A natural tandem array alleviates epigenetic repression of IPA1 and leads to superior yielding rice

Lin Zhang; Hong Yu; Bin Ma; Guifu Liu; Jianjun Wang; Junmin Wang; Rongcun Gao; Jinjun Li; Jiyun Liu; Jing Xu; Yingying Zhang; Qun Li; Xuehui Huang; Jianlong Xu; Jianming Li; Qian Qian; Bin Han; Zuhua He; Jiayang Li

doi:10.1038/ncomms14789

A natural tandem array alleviates epigenetic repression of IPA1 and leads to superior yielding rice

Lin Zhang
, Hong Yu
, Bin Ma
, Guifu Liu
, Jianjun Wang
, Junmin Wang
, Rongcun Gao
, Jinjun Li
, Jiyun Liu
, Jing Xu
, Yingying Zhang
, Qun Li
, Xuehui Huang
, Jianlong Xu
, Jianming Li
, Qian Qian
, Bin Han
, Zuhua He^*
, Jiayang Li

^*Corresponding author for this work

Department of Biology

Research output: Contribution to journal › Journal article › peer-review

203 Citations (Scopus)

Abstract

Super hybrid rice varieties with ideal plant architecture (IPA) have been critical in enhancing food security worldwide. However, the molecular mechanisms underlying their improved yield remain unclear. Here, we report the identification of a QTL, qWS8/ipa1-2D, in the super rice Yongyou12 (YY12) and related varieties. In-depth genetic molecular characterization of qWS8/ipa1-2D reveals that this newly identified QTL results from three distal naturally occurring tandem repeats upstream of IPA1, a key gene/locus previously shown to shape rice ideal plant architecture and greatly enhance grain yield. The qWS8/ipa1-2D locus is associated with reduced DNA methylation and a more open chromatin state at the IPA1 promoter, thus alleviating the epigenetic repression of IPA1 mediated by nearby heterochromatin. Our findings reveal that IPA traits can be fine-tuned by manipulating IPA1 expression and that an optimal IPA1 expression/dose may lead to an ideal yield, demonstrating a practical approach to efficiently design elite super rice varieties.

Original language	English
Article number	14789
Number of pages	10
Journal	Nature Communications
Volume	8
DOIs	https://doi.org/10.1038/ncomms14789
Publication status	Published - 20 Mar 2017

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1038/ncomms14789

Cite this

@article{dc8e70cdd8634af2a2c9f6fde6abfc11,

title = "A natural tandem array alleviates epigenetic repression of IPA1 and leads to superior yielding rice",

abstract = "Super hybrid rice varieties with ideal plant architecture (IPA) have been critical in enhancing food security worldwide. However, the molecular mechanisms underlying their improved yield remain unclear. Here, we report the identification of a QTL, qWS8/ipa1-2D, in the super rice Yongyou12 (YY12) and related varieties. In-depth genetic molecular characterization of qWS8/ipa1-2D reveals that this newly identified QTL results from three distal naturally occurring tandem repeats upstream of IPA1, a key gene/locus previously shown to shape rice ideal plant architecture and greatly enhance grain yield. The qWS8/ipa1-2D locus is associated with reduced DNA methylation and a more open chromatin state at the IPA1 promoter, thus alleviating the epigenetic repression of IPA1 mediated by nearby heterochromatin. Our findings reveal that IPA traits can be fine-tuned by manipulating IPA1 expression and that an optimal IPA1 expression/dose may lead to an ideal yield, demonstrating a practical approach to efficiently design elite super rice varieties.",

author = "Lin Zhang and Hong Yu and Bin Ma and Guifu Liu and Jianjun Wang and Junmin Wang and Rongcun Gao and Jinjun Li and Jiyun Liu and Jing Xu and Yingying Zhang and Qun Li and Xuehui Huang and Jianlong Xu and Jianming Li and Qian Qian and Bin Han and Zuhua He and Jiayang Li",

note = "We thank Linyou Wang, Lixia Zhang and Yongbin Qi for rice growth and paddy field tests, Zhikang Li for providing rice germplasms, Ertao Wang for valuable suggestions. This work was supported by grants from Ministry of Science and Technology of China (2013ZX08009-003-001, 2016YFD0101800, 2014AA10A600), the Chinese Academy of Sciences (XDA0801 and XDA0803), the National Natural Science Foundation of China (31600990). Publisher Copyright: {\textcopyright} The Author(s) 2017.",

year = "2017",

month = mar,

day = "20",

doi = "10.1038/ncomms14789",

language = "English",

volume = "8",

journal = "Nature Communications",

issn = "2041-1723",

publisher = "Nature Research",

}

TY - JOUR

T1 - A natural tandem array alleviates epigenetic repression of IPA1 and leads to superior yielding rice

AU - Zhang, Lin

AU - Yu, Hong

AU - Ma, Bin

AU - Liu, Guifu

AU - Wang, Jianjun

AU - Wang, Junmin

AU - Gao, Rongcun

AU - Li, Jinjun

AU - Liu, Jiyun

AU - Xu, Jing

AU - Zhang, Yingying

AU - Li, Qun

AU - Huang, Xuehui

AU - Xu, Jianlong

AU - Li, Jianming

AU - Qian, Qian

AU - Han, Bin

AU - He, Zuhua

AU - Li, Jiayang

N1 - We thank Linyou Wang, Lixia Zhang and Yongbin Qi for rice growth and paddy field tests, Zhikang Li for providing rice germplasms, Ertao Wang for valuable suggestions. This work was supported by grants from Ministry of Science and Technology of China (2013ZX08009-003-001, 2016YFD0101800, 2014AA10A600), the Chinese Academy of Sciences (XDA0801 and XDA0803), the National Natural Science Foundation of China (31600990). Publisher Copyright: © The Author(s) 2017.

PY - 2017/3/20

Y1 - 2017/3/20

N2 - Super hybrid rice varieties with ideal plant architecture (IPA) have been critical in enhancing food security worldwide. However, the molecular mechanisms underlying their improved yield remain unclear. Here, we report the identification of a QTL, qWS8/ipa1-2D, in the super rice Yongyou12 (YY12) and related varieties. In-depth genetic molecular characterization of qWS8/ipa1-2D reveals that this newly identified QTL results from three distal naturally occurring tandem repeats upstream of IPA1, a key gene/locus previously shown to shape rice ideal plant architecture and greatly enhance grain yield. The qWS8/ipa1-2D locus is associated with reduced DNA methylation and a more open chromatin state at the IPA1 promoter, thus alleviating the epigenetic repression of IPA1 mediated by nearby heterochromatin. Our findings reveal that IPA traits can be fine-tuned by manipulating IPA1 expression and that an optimal IPA1 expression/dose may lead to an ideal yield, demonstrating a practical approach to efficiently design elite super rice varieties.

AB - Super hybrid rice varieties with ideal plant architecture (IPA) have been critical in enhancing food security worldwide. However, the molecular mechanisms underlying their improved yield remain unclear. Here, we report the identification of a QTL, qWS8/ipa1-2D, in the super rice Yongyou12 (YY12) and related varieties. In-depth genetic molecular characterization of qWS8/ipa1-2D reveals that this newly identified QTL results from three distal naturally occurring tandem repeats upstream of IPA1, a key gene/locus previously shown to shape rice ideal plant architecture and greatly enhance grain yield. The qWS8/ipa1-2D locus is associated with reduced DNA methylation and a more open chromatin state at the IPA1 promoter, thus alleviating the epigenetic repression of IPA1 mediated by nearby heterochromatin. Our findings reveal that IPA traits can be fine-tuned by manipulating IPA1 expression and that an optimal IPA1 expression/dose may lead to an ideal yield, demonstrating a practical approach to efficiently design elite super rice varieties.

UR - https://www.scopus.com/pages/publications/85015747405

U2 - 10.1038/ncomms14789

DO - 10.1038/ncomms14789

M3 - Journal article

C2 - 28317902

AN - SCOPUS:85015747405

SN - 2041-1723

VL - 8

JO - Nature Communications

JF - Nature Communications

M1 - 14789

ER -

A natural tandem array alleviates epigenetic repression of IPA1 and leads to superior yielding rice

Abstract

UN SDGs

Access to Document

Other files and links

Fingerprint

Cite this