A natural tandem array alleviates epigenetic repression of IPA1 and leads to superior yielding rice.
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.
National Key Laboratory of Plant Molecular Genetics and National Center of Plant Gene Research, Institute of Plant Physiology &Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.|Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China.|University of the Chinese Academy of Sciences, Beijing 100049, China.
Lin
L
Zhang
State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
Hong
0000-0002-1748-8693
H
Yu
School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China.
Bin
B
Ma
State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
Guifu
G
Liu
Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
Jianjun
J
Wang
Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
Junmin
J
Wang
Jiaxing Academy of Agricultural Sciences, Jiaxing, Zhejiang 314016, China.
Rongcun
R
Gao
Jiaxing Academy of Agricultural Sciences, Jiaxing, Zhejiang 314016, China.
Jinjun
J
Li
National Key Laboratory of Plant Molecular Genetics and National Center of Plant Gene Research, Institute of Plant Physiology &Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
Jiyun
J
Liu
National Key Laboratory of Plant Molecular Genetics and National Center of Plant Gene Research, Institute of Plant Physiology &Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
Jing
J
Xu
National Key Laboratory of Plant Molecular Genetics and National Center of Plant Gene Research, Institute of Plant Physiology &Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
Yingying
Y
Zhang
National Key Laboratory of Plant Molecular Genetics and National Center of Plant Gene Research, Institute of Plant Physiology &Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
Qun
Q
Li
National Center for Gene Research, CAS Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology &Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China.
Xuehui
X
Huang
Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
Jianlong
J
Xu
Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China.
Jianming
J
Li
Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
Qian
Q
Qian
National Center for Gene Research, CAS Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology &Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China.
Bin
B
Han
National Key Laboratory of Plant Molecular Genetics and National Center of Plant Gene Research, Institute of Plant Physiology &Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.|University of the Chinese Academy of Sciences, Beijing 100049, China.
Zuhua
0000-0002-6098-7893
Z
He
University of the Chinese Academy of Sciences, Beijing 100049, China.|State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
Jiayang
0000-0002-0487-6574
J
Li
D019175:DNA Methylation; D002523:Edible Grain / Q000235:genetics / Q000254:growth & development; D063185:Epigenetic Repression; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant / Q000235:genetics*; D012275:Oryza / Q000235:genetics* / Q000254:growth & development; D030821:Plants, Genetically Modified; D011401:Promoter Regions, Genetic / Q000235:genetics; D040641:Quantitative Trait Loci / Q000235:genetics*