Genetic basis of sRNA quantitative variation analyzed using an experimental population derived from an elite rice hybrid
We performed a genetic analysis of sRNA abundance in flag leaf from an immortalized F2 (IMF2) population in rice. We identified 53,613,739 unique sRNAs and 165,797 sRNA expression traits (s-traits). A total of 66,649 s-traits mapped 40,049 local-sQTLs and 30,809 distant-sQTLs. By defining 80,362 sRN...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2015-03-01
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| Series: | eLife |
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| Online Access: | https://elifesciences.org/articles/03913 |
| _version_ | 1811235865601507328 |
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| author | Jia Wang Wen Yao Dan Zhu Weibo Xie Qifa Zhang |
| author_facet | Jia Wang Wen Yao Dan Zhu Weibo Xie Qifa Zhang |
| author_sort | Jia Wang |
| collection | DOAJ |
| description | We performed a genetic analysis of sRNA abundance in flag leaf from an immortalized F2 (IMF2) population in rice. We identified 53,613,739 unique sRNAs and 165,797 sRNA expression traits (s-traits). A total of 66,649 s-traits mapped 40,049 local-sQTLs and 30,809 distant-sQTLs. By defining 80,362 sRNA clusters, 22,263 sRNA cluster QTLs (scQTLs) were recovered for 20,249 of all the 50,139 sRNA cluster expression traits (sc-traits). The expression levels for most of s-traits from the same genes or the same sRNA clusters were slightly positively correlated. While genetic co-regulation between sRNAs from the same mother genes and between sRNAs and their mother genes was observed for a portion of the sRNAs, most of the sRNAs and their mother genes showed little co-regulation. Some sRNA biogenesis genes were located in distant-sQTL hotspots and showed correspondence with specific length classes of sRNAs suggesting their important roles in the regulation and biogenesis of the sRNAs. |
| first_indexed | 2024-04-12T11:59:25Z |
| format | Article |
| id | doaj.art-b1222685c42c4d1c8319e9692b8a3acb |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-12T11:59:25Z |
| publishDate | 2015-03-01 |
| publisher | eLife Sciences Publications Ltd |
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| spelling | doaj.art-b1222685c42c4d1c8319e9692b8a3acb2022-12-22T03:33:53ZengeLife Sciences Publications LtdeLife2050-084X2015-03-01410.7554/eLife.03913Genetic basis of sRNA quantitative variation analyzed using an experimental population derived from an elite rice hybridJia Wang0Wen Yao1Dan Zhu2Weibo Xie3Qifa Zhang4National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China; National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, ChinaNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China; National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, ChinaNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China; National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, ChinaNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China; National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, ChinaNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China; National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, ChinaWe performed a genetic analysis of sRNA abundance in flag leaf from an immortalized F2 (IMF2) population in rice. We identified 53,613,739 unique sRNAs and 165,797 sRNA expression traits (s-traits). A total of 66,649 s-traits mapped 40,049 local-sQTLs and 30,809 distant-sQTLs. By defining 80,362 sRNA clusters, 22,263 sRNA cluster QTLs (scQTLs) were recovered for 20,249 of all the 50,139 sRNA cluster expression traits (sc-traits). The expression levels for most of s-traits from the same genes or the same sRNA clusters were slightly positively correlated. While genetic co-regulation between sRNAs from the same mother genes and between sRNAs and their mother genes was observed for a portion of the sRNAs, most of the sRNAs and their mother genes showed little co-regulation. Some sRNA biogenesis genes were located in distant-sQTL hotspots and showed correspondence with specific length classes of sRNAs suggesting their important roles in the regulation and biogenesis of the sRNAs.https://elifesciences.org/articles/03913ricegeneticsRNA |
| spellingShingle | Jia Wang Wen Yao Dan Zhu Weibo Xie Qifa Zhang Genetic basis of sRNA quantitative variation analyzed using an experimental population derived from an elite rice hybrid eLife rice genetic sRNA |
| title | Genetic basis of sRNA quantitative variation analyzed using an experimental population derived from an elite rice hybrid |
| title_full | Genetic basis of sRNA quantitative variation analyzed using an experimental population derived from an elite rice hybrid |
| title_fullStr | Genetic basis of sRNA quantitative variation analyzed using an experimental population derived from an elite rice hybrid |
| title_full_unstemmed | Genetic basis of sRNA quantitative variation analyzed using an experimental population derived from an elite rice hybrid |
| title_short | Genetic basis of sRNA quantitative variation analyzed using an experimental population derived from an elite rice hybrid |
| title_sort | genetic basis of srna quantitative variation analyzed using an experimental population derived from an elite rice hybrid |
| topic | rice genetic sRNA |
| url | https://elifesciences.org/articles/03913 |
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