title: 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.
authors.affiliation: Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom.
authors.forename: Gareth J
authors.initials: GJ
authors.lastname: Norton
authors.affiliation: Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom.
authors.forename: Alex
authors.initials: A
authors.lastname: Douglas
authors.affiliation: Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, United States of America.
authors.forename: Brett
authors.initials: B
authors.lastname: Lahner
authors.affiliation: Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, United States of America.
authors.forename: Elena
authors.initials: E
authors.lastname: Yakubova
authors.affiliation: Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, United States of America.
authors.forename: Mary Lou
authors.initials: ML
authors.lastname: Guerinot
authors.affiliation: USDA ARS, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas, United States of America.
authors.forename: Shannon R M
authors.initials: SR
authors.lastname: Pinson
authors.affiliation: Texas A&M University System, Texas A&M AgriLife Research, Beaumont, Texas, United States of America.
authors.forename: Lee
authors.initials: L
authors.lastname: Tarpley
authors.affiliation: USDA ARS, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas, United States of America.
authors.forename: Georgia C
authors.initials: GC
authors.lastname: Eizenga
authors.affiliation: Rothamsted Research, Harpenden, Hertfordshire, United Kingdom.
authors.forename: Steve P
authors.initials: SP
authors.lastname: McGrath
authors.affiliation: Rothamsted Research, Harpenden, Hertfordshire, United Kingdom ; College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China.
authors.forename: Fang-Jie
authors.initials: FJ
authors.lastname: Zhao
authors.affiliation: Department of Soil Science, Bangladesh Agricultural University, Mymensingh, Bangladesh.
authors.forename: M Rafiqul
authors.initials: MR
authors.lastname: Islam
authors.affiliation: Department of Soil Science, Bangladesh Agricultural University, Mymensingh, Bangladesh.
authors.forename: Shofiqul
authors.initials: S
authors.lastname: Islam
authors.affiliation: Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, China.
authors.forename: Guilan
authors.initials: G
authors.lastname: Duan
authors.affiliation: Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, China.
authors.forename: Yongguan
authors.initials: Y
authors.lastname: Zhu
authors.affiliation: Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom.
authors.forename: David E
authors.initials: DE
authors.lastname: Salt
authors.affiliation: Institute for Global Food Security, Queen's University Belfast, David Keir Building, Belfast, United Kingdom.
authors.forename: Andrew A
authors.initials: AA
authors.lastname: Meharg
authors.affiliation: Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom.
authors.forename: Adam H
authors.initials: AH
authors.lastname: Price
mesh_terms: D027321:Anion Transport Proteins / Q000235:genetics; D001151:Arsenic; D001459:Bangladesh; D027682:Cation Transport Proteins / Q000235:genetics; D002681:China; D003300:Copper; D004777:Environment; D055106:Genome-Wide Association Study; D008982:Molybdenum; D012275:Oryza / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D014481:United States; D015032:Zinc
chemical_list: D027321:Anion Transport Proteins; D027682:Cation Transport Proteins; D003300:Copper; D008982:Molybdenum; D015032:Zinc; D001151:Arsenic