title: Global RNA sequencing reveals that genotype-dependent allele-specific expression contributes to differential expression in rice F1 hybrids.
abstract: BACKGROUND
  Extensive studies on heterosis in plants using transcriptome analysis have identified differentially expressed genes (DEGs) in F1 hybrids. However, it is not clear why yield in heterozygotes is superior to that of the homozygous parents or how DEGs are produced. Global allele-specific expression analysis in hybrid rice has the potential to answer these questions.
  
  
  RESULTS
  We report a genome-wide allele-specific expression analysis using RNA-sequencing technology of 3,637-3,824 genes from three rice F1 hybrids. Of the expressed genes, 3.7% exhibited an unexpected type of monoallelic expression and 23.8% showed preferential allelic expression that was genotype-dependent in reciprocal crosses. Those genes exhibiting allele-specific expression comprised 42.4% of the genes differentially expressed between F1 hybrids and their parents. Allele-specific expression accounted for 79.8% of the genes displaying more than a 10-fold expression level difference between an F1 and its parents, and almost all (97.3%) of the genes expressed in F1, but non-expressed in one parent. Significant allelic complementary effects were detected in the F1 hybrids of rice.
  
  
  CONCLUSIONS
  Analysis of the allelic expression profiles of genes at the critical stage for highest biomass production from the leaves of three different rice F1 hybrids identified genotype-dependent allele-specific expression genes. A cis-regulatory mechanism was identified that contributes to allele-specific expression, leading to differential gene expression and allelic complementary effects in F1 hybrids.
authors.forename: Gaoyuan
authors.initials: G
authors.lastname: Song
authors.forename: Zhibin
authors.initials: Z
authors.lastname: Guo
authors.forename: Zhenwei
authors.initials: Z
authors.lastname: Liu
authors.forename: Qin
authors.initials: Q
authors.lastname: Cheng
authors.forename: Xuefeng
authors.initials: X
authors.lastname: Qu
authors.forename: Rong
authors.initials: R
authors.lastname: Chen
authors.forename: Daiming
authors.initials: D
authors.lastname: Jiang
authors.forename: Chuan
authors.initials: C
authors.lastname: Liu
authors.forename: Wei
authors.initials: W
authors.lastname: Wang
authors.forename: Yunfang
authors.initials: Y
authors.lastname: Sun
authors.forename: Liping
authors.initials: L
authors.lastname: Zhang
authors.forename: Yingguo
authors.initials: Y
authors.lastname: Zhu
authors.affiliation: State Key Laboratory of Hybrid Rice and College of Life Sciences, Wuhan University, Luojia Hill, Wuhan, Hubei Province 430072, China. dyang@whu.edu.cn.
authors.forename: Daichang
authors.initials: D
authors.lastname: Yang
mesh_terms: D000483:Alleles; D018506:Gene Expression Regulation, Plant / Q000235:genetics*; D005838:Genotype; D006824:Hybridization, Genetic / Q000235:genetics; D012275:Oryza / Q000235:genetics*; D017423:Sequence Analysis, RNA