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Proceedings of the National Academy of Sciences of the United States of America
10 11, 2016;113 (41): E6026-E6035.

Integrated analysis of phenome, genome, and transcriptome of hybrid rice uncovered multiple heterosis-related loci for yield increase.

Dayong Li, Zhiyuan Huang, Shuhui Song, Yeyun Xin, Donghai Mao, Qiming Lv, Ming Zhou, Dongmei Tian, Mingfeng Tang, Qi Wu, Xue Liu, Tingting Chen, Xianwei Song, Xiqin Fu, Bingran Zhao, Chengzhi Liang, Aihong Li, Guozhen Liu, Shigui Li, Songnian Hu, Xiaofeng Cao, Jun Yu, Longping Yuan, Caiyan Chen, Lihuang Zhu
Author Information
  1. Dayong Li: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
  2. Zhiyuan Huang: State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China.
  3. Shuhui Song: BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; lhzhu@genetics.ac.cn cychen@isa.ac.cn lpyuan@hhrrc.ac.cn songshh@big.ac.cn xinyeyun@hhrrc.ac.cn.
  4. Yeyun Xin: State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China; lhzhu@genetics.ac.cn cychen@isa.ac.cn lpyuan@hhrrc.ac.cn songshh@big.ac.cn xinyeyun@hhrrc.ac.cn.
  5. Donghai Mao: Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China.
  6. Qiming Lv: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China.
  7. Ming Zhou: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
  8. Dongmei Tian: BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
  9. Mingfeng Tang: Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China.
  10. Qi Wu: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
  11. Xue Liu: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
  12. Tingting Chen: BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
  13. Xianwei Song: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
  14. Xiqin Fu: State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China.
  15. Bingran Zhao: State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China.
  16. Chengzhi Liang: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
  17. Aihong Li: Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou 225007, China.
  18. Guozhen Liu: College of Life Sciences, Hebei Agricultural University, Baoding 071001, China.
  19. Shigui Li: Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China.
  20. Songnian Hu: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
  21. Xiaofeng Cao: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
  22. Jun Yu: Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
  23. Longping Yuan: State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China; lhzhu@genetics.ac.cn cychen@isa.ac.cn lpyuan@hhrrc.ac.cn songshh@big.ac.cn xinyeyun@hhrrc.ac.cn.
  24. Caiyan Chen: Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; lhzhu@genetics.ac.cn cychen@isa.ac.cn lpyuan@hhrrc.ac.cn songshh@big.ac.cn xinyeyun@hhrrc.ac.cn.
  25. Lihuang Zhu: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China; lhzhu@genetics.ac.cn cychen@isa.ac.cn lpyuan@hhrrc.ac.cn songshh@big.ac.cn xinyeyun@hhrrc.ac.cn.
PMID: 27663737 DOI: 10.1073/pnas.1610115113

Abstract

Hybrid rice is the dominant form of rice planted in China, and its use has extended worldwide since the 1970s. It offers great yield advantages and has contributed greatly to the world's food security. However, the molecular mechanisms underlying heterosis have remained a mystery. In this study we integrated genetics and omics analyses to determine the candidate genes for yield heterosis in a model two-line rice hybrid system, Liang-you-pei 9 (LYP9) and its parents. Phenomics study revealed that the better parent heterosis (BPH) of yield in hybrid is not ascribed to BPH of all the yield components but is specific to the BPH of spikelet number per panicle (SPP) and paternal parent heterosis (PPH) of effective panicle number (EPN). Genetic analyses then identified multiple quantitative trait loci (QTLs) for these two components. Moreover, a number of differentially expressed genes and alleles in the hybrid were mapped by transcriptome profiling to the QTL regions as possible candidate genes. In parallel, a major QTL for yield heterosis, rice heterosis 8 (RH8), was found to be the DTH8/Ghd8/LHD1 gene. Based on the shared allelic heterozygosity of RH8 in many hybrid rice cultivars, a common mechanism for yield heterosis in the present commercial hybrid rice is proposed.

Keywords

QTL RH8 heterosis hybrid rice yield

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MeSH Term

Alleles
Chromosome Mapping
Gene Expression Profiling
Gene Expression Regulation, Plant
Genes, Plant
Genetic Linkage
Genome, Plant
Genomics
Genotype
Hybrid Vigor
Hybridization, Genetic
Oryza
Phenotype
Polymorphism, Single Nucleotide
Quantitative Trait Loci
Quantitative Trait, Heritable
Transcriptome
Journal Article Research Support, Non-U.S. Gov't

Links to CNCB-NGDC Resources

GSA: CRA000026 (CRA_26)
BioProject: PRJCA000131 (Rice Heterosis)

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