Integrated analysis of phenome, genome, and transcriptome of hybrid rice uncovered multiple heterosis-related loci for yield increase.
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.
State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
Dayong
D
Li
State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China.
Zhiyuan
Z
Huang
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.
Shuhui
S
Song
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.
Yeyun
Y
Xin
Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China.
Donghai
D
Mao
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.
Qiming
Q
Lv
State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
Ming
M
Zhou
BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
Dongmei
D
Tian
Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China.
Mingfeng
M
Tang
State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
Qi
Q
Wu
Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
Xue
X
Liu
BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
Tingting
T
Chen
State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
Xianwei
X
Song
State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China.
Xiqin
X
Fu
State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China.
Bingran
B
Zhao
State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
Chengzhi
C
Liang
Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou 225007, China.
Aihong
A
Li
College of Life Sciences, Hebei Agricultural University, Baoding 071001, China.
Guozhen
G
Liu
Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China.
Shigui
S
Li
Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
Songnian
S
Hu
State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
Xiaofeng
X
Cao
Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
Jun
J
Yu
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.
Longping
L
Yuan
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.
Caiyan
C
Chen
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.
Lihuang
L
Zhu
D000483:Alleles; D002874:Chromosome Mapping; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D008040:Genetic Linkage; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D005838:Genotype; D006823:Hybrid Vigor / Q000235:genetics*; D006824:Hybridization, Genetic; D012275:Oryza / Q000235:genetics* / Q000378:metabolism*; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable; D059467:Transcriptome
QTL; RH8; heterosis; hybrid rice; yield
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