Genome wide association mapping of grain arsenic, copper, molybdenum and zinc in rice (Oryza sativa L.) grown at four international field sites.
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-wi...
| Main Authors: | , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2014-01-01
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| Series: | PLoS ONE |
| Online Access: | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0089685&type=printable |
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| author | Gareth J Norton Alex Douglas Brett Lahner Elena Yakubova Mary Lou Guerinot Shannon R M Pinson Lee Tarpley Georgia C Eizenga Steve P McGrath Fang-Jie Zhao M Rafiqul Islam Shofiqul Islam Guilan Duan Yongguan Zhu David E Salt Andrew A Meharg Adam H Price |
| author_facet | Gareth J Norton Alex Douglas Brett Lahner Elena Yakubova Mary Lou Guerinot Shannon R M Pinson Lee Tarpley Georgia C Eizenga Steve P McGrath Fang-Jie Zhao M Rafiqul Islam Shofiqul Islam Guilan Duan Yongguan Zhu David E Salt Andrew A Meharg Adam H Price |
| author_sort | Gareth J Norton |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-11T11:56:56Z |
| format | Article |
| id | doaj.art-f8942c5373f046dd954204b520965d15 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2025-03-14T16:44:32Z |
| publishDate | 2014-01-01 |
| publisher | Public Library of Science (PLoS) |
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| series | PLoS ONE |
| spelling | doaj.art-f8942c5373f046dd954204b520965d152025-02-21T05:37:54ZengPublic Library of Science (PLoS)PLoS ONE1932-62032014-01-0192e8968510.1371/journal.pone.0089685Genome wide association mapping of grain arsenic, copper, molybdenum and zinc in rice (Oryza sativa L.) grown at four international field sites.Gareth J NortonAlex DouglasBrett LahnerElena YakubovaMary Lou GuerinotShannon R M PinsonLee TarpleyGeorgia C EizengaSteve P McGrathFang-Jie ZhaoM Rafiqul IslamShofiqul IslamGuilan DuanYongguan ZhuDavid E SaltAndrew A MehargAdam H PriceThe 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.https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0089685&type=printable |
| spellingShingle | Gareth J Norton Alex Douglas Brett Lahner Elena Yakubova Mary Lou Guerinot Shannon R M Pinson Lee Tarpley Georgia C Eizenga Steve P McGrath Fang-Jie Zhao M Rafiqul Islam Shofiqul Islam Guilan Duan Yongguan Zhu David E Salt Andrew A Meharg Adam H Price Genome wide association mapping of grain arsenic, copper, molybdenum and zinc in rice (Oryza sativa L.) grown at four international field sites. PLoS ONE |
| title | Genome wide association mapping of grain arsenic, copper, molybdenum and zinc in rice (Oryza sativa L.) grown at four international field sites. |
| title_full | Genome wide association mapping of grain arsenic, copper, molybdenum and zinc in rice (Oryza sativa L.) grown at four international field sites. |
| title_fullStr | Genome wide association mapping of grain arsenic, copper, molybdenum and zinc in rice (Oryza sativa L.) grown at four international field sites. |
| title_full_unstemmed | Genome wide association mapping of grain arsenic, copper, molybdenum and zinc in rice (Oryza sativa L.) grown at four international field sites. |
| title_short | Genome wide association mapping of grain arsenic, copper, molybdenum and zinc in rice (Oryza sativa L.) grown at four international field sites. |
| title_sort | genome wide association mapping of grain arsenic copper molybdenum and zinc in rice oryza sativa l grown at four international field sites |
| url | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0089685&type=printable |
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