PMID- 27663737
OWN - NLM
STAT- MEDLINE
DCOM- 20180130
LR  - 20220317
IS  - 1091-6490 (Electronic)
IS  - 0027-8424 (Print)
IS  - 0027-8424 (Linking)
VI  - 113
IP  - 41
DP  - 2016 Oct 11
TI  - Integrated analysis of phenome, genome, and transcriptome of hybrid rice 
      uncovered multiple heterosis-related loci for yield increase.
PG  - E6026-E6035
AB  - 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.
FAU - Li, Dayong
AU  - Li D
AD  - State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental 
      Biology, Chinese Academy of Sciences, Beijing 100101, China.
FAU - Huang, Zhiyuan
AU  - Huang Z
AD  - State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 
      410125, China.
FAU - Song, Shuhui
AU  - Song S
AD  - 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.
FAU - Xin, Yeyun
AU  - Xin Y
AD  - 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.
FAU - Mao, Donghai
AU  - Mao D
AD  - Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of 
      Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China.
FAU - Lv, Qiming
AU  - Lv Q
AD  - 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.
FAU - Zhou, Ming
AU  - Zhou M
AD  - State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental 
      Biology, Chinese Academy of Sciences, Beijing 100101, China.
FAU - Tian, Dongmei
AU  - Tian D
AD  - BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, 
      Beijing 100101, China.
FAU - Tang, Mingfeng
AU  - Tang M
AD  - Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of 
      Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China.
FAU - Wu, Qi
AU  - Wu Q
AD  - State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental 
      Biology, Chinese Academy of Sciences, Beijing 100101, China.
FAU - Liu, Xue
AU  - Liu X
AD  - Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, 
      Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, 
      China.
FAU - Chen, Tingting
AU  - Chen T
AD  - BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, 
      Beijing 100101, China.
FAU - Song, Xianwei
AU  - Song X
AD  - State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental 
      Biology, Chinese Academy of Sciences, Beijing 100101, China.
FAU - Fu, Xiqin
AU  - Fu X
AD  - State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 
      410125, China.
FAU - Zhao, Bingran
AU  - Zhao B
AD  - State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 
      410125, China.
FAU - Liang, Chengzhi
AU  - Liang C
AD  - State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental 
      Biology, Chinese Academy of Sciences, Beijing 100101, China.
FAU - Li, Aihong
AU  - Li A
AD  - Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou 225007, 
      China.
FAU - Liu, Guozhen
AU  - Liu G
AD  - College of Life Sciences, Hebei Agricultural University, Baoding 071001, China.
FAU - Li, Shigui
AU  - Li S
AD  - Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China.
FAU - Hu, Songnian
AU  - Hu S
AD  - Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, 
      Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, 
      China.
FAU - Cao, Xiaofeng
AU  - Cao X
AD  - State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental 
      Biology, Chinese Academy of Sciences, Beijing 100101, China.
FAU - Yu, Jun
AU  - Yu J
AD  - Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, 
      Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, 
      China.
FAU - Yuan, Longping
AU  - Yuan L
AD  - 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.
FAU - Chen, Caiyan
AU  - Chen C
AD  - 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.
FAU - Zhu, Lihuang
AU  - Zhu L
AD  - 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.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20160923
PL  - United States
TA  - Proc Natl Acad Sci U S A
JT  - Proceedings of the National Academy of Sciences of the United States of America
JID - 7505876
SB  - IM
MH  - Alleles
MH  - Chromosome Mapping
MH  - Gene Expression Profiling
MH  - Gene Expression Regulation, Plant
MH  - Genes, Plant
MH  - Genetic Linkage
MH  - *Genome, Plant
MH  - Genomics/methods
MH  - Genotype
MH  - Hybrid Vigor/*genetics
MH  - *Hybridization, Genetic
MH  - Oryza/*genetics/*metabolism
MH  - *Phenotype
MH  - Polymorphism, Single Nucleotide
MH  - *Quantitative Trait Loci
MH  - Quantitative Trait, Heritable
MH  - *Transcriptome
PMC - PMC5068331
OTO - NOTNLM
OT  - QTL
OT  - RH8
OT  - heterosis
OT  - hybrid rice
OT  - yield
COIS- The authors declare no conflict of interest.
EDAT- 2016/09/25 06:00
MHDA- 2018/01/31 06:00
PMCR- 2016/09/23
CRDT- 2016/09/25 06:00
PHST- 2016/09/25 06:00 [pubmed]
PHST- 2018/01/31 06:00 [medline]
PHST- 2016/09/25 06:00 [entrez]
PHST- 2016/09/23 00:00 [pmc-release]
AID - 1610115113 [pii]
AID - 201610115 [pii]
AID - 10.1073/pnas.1610115113 [doi]
PST - ppublish
SO  - Proc Natl Acad Sci U S A. 2016 Oct 11;113(41):E6026-E6035. doi: 
      10.1073/pnas.1610115113. Epub 2016 Sep 23.