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Population genetic structure of Oryza sativa in East and Southeast Asia and the discovery of elite alleles for grain traits
We investigated the nuclear simple sequence repeat (SSR) genotypes of 532 rice (Oryza sativa L.) accessions collected from East and Southeast Asia and detected abundant genetic diversity within the population. We identified 6 subpopulations and found a tendency towards directional evolution in O. sa...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4462027/ https://www.ncbi.nlm.nih.gov/pubmed/26059752 http://dx.doi.org/10.1038/srep11254 |
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author | Dang, Xiaojing Giang Tran Thi, Thu Mawuli Edzesi, Wisdom Liang, Lijun Liu, Qiangming Liu, Erbao Wang, Yang Qiang, Sheng Liu, Linglong Hong, Delin |
author_facet | Dang, Xiaojing Giang Tran Thi, Thu Mawuli Edzesi, Wisdom Liang, Lijun Liu, Qiangming Liu, Erbao Wang, Yang Qiang, Sheng Liu, Linglong Hong, Delin |
author_sort | Dang, Xiaojing |
collection | PubMed |
description | We investigated the nuclear simple sequence repeat (SSR) genotypes of 532 rice (Oryza sativa L.) accessions collected from East and Southeast Asia and detected abundant genetic diversity within the population. We identified 6 subpopulations and found a tendency towards directional evolution in O. sativa from low to high latitudes, with levels of linkage disequilibrium (LD) in the 6 subpopulations ranging from 10 to 30 cM. We then investigated the phenotypic data for grain length, grain width, grain thickness and 1,000-grain weight over 4 years. Using a genome-wide association analysis, we identified 17 marker-trait associations involving 14 SSR markers on 12 chromosome arms, and 8 of the 17 associations were novel. The elite alleles were mined based on the phenotypic effects of the detected quantitative trait loci (QTLs). These elite alleles could be used to improve target traits through optimal cross designs, with the expected results obtained by pyramiding or substituting the elite alleles per QTL (independent of possible epistatic effects). Together, these results provide an in-depth understanding of the genetic diversity pattern among rice-grain traits across a broad geographic scale, which has potential use in future research work, including studies related to germplasm conservation and molecular breeding by design. |
format | Online Article Text |
id | pubmed-4462027 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Nature Publishing Group |
record_format | MEDLINE/PubMed |
spelling | pubmed-44620272015-06-12 Population genetic structure of Oryza sativa in East and Southeast Asia and the discovery of elite alleles for grain traits Dang, Xiaojing Giang Tran Thi, Thu Mawuli Edzesi, Wisdom Liang, Lijun Liu, Qiangming Liu, Erbao Wang, Yang Qiang, Sheng Liu, Linglong Hong, Delin Sci Rep Article We investigated the nuclear simple sequence repeat (SSR) genotypes of 532 rice (Oryza sativa L.) accessions collected from East and Southeast Asia and detected abundant genetic diversity within the population. We identified 6 subpopulations and found a tendency towards directional evolution in O. sativa from low to high latitudes, with levels of linkage disequilibrium (LD) in the 6 subpopulations ranging from 10 to 30 cM. We then investigated the phenotypic data for grain length, grain width, grain thickness and 1,000-grain weight over 4 years. Using a genome-wide association analysis, we identified 17 marker-trait associations involving 14 SSR markers on 12 chromosome arms, and 8 of the 17 associations were novel. The elite alleles were mined based on the phenotypic effects of the detected quantitative trait loci (QTLs). These elite alleles could be used to improve target traits through optimal cross designs, with the expected results obtained by pyramiding or substituting the elite alleles per QTL (independent of possible epistatic effects). Together, these results provide an in-depth understanding of the genetic diversity pattern among rice-grain traits across a broad geographic scale, which has potential use in future research work, including studies related to germplasm conservation and molecular breeding by design. Nature Publishing Group 2015-06-10 /pmc/articles/PMC4462027/ /pubmed/26059752 http://dx.doi.org/10.1038/srep11254 Text en Copyright © 2015, Macmillan Publishers Limited http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ |
spellingShingle | Article Dang, Xiaojing Giang Tran Thi, Thu Mawuli Edzesi, Wisdom Liang, Lijun Liu, Qiangming Liu, Erbao Wang, Yang Qiang, Sheng Liu, Linglong Hong, Delin Population genetic structure of Oryza sativa in East and Southeast Asia and the discovery of elite alleles for grain traits |
title | Population genetic structure of Oryza sativa in East and Southeast Asia and the discovery of elite alleles for grain traits |
title_full | Population genetic structure of Oryza sativa in East and Southeast Asia and the discovery of elite alleles for grain traits |
title_fullStr | Population genetic structure of Oryza sativa in East and Southeast Asia and the discovery of elite alleles for grain traits |
title_full_unstemmed | Population genetic structure of Oryza sativa in East and Southeast Asia and the discovery of elite alleles for grain traits |
title_short | Population genetic structure of Oryza sativa in East and Southeast Asia and the discovery of elite alleles for grain traits |
title_sort | population genetic structure of oryza sativa in east and southeast asia and the discovery of elite alleles for grain traits |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4462027/ https://www.ncbi.nlm.nih.gov/pubmed/26059752 http://dx.doi.org/10.1038/srep11254 |
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