QTL map meets population genomics: an application to rice.
Genes involved in the transition from wild to cultivated crop species should be of great agronomic importance. Population genomic approaches utilizing genome resequencing data have been recently applied for this purpose, although it only reports a large list of candidate genes with no biological inf...
| Main Authors: | , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2013-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3871663?pdf=render |
| _version_ | 1818995596168527872 |
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| author | Jeffrey A Fawcett Tomoyuki Kado Eriko Sasaki Shohei Takuno Kentaro Yoshida Ryuichi P Sugino Shunichi Kosugi Satoshi Natsume Chikako Mitsuoka Aiko Uemura Hiroki Takagi Akira Abe Takashige Ishii Ryohei Terauchi Hideki Innan |
| author_facet | Jeffrey A Fawcett Tomoyuki Kado Eriko Sasaki Shohei Takuno Kentaro Yoshida Ryuichi P Sugino Shunichi Kosugi Satoshi Natsume Chikako Mitsuoka Aiko Uemura Hiroki Takagi Akira Abe Takashige Ishii Ryohei Terauchi Hideki Innan |
| author_sort | Jeffrey A Fawcett |
| collection | DOAJ |
| description | Genes involved in the transition from wild to cultivated crop species should be of great agronomic importance. Population genomic approaches utilizing genome resequencing data have been recently applied for this purpose, although it only reports a large list of candidate genes with no biological information. Here, by resequencing more than 30 genomes altogether of wild rice Oryza rufipogon and cultivated rice O. sativa, we identified a number of regions with clear footprints of selection during the domestication process. We then focused on identifying candidate domestication genes in these regions by utilizing the wealth of QTL information in rice. We were able to identify a number of interesting candidates such as transcription factors that should control key domestication traits such as shattering, awn length, and seed dormancy. Other candidates include those that might have been related to the improvement of grain quality and those that might have been involved in the local adaptation to dry conditions and colder environments. Our study shows that population genomic approaches and QTL mapping information can be used together to identify genes that might be of agronomic importance. |
| first_indexed | 2024-12-20T21:16:21Z |
| format | Article |
| id | doaj.art-6c43896a9c3b43c197bff454a9836b9c |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-20T21:16:21Z |
| publishDate | 2013-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-6c43896a9c3b43c197bff454a9836b9c2022-12-21T19:26:24ZengPublic Library of Science (PLoS)PLoS ONE1932-62032013-01-01812e8372010.1371/journal.pone.0083720QTL map meets population genomics: an application to rice.Jeffrey A FawcettTomoyuki KadoEriko SasakiShohei TakunoKentaro YoshidaRyuichi P SuginoShunichi KosugiSatoshi NatsumeChikako MitsuokaAiko UemuraHiroki TakagiAkira AbeTakashige IshiiRyohei TerauchiHideki InnanGenes involved in the transition from wild to cultivated crop species should be of great agronomic importance. Population genomic approaches utilizing genome resequencing data have been recently applied for this purpose, although it only reports a large list of candidate genes with no biological information. Here, by resequencing more than 30 genomes altogether of wild rice Oryza rufipogon and cultivated rice O. sativa, we identified a number of regions with clear footprints of selection during the domestication process. We then focused on identifying candidate domestication genes in these regions by utilizing the wealth of QTL information in rice. We were able to identify a number of interesting candidates such as transcription factors that should control key domestication traits such as shattering, awn length, and seed dormancy. Other candidates include those that might have been related to the improvement of grain quality and those that might have been involved in the local adaptation to dry conditions and colder environments. Our study shows that population genomic approaches and QTL mapping information can be used together to identify genes that might be of agronomic importance.http://europepmc.org/articles/PMC3871663?pdf=render |
| spellingShingle | Jeffrey A Fawcett Tomoyuki Kado Eriko Sasaki Shohei Takuno Kentaro Yoshida Ryuichi P Sugino Shunichi Kosugi Satoshi Natsume Chikako Mitsuoka Aiko Uemura Hiroki Takagi Akira Abe Takashige Ishii Ryohei Terauchi Hideki Innan QTL map meets population genomics: an application to rice. PLoS ONE |
| title | QTL map meets population genomics: an application to rice. |
| title_full | QTL map meets population genomics: an application to rice. |
| title_fullStr | QTL map meets population genomics: an application to rice. |
| title_full_unstemmed | QTL map meets population genomics: an application to rice. |
| title_short | QTL map meets population genomics: an application to rice. |
| title_sort | qtl map meets population genomics an application to rice |
| url | http://europepmc.org/articles/PMC3871663?pdf=render |
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