Genetic basis of sRNA quantitative variation analyzed using an experimental population derived from an elite rice hybrid

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Cite this article as: eLife 2015;4:e03913 doi: 10.7554/eLife.03913

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Abstract

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.

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Jia Wang

National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China

Competing interests
The authors declare that no competing interests exist.
Wen Yao

National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China

Competing interests
The authors declare that no competing interests exist.
Dan Zhu

National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China

Competing interests
The authors declare that no competing interests exist.
Weibo Xie

National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China

Competing interests
The authors declare that no competing interests exist.
Qifa Zhang

National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China

For correspondence
qifazh@mail.hzau.edu.cn

Competing interests
The authors declare that no competing interests exist.

Reviewing Editor

Justin Borevitz, Australian National University, Australia

Publication history

Received: July 7, 2014
Accepted: March 30, 2015
Accepted Manuscript published: March 30, 2015 (version 1)
Version of Record published: May 5, 2015 (version 2)

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This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.