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Genome-wide association study to identify candidate loci and genes for Mn toxicity tolerance in rice
Manganese (Mn) is an essential micro-nutrient for plants, but flooded rice fields can accumulate high levels of Mn(2+) leading to Mn toxicity. Here, we present a genome-wide association study (GWAS) to identify candidate loci conferring Mn toxicity tolerance in rice (Oryza sativa L.). A diversity pa...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5806864/ https://www.ncbi.nlm.nih.gov/pubmed/29425206 http://dx.doi.org/10.1371/journal.pone.0192116 |
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author | Shrestha, Asis Dziwornu, Ambrose Kwaku Ueda, Yoshiaki Wu, Lin-Bo Mathew, Boby Frei, Michael |
author_facet | Shrestha, Asis Dziwornu, Ambrose Kwaku Ueda, Yoshiaki Wu, Lin-Bo Mathew, Boby Frei, Michael |
author_sort | Shrestha, Asis |
collection | PubMed |
description | Manganese (Mn) is an essential micro-nutrient for plants, but flooded rice fields can accumulate high levels of Mn(2+) leading to Mn toxicity. Here, we present a genome-wide association study (GWAS) to identify candidate loci conferring Mn toxicity tolerance in rice (Oryza sativa L.). A diversity panel of 288 genotypes was grown in hydroponic solutions in a greenhouse under optimal and toxic Mn concentrations. We applied a Mn toxicity treatment (5 ppm Mn(2+), 3 weeks) at twelve days after transplanting. Mn toxicity caused moderate damage in rice in terms of biomass loss and symptom formation despite extremely high shoot Mn concentrations ranging from 2.4 to 17.4 mg g(-1). The tropical japonica subpopulation was more sensitive to Mn toxicity than other subpopulations. Leaf damage symptoms were significantly correlated with Mn uptake into shoots. Association mapping was conducted for seven traits using 416741 single nucleotide polymorphism (SNP) markers using a mixed linear model, and detected six significant associations for the traits shoot manganese concentration and relative shoot length. Candidate regions contained genes coding for a heavy metal transporter, peroxidase precursor and Mn(2+) ion binding proteins. The significant marker SNP-2.22465867 caused an amino acid change in a gene (LOC_Os02g37170) with unknown function. This study demonstrated significant natural variation in rice for Mn toxicity tolerance and the possibility of using GWAS to unravel genetic factors responsible for such complex traits. |
format | Online Article Text |
id | pubmed-5806864 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-58068642018-02-23 Genome-wide association study to identify candidate loci and genes for Mn toxicity tolerance in rice Shrestha, Asis Dziwornu, Ambrose Kwaku Ueda, Yoshiaki Wu, Lin-Bo Mathew, Boby Frei, Michael PLoS One Research Article Manganese (Mn) is an essential micro-nutrient for plants, but flooded rice fields can accumulate high levels of Mn(2+) leading to Mn toxicity. Here, we present a genome-wide association study (GWAS) to identify candidate loci conferring Mn toxicity tolerance in rice (Oryza sativa L.). A diversity panel of 288 genotypes was grown in hydroponic solutions in a greenhouse under optimal and toxic Mn concentrations. We applied a Mn toxicity treatment (5 ppm Mn(2+), 3 weeks) at twelve days after transplanting. Mn toxicity caused moderate damage in rice in terms of biomass loss and symptom formation despite extremely high shoot Mn concentrations ranging from 2.4 to 17.4 mg g(-1). The tropical japonica subpopulation was more sensitive to Mn toxicity than other subpopulations. Leaf damage symptoms were significantly correlated with Mn uptake into shoots. Association mapping was conducted for seven traits using 416741 single nucleotide polymorphism (SNP) markers using a mixed linear model, and detected six significant associations for the traits shoot manganese concentration and relative shoot length. Candidate regions contained genes coding for a heavy metal transporter, peroxidase precursor and Mn(2+) ion binding proteins. The significant marker SNP-2.22465867 caused an amino acid change in a gene (LOC_Os02g37170) with unknown function. This study demonstrated significant natural variation in rice for Mn toxicity tolerance and the possibility of using GWAS to unravel genetic factors responsible for such complex traits. Public Library of Science 2018-02-09 /pmc/articles/PMC5806864/ /pubmed/29425206 http://dx.doi.org/10.1371/journal.pone.0192116 Text en © 2018 Shrestha et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Shrestha, Asis Dziwornu, Ambrose Kwaku Ueda, Yoshiaki Wu, Lin-Bo Mathew, Boby Frei, Michael Genome-wide association study to identify candidate loci and genes for Mn toxicity tolerance in rice |
title | Genome-wide association study to identify candidate loci and genes for Mn toxicity tolerance in rice |
title_full | Genome-wide association study to identify candidate loci and genes for Mn toxicity tolerance in rice |
title_fullStr | Genome-wide association study to identify candidate loci and genes for Mn toxicity tolerance in rice |
title_full_unstemmed | Genome-wide association study to identify candidate loci and genes for Mn toxicity tolerance in rice |
title_short | Genome-wide association study to identify candidate loci and genes for Mn toxicity tolerance in rice |
title_sort | genome-wide association study to identify candidate loci and genes for mn toxicity tolerance in rice |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5806864/ https://www.ncbi.nlm.nih.gov/pubmed/29425206 http://dx.doi.org/10.1371/journal.pone.0192116 |
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