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

Author

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  • 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)

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.

Suggested Citation

  • 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 Z, 2015. "Genomic analysis of hybrid rice varieties reveals numerous superior alleles that contribute to heterosis," Nature Communications, Nature, vol. 6(1), pages 1-9, May.
    • Handle: RePEc:nat:natcom:v:6:y:2015:i:1:d:10.1038_ncomms7258
    DOI: 10.1038/ncomms7258
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    Cited by:

    1. Lanzhi Li & Xingfei Zheng & Jiabo Wang & Xueli Zhang & Xiaogang He & Liwen Xiong & Shufeng Song & Jing Su & Ying Diao & Zheming Yuan & Zhiwu Zhang & Zhongli Hu, 2023. "Joint analysis of phenotype-effect-generation identifies loci associated with grain quality traits in rice hybrids," Nature Communications, Nature, vol. 14(1), pages 1-9, December.
    2. Luchang Ming & Debao Fu & Zhaona Wu & Hu Zhao & Xingbing Xu & Tingting Xu & Xiaohu Xiong & Mu Li & Yi Zheng & Ge Li & Ling Yang & Chunjiao Xia & Rongfang Zhou & Keyan Liao & Qian Yu & Wenqi Chai & Sij, 2023. "Transcriptome-wide association analyses reveal the impact of regulatory variants on rice panicle architecture and causal gene regulatory networks," Nature Communications, Nature, vol. 14(1), pages 1-15, December.

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