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

doi:10.1073/pnas.1610115113

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

Proc Natl Acad Sci U S A. 2016 Oct 11;113(41):E6026-E6035. doi: 10.1073/pnas.1610115113. Epub 2016 Sep 23.

Authors

Dayong Li¹, Zhiyuan Huang², Shuhui Song³, Yeyun Xin⁴, Donghai Mao⁵, Qiming Lv⁶, Ming Zhou¹, Dongmei Tian⁷, Mingfeng Tang⁵, Qi Wu¹, Xue Liu⁸, Tingting Chen⁷, Xianwei Song¹, Xiqin Fu², Bingran Zhao², Chengzhi Liang¹, Aihong Li⁹, Guozhen Liu¹⁰, Shigui Li¹¹, Songnian Hu⁸, Xiaofeng Cao¹, Jun Yu⁸, Longping Yuan⁴, Caiyan Chen¹², Lihuang Zhu¹³

Affiliations

¹ State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
² State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China.
³ 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 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 Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China.
⁶ 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 BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
⁸ Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
⁹ Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou 225007, China.
¹⁰ College of Life Sciences, Hebei Agricultural University, Baoding 071001, China.
¹¹ Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China.
¹² 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.
¹³ 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.

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Alleles
Chromosome Mapping
Gene Expression Profiling
Gene Expression Regulation, Plant
Genes, Plant
Genetic Linkage
Genome, Plant*
Genomics / methods
Genotype
Hybrid Vigor / genetics*
Hybridization, Genetic*
Oryza / genetics*
Oryza / metabolism*
Phenotype*
Polymorphism, Single Nucleotide
Quantitative Trait Loci*
Quantitative Trait, Heritable
Transcriptome*