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

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 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.

Figure 1. GWA mapping of grain arsenic concentration at the five field sites across the 12 rice chromosomes.

Data points represent SNPs significantly associated (p<0.0001) with the trait and which have a MAF >5%. Significant SNPs from different experiments are displayed with different coloured symbols: 2006 Arkansas are red, 2007 Arkansas are black, 2009 Texas are blue, Faridpur are green, and Qiyang are grey. Analyses of the combined subpopulation groups and separate subpopulations are represented by different symbols: combined analysis = X, aus = circle, indica = square, tropical japonica = triangle, temperate japonica = inverted triangle. Yellow highlighted bars indicate regions of mapped QTLs for grain arsenic concentration (21, 22). Dotted lines indicate chromosome ends.

Figure 2. GWA mapping of copper concentration at the five field sites across the 12 rice chromosomes.

Data points represent SNPs significantly associated (p<0.0001) with the trait and which have a MAF >5%. Significant SNPs from different experiments are displayed with different coloured symbols: 2006 Arkansas are red, 2007 Arkansas are black, 2009 Texas are blue, Faridpur are green, and Qiyang are grey. Analyses of the combined subpopulation groups and separate subpopulations are represented by different symbols: combined analysis = X, aus = circle, indica = square, tropical japonica = triangle, temperate japonica = inverted triangle. Yellow highlighted bars indicate regions of mapped QTLs for grain copper concentration (17, 21, 22). Dotted lines indicate chromosome ends.

Figure 3. GWA mapping of molybdenum concentration at the five field sites across the 12 rice chromosomes.

Data points represent SNPs significantly associated (p<0.0001) with the trait and which have a MAF >5%. Significant SNPs from different experiments are displayed with different coloured symbols: 2006 Arkansas are red, 2007 Arkansas are black, 2009 Texas are blue, Faridpur are green, and Qiyang are grey. Analyses of the combined subpopulation groups and separate subpopulations are represented by different symbols: combined analysi = Xs, aus = circle, indica = square, tropical japonica = triangle, temperate japonica = inverted triangle. Yellow highlighted bars indicate regions of mapped QTLs for grain molybdenum concentration (17, 21, 22). Dotted lines indicate chromosome ends.

Figure 4. GWA mapping of zinc concentration at the five field sites across the 12 rice chromosomes.

Data points represent SNPs significantly associated (p<0.0001) with the trait and which have a MAF >5%. Significant SNPs from different experiments are displayed with different coloured symbols: 2006 Arkansas are red, 2007 Arkansas are black, 2009 Texas are blue, Faridpur are green, and Qiyang are grey. Analyses of the combined subpopulation groups and separate subpopulations are represented by different symbols: combined analysis = X, aus = circle, indica = square, tropical japonica = triangle, temperate japonica = inverted triangle. Yellow highlighted bars indicate regions of mapped QTLs for grain zinc concentration (15–17, 20, 21, 22). Dotted lines indicate chromosome ends.