Genomic analysis of hybrid rice varieties reveals numerous superior alleles that contribute to heterosis

Xuehui Huang, Shihua Yang, Junyi Gong, Yan Zhao, Qi Feng, Hao Gong, Wenjun Li, Qilin Zhan, Benyi Cheng, Junhui Xia, Neng Chen, Zhongna Hao, Kunyan Liu, Chuanrang Zhu, Tao Huang, Qiang Zhao, Lei Zhang, Danlin Fan, Congcong Zhou, Yiqi Lu, Qijun Weng, Zi-Xuan Wang, Jiayang Li and Bin Han ()
Additional contact information
Xuehui Huang: National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
Shihua Yang: State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences
Junyi Gong: State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences
Yan Zhao: National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
Qi Feng: National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
Hao Gong: National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
Wenjun Li: National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
Qilin Zhan: National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
Benyi Cheng: State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences
Junhui Xia: State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences
Neng Chen: State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences
Zhongna Hao: Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences
Kunyan Liu: National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
Chuanrang Zhu: National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
Tao Huang: National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
Qiang Zhao: National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
Lei Zhang: National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
Danlin Fan: National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
Congcong Zhou: National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
Yiqi Lu: National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
Qijun Weng: National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
Zi-Xuan Wang: National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
Jiayang Li: National Center for Plant Gene Research, State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
Bin Han: National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

Nature Communications, 2015, vol. 6, issue 1, 1-9

Abstract: Abstract Exploitation of heterosis is one of the most important applications of genetics in agriculture. However, the genetic mechanisms of heterosis are only partly understood, and a global view of heterosis from a representative number of hybrid combinations is lacking. Here we develop an integrated genomic approach to construct a genome map for 1,495 elite hybrid rice varieties and their inbred parental lines. We investigate 38 agronomic traits and identify 130 associated loci. In-depth analyses of the effects of heterozygous genotypes reveal that there are only a few loci with strong overdominance effects in hybrids, but a strong correlation is observed between the yield and the number of superior alleles. While most parental inbred lines have only a small number of superior alleles, high-yielding hybrid varieties have several. We conclude that the accumulation of numerous rare superior alleles with positive dominance is an important contributor to the heterotic phenomena.

Date: 2015
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DOI: 10.1038/ncomms7258

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