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The genetic diversity and structure of indica rice in China as detected by single nucleotide polymorphism analysis

BACKGROUND: Rice (Oryza sativa L.) is the staple food of more than half of the world’s population. The identification of genetic diversity in local varieties of rice compared with that of improved or introduced varieties is important in breeding elite varieties for sustainable agriculture. Array-bas...

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Autores principales: Xu, Qun, Yuan, Xiaoping, Wang, Shan, Feng, Yue, Yu, Hanyong, Wang, Yiping, Yang, Yaolong, Wei, Xinghua, Li, Ximing
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4793538/
https://www.ncbi.nlm.nih.gov/pubmed/26979342
http://dx.doi.org/10.1186/s12863-016-0361-x
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author Xu, Qun
Yuan, Xiaoping
Wang, Shan
Feng, Yue
Yu, Hanyong
Wang, Yiping
Yang, Yaolong
Wei, Xinghua
Li, Ximing
author_facet Xu, Qun
Yuan, Xiaoping
Wang, Shan
Feng, Yue
Yu, Hanyong
Wang, Yiping
Yang, Yaolong
Wei, Xinghua
Li, Ximing
author_sort Xu, Qun
collection PubMed
description BACKGROUND: Rice (Oryza sativa L.) is the staple food of more than half of the world’s population. The identification of genetic diversity in local varieties of rice compared with that of improved or introduced varieties is important in breeding elite varieties for sustainable agriculture. Array-based single nucleotide polymorphism (SNP) detection is a useful technique for such studies and breeding applications. RESULTS: We developed a 5291-SNP genome-wide array and used it to genotype 471 indica rice accessions in China using Illumina’s Infinium technology. Local, introduced, and improved rice varieties were clustered into three sub-groups, with some overlapping shown in principal component analysis and neighbor-joining tree, also confirmed by model-based structure. A minor allele frequency ≥0.2 was observed in 72 % of polymorphic SNPs in local rice varieties, which was higher than that in other sub-groups. Local rice varieties also had the highest mean polymorphism information content (PIC) and genetic diversity. Analysis of molecular variance showed that 90.61 % of genetic variation was a result of differences within sub-groups. CONCLUSIONS: Our results revealed that SNP analysis clustered local varieties, introduced varieties, and improved varieties into three clear sub-groups. The distribution of parameter PIC values on sub-group genomes revealed that genetic differentiation among them might not be on a genome-wide scale, but rather on selected loci or chromosomal intervals. The result of Gene Ontology enrichment analysis showed that genes nearby those selected SNPs associated different molecular functions or various traits among sub-groups. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12863-016-0361-x) contains supplementary material, which is available to authorized users.
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spelling pubmed-47935382016-03-16 The genetic diversity and structure of indica rice in China as detected by single nucleotide polymorphism analysis Xu, Qun Yuan, Xiaoping Wang, Shan Feng, Yue Yu, Hanyong Wang, Yiping Yang, Yaolong Wei, Xinghua Li, Ximing BMC Genet Research Article BACKGROUND: Rice (Oryza sativa L.) is the staple food of more than half of the world’s population. The identification of genetic diversity in local varieties of rice compared with that of improved or introduced varieties is important in breeding elite varieties for sustainable agriculture. Array-based single nucleotide polymorphism (SNP) detection is a useful technique for such studies and breeding applications. RESULTS: We developed a 5291-SNP genome-wide array and used it to genotype 471 indica rice accessions in China using Illumina’s Infinium technology. Local, introduced, and improved rice varieties were clustered into three sub-groups, with some overlapping shown in principal component analysis and neighbor-joining tree, also confirmed by model-based structure. A minor allele frequency ≥0.2 was observed in 72 % of polymorphic SNPs in local rice varieties, which was higher than that in other sub-groups. Local rice varieties also had the highest mean polymorphism information content (PIC) and genetic diversity. Analysis of molecular variance showed that 90.61 % of genetic variation was a result of differences within sub-groups. CONCLUSIONS: Our results revealed that SNP analysis clustered local varieties, introduced varieties, and improved varieties into three clear sub-groups. The distribution of parameter PIC values on sub-group genomes revealed that genetic differentiation among them might not be on a genome-wide scale, but rather on selected loci or chromosomal intervals. The result of Gene Ontology enrichment analysis showed that genes nearby those selected SNPs associated different molecular functions or various traits among sub-groups. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12863-016-0361-x) contains supplementary material, which is available to authorized users. BioMed Central 2016-03-15 /pmc/articles/PMC4793538/ /pubmed/26979342 http://dx.doi.org/10.1186/s12863-016-0361-x Text en © Xu et al. 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Xu, Qun
Yuan, Xiaoping
Wang, Shan
Feng, Yue
Yu, Hanyong
Wang, Yiping
Yang, Yaolong
Wei, Xinghua
Li, Ximing
The genetic diversity and structure of indica rice in China as detected by single nucleotide polymorphism analysis
title The genetic diversity and structure of indica rice in China as detected by single nucleotide polymorphism analysis
title_full The genetic diversity and structure of indica rice in China as detected by single nucleotide polymorphism analysis
title_fullStr The genetic diversity and structure of indica rice in China as detected by single nucleotide polymorphism analysis
title_full_unstemmed The genetic diversity and structure of indica rice in China as detected by single nucleotide polymorphism analysis
title_short The genetic diversity and structure of indica rice in China as detected by single nucleotide polymorphism analysis
title_sort genetic diversity and structure of indica rice in china as detected by single nucleotide polymorphism analysis
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4793538/
https://www.ncbi.nlm.nih.gov/pubmed/26979342
http://dx.doi.org/10.1186/s12863-016-0361-x
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