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...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2018-01-01
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| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/article/10.3389/fpls.2017.02213/full |
| _version_ | 1811342734167900160 |
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| author | Qing Lu Qing Lu Xiaojun Niu Mengchen Zhang Caihong Wang Qun Xu Yue Feng Yaolong Yang Shan Wang Xiaoping Yuan Hanyong Yu Yiping Wang Xiaoping Chen Xuanqiang Liang Xinghua Wei |
| author_facet | Qing Lu Qing Lu Xiaojun Niu Mengchen Zhang Caihong Wang Qun Xu Yue Feng Yaolong Yang Shan Wang Xiaoping Yuan Hanyong Yu Yiping Wang Xiaoping Chen Xuanqiang Liang Xinghua Wei |
| author_sort | Qing Lu |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-04-13T19:15:57Z |
| format | Article |
| id | doaj.art-c3484386369740169f9515a5f58b7f96 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-13T19:15:57Z |
| publishDate | 2018-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-c3484386369740169f9515a5f58b7f962022-12-22T02:33:41ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2018-01-01810.3389/fpls.2017.02213320907Genome-Wide Association Study of Seed Dormancy and the Genomic Consequences of Improvement Footprints in Rice (Oryza sativa L.)Qing Lu0Qing Lu1Xiaojun Niu2Mengchen Zhang3Caihong Wang4Qun Xu5Yue Feng6Yaolong Yang7Shan Wang8Xiaoping Yuan9Hanyong Yu10Yiping Wang11Xiaoping Chen12Xuanqiang Liang13Xinghua Wei14State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, ChinaCrops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement and Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, ChinaState Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, ChinaState Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, ChinaState Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, ChinaState Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, ChinaState Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, ChinaState Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, ChinaState Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, ChinaState Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, ChinaState Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, ChinaState Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, ChinaCrops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement and Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, ChinaCrops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement and Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, ChinaState Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, ChinaSeed 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.http://journal.frontiersin.org/article/10.3389/fpls.2017.02213/fullgenome-wide association studyseed dormancyselective sweepsimprovement footprintsrice (Oryza sativa L.) |
| spellingShingle | Qing Lu Qing Lu Xiaojun Niu Mengchen Zhang Caihong Wang Qun Xu Yue Feng Yaolong Yang Shan Wang Xiaoping Yuan Hanyong Yu Yiping Wang Xiaoping Chen Xuanqiang Liang Xinghua Wei Genome-Wide Association Study of Seed Dormancy and the Genomic Consequences of Improvement Footprints in Rice (Oryza sativa L.) Frontiers in Plant Science genome-wide association study seed dormancy selective sweeps improvement footprints 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 | genome-wide association study seed dormancy selective sweeps improvement footprints rice (Oryza sativa L.) |
| url | http://journal.frontiersin.org/article/10.3389/fpls.2017.02213/full |
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