sativa L.) grown at four international field sites

Authors: NORTON, GARETH - University Of Aberdeen; DOUGLAS, ALEX - University Of Aberdeen; LAHNER, BRETT - Purdue University; YAKUBOVA, ELENA - Purdue University; GUERINOT, MARY LOU - Dartmouth College; Pinson, Shannon; TARPLEY, LEE - Texas Agrilife Research; Eizenga, Georgia; MCGRATH, STEVE - Rothamsted Research; ZHAO, FANG-JIE - Rothamsted Research; ISLAM, M. RAFIQUL - Bangladesh Agricultural University; ISLAM, SHOFIQUL - Bangladesh Agricultural University; DUAN, GUILAN - Chinese Academy Of Sciences; ZHU, YONGGUAN - Chinese Academy Of Sciences; SALT, DAVID - University Of Aberdeen; MEHARG, ANDREW - Queen'S University - Ireland; PRICE, ADAM - University Of Aberdeen

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/27/2014
Publication Date: 2/25/2014
Citation: Norton, G.J., Douglas, A., Lahner, B., Yakubova, E., Guerinot, M., Pinson, S.R., Tarpley, L., Eizenga, G.C., Mcgrath, S.P., Zhao, F., Islam, M., Islam, S., Duan, G., Zhu, Y., Salt, D.E., Meharg, A.A., Price, A.H. 2014. Genome wide association mapping of grain arsenic, copper, molybdenum, and zinc in rice (Oryza sativa L.) grown at four international field sites. PLoS One. 9(2):e89685.

Interpretive Summary: For people who rely on rice as their dietary staple, a large proportion of their micronutrients come from rice grains. Some of these nutrients are essential (e.g., zinc) while others are unwanted (e.g., arsenic). The identification of genes controlling how much of an element is taken up by the plant and ultimately accumulated in the grain is an important first step toward breeding new rice varieties with enhanced grain nutritional value. Because of genetic similarity between rice and other cereal crops, knowledge on genes that enhance the nutritional value of rice can also be used to enhance the nutritional value of other grains, such as wheat, oats, and barley. We identified chromosomal regions containing genes affecting rice grain element concentrations by comparing grains from a diverse set of 300 rice varieties originally adapted to production conditions in a wide range of geographic regions. The 300 varieties were first grown side-by-side in four diverse soils and field environments, namely Texas and Arkansas in the USA, and one field site each in China and Bangladesh. Since soil chemistry has a significant effect on plant mineral uptake rates, studying the mapping population under a wide range of environments allowed us to determine which genes affected grain element concentrations in multiple as opposed to single environments or field conditions. This study identified a number of interesting genomic regions and candidate genes for further research, such as a location on chromosome 2 whose genomic sequence shows similarity with genes known to code for metal transporters in animals as well as plants.

Technical Abstract: 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 carried 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 approx. 300 accessions and 36.9k SNP. The study was performed across five dissimilar environments being field sites in Bangladesh, China, and two in the USA, with one of the USA sites repeated over two years. GWA mapping on the whole dataset and on separate subpopulations (or ancestral lineages) 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-localize with previously identified quantitative trait loci. Additionally, a number of significantly associated SNPs were located near (within 200 kb) candidate genes for the uptake or transport of these elements. This analysis highlights a number of genomic regions and candidate genes for further analysis, such as a location on chromosome 2 whose genomic sequence shows similarity with genes known to code for metal transporters in animals as well as plants.