title: A genome-wide transcription analysis reveals a close correlation of promoter INDEL polymorphism and heterotic gene expression in rice hybrids.
abstract: Heterosis, or hybrid vigor, refers to the phenomenon in which hybrid progeny of two inbred varieties exhibits enhanced growth or agronomic performance. Although a century-long history of research has generated several hypotheses regarding the genetic basis of heterosis, the molecular mechanisms underlying heterosis and heterotic gene expression remain elusive. Here, we report a genome-wide gene expression analysis of two heterotic crosses in rice, taking advantage of its fully sequenced genomes. Approximately 7-9% of the genes were differentially expressed in the seedling shoots from two sets of heterotic crosses, including many transcription factor genes, and exhibited multiple modes of gene action. Comparison of the putative promoter regions of the ortholog genes between inbred parents revealed extensive sequence variation, particularly small insertions/deletions (INDELs), many of which result in the formation/disruption of putative cis-regulatory elements. Together, these results suggest that a combinatorial interplay between expression of transcription factors and polymorphic promoter cis-regulatory elements in the hybrids is one plausible molecular mechanism underlying heterotic gene action and thus heterosis in rice.
authors.affiliation: National Institute of Biological Sciences, Zhongguancun Life Science Park, Beijing 102206, China.
authors.forename: Hui-Yong
authors.initials: HY
authors.lastname: Zhang
authors.forename: Hang
authors.initials: H
authors.lastname: He
authors.forename: Liang-Bi
authors.initials: LB
authors.lastname: Chen
authors.forename: Lei
authors.initials: L
authors.lastname: Li
authors.forename: Man-Zhong
authors.initials: MZ
authors.lastname: Liang
authors.forename: Xiang-Feng
authors.initials: XF
authors.lastname: Wang
authors.forename: Xi-Gang
authors.initials: XG
authors.lastname: Liu
authors.forename: Guang-Ming
authors.initials: GM
authors.lastname: He
authors.forename: Run-Sheng
authors.initials: RS
authors.lastname: Chen
authors.forename: Li-Geng
authors.initials: LG
authors.lastname: Ma
authors.forename: Xing Wang
authors.initials: XW
authors.lastname: Deng
mesh_terms: D001483:Base Sequence; D003433:Crosses, Genetic; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018745:Genome, Plant / Q000235:genetics*; D006823:Hybrid Vigor / Q000235:genetics*; D006824:Hybridization, Genetic; D054643:INDEL Mutation / Q000235:genetics*; D053858:Metabolic Networks and Pathways / Q000235:genetics; D008957:Models, Genetic; D008969:Molecular Sequence Data; D012275:Oryza / Q000235:genetics* / Q000378:metabolism; D011110:Polymorphism, Genetic; D011401:Promoter Regions, Genetic / Q000235:genetics*