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Genome-Wide Association Study of Seed Dormancy and the Genomic Consequences of Improvement Footprints in Rice (Oryza sativa L.)
Seed dormancy is an important agronomic trait affecting grain yield and quality because of pre-harvest germination and is influenced by both environmental and genetic factors. However, our knowledge of the factors controlling seed dormancy remains limited. To better reveal the molecular mechanism un...
Autores principales: | , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5760558/ https://www.ncbi.nlm.nih.gov/pubmed/29354150 http://dx.doi.org/10.3389/fpls.2017.02213 |
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author | Lu, Qing Niu, Xiaojun Zhang, Mengchen Wang, Caihong Xu, Qun Feng, Yue Yang, Yaolong Wang, Shan Yuan, Xiaoping Yu, Hanyong Wang, Yiping Chen, Xiaoping Liang, Xuanqiang Wei, Xinghua |
author_facet | Lu, Qing Niu, Xiaojun Zhang, Mengchen Wang, Caihong Xu, Qun Feng, Yue Yang, Yaolong Wang, Shan Yuan, Xiaoping Yu, Hanyong Wang, Yiping Chen, Xiaoping Liang, Xuanqiang Wei, Xinghua |
author_sort | Lu, Qing |
collection | PubMed |
description | Seed dormancy is an important agronomic trait affecting grain yield and quality because of pre-harvest germination and is influenced by both environmental and genetic factors. However, our knowledge of the factors controlling seed dormancy remains limited. To better reveal the molecular mechanism underlying this trait, a genome-wide association study was conducted in an indica-only population consisting of 453 accessions genotyped using 5,291 SNPs. Nine known and new significant SNPs were identified on eight chromosomes. These lead SNPs explained 34.9% of the phenotypic variation, and four of them were designed as dCAPS markers in the hope of accelerating molecular breeding. Moreover, a total of 212 candidate genes was predicted and eight candidate genes showed plant tissue-specific expression in expression profile data from different public bioinformatics databases. In particular, LOC_Os03g10110, which had a maize homolog involved in embryo development, was identified as a candidate regulator for further biological function investigations. Additionally, a polymorphism information content ratio method was used to screen improvement footprints and 27 selective sweeps were identified, most of which harbored domestication-related genes. Further studies suggested that three significant SNPs were adjacent to the candidate selection signals, supporting the accuracy of our genome-wide association study (GWAS) results. These findings show that genome-wide screening for selective sweeps can be used to identify new improvement-related DNA regions, although the phenotypes are unknown. This study enhances our knowledge of the genetic variation in seed dormancy, and the new dormancy-associated SNPs will provide real benefits in molecular breeding. |
format | Online Article Text |
id | pubmed-5760558 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-57605582018-01-19 Genome-Wide Association Study of Seed Dormancy and the Genomic Consequences of Improvement Footprints in Rice (Oryza sativa L.) Lu, Qing Niu, Xiaojun Zhang, Mengchen Wang, Caihong Xu, Qun Feng, Yue Yang, Yaolong Wang, Shan Yuan, Xiaoping Yu, Hanyong Wang, Yiping Chen, Xiaoping Liang, Xuanqiang Wei, Xinghua Front Plant Sci Plant Science Seed dormancy is an important agronomic trait affecting grain yield and quality because of pre-harvest germination and is influenced by both environmental and genetic factors. However, our knowledge of the factors controlling seed dormancy remains limited. To better reveal the molecular mechanism underlying this trait, a genome-wide association study was conducted in an indica-only population consisting of 453 accessions genotyped using 5,291 SNPs. Nine known and new significant SNPs were identified on eight chromosomes. These lead SNPs explained 34.9% of the phenotypic variation, and four of them were designed as dCAPS markers in the hope of accelerating molecular breeding. Moreover, a total of 212 candidate genes was predicted and eight candidate genes showed plant tissue-specific expression in expression profile data from different public bioinformatics databases. In particular, LOC_Os03g10110, which had a maize homolog involved in embryo development, was identified as a candidate regulator for further biological function investigations. Additionally, a polymorphism information content ratio method was used to screen improvement footprints and 27 selective sweeps were identified, most of which harbored domestication-related genes. Further studies suggested that three significant SNPs were adjacent to the candidate selection signals, supporting the accuracy of our genome-wide association study (GWAS) results. These findings show that genome-wide screening for selective sweeps can be used to identify new improvement-related DNA regions, although the phenotypes are unknown. This study enhances our knowledge of the genetic variation in seed dormancy, and the new dormancy-associated SNPs will provide real benefits in molecular breeding. Frontiers Media S.A. 2018-01-05 /pmc/articles/PMC5760558/ /pubmed/29354150 http://dx.doi.org/10.3389/fpls.2017.02213 Text en Copyright © 2018 Lu, Niu, Zhang, Wang, Xu, Feng, Yang, Wang, Yuan, Yu, Wang, Chen, Liang and Wei. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Plant Science Lu, Qing Niu, Xiaojun Zhang, Mengchen Wang, Caihong Xu, Qun Feng, Yue Yang, Yaolong Wang, Shan Yuan, Xiaoping Yu, Hanyong Wang, Yiping Chen, Xiaoping Liang, Xuanqiang Wei, Xinghua Genome-Wide Association Study of Seed Dormancy and the Genomic Consequences of Improvement Footprints in Rice (Oryza sativa L.) |
title | Genome-Wide Association Study of Seed Dormancy and the Genomic Consequences of Improvement Footprints in Rice (Oryza sativa L.) |
title_full | Genome-Wide Association Study of Seed Dormancy and the Genomic Consequences of Improvement Footprints in Rice (Oryza sativa L.) |
title_fullStr | Genome-Wide Association Study of Seed Dormancy and the Genomic Consequences of Improvement Footprints in Rice (Oryza sativa L.) |
title_full_unstemmed | Genome-Wide Association Study of Seed Dormancy and the Genomic Consequences of Improvement Footprints in Rice (Oryza sativa L.) |
title_short | Genome-Wide Association Study of Seed Dormancy and the Genomic Consequences of Improvement Footprints in Rice (Oryza sativa L.) |
title_sort | genome-wide association study of seed dormancy and the genomic consequences of improvement footprints in rice (oryza sativa l.) |
topic | Plant Science |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5760558/ https://www.ncbi.nlm.nih.gov/pubmed/29354150 http://dx.doi.org/10.3389/fpls.2017.02213 |
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