title: Small RNAs as important regulators for the hybrid vigour of super-hybrid rice.
abstract: Heterosis is an important biological phenomenon; however, the role of small RNA (sRNA) in heterosis of hybrid rice remains poorly described. Here, we performed sRNA profiling of F1 super-hybrid rice LYP9 and its parents using high-throughput sequencing technology, and identified 355 distinct mature microRNAs and trans-acting small interfering RNAs, 69 of which were differentially expressed sRNAs (DES) between the hybrid and the mid-parental value. Among these, 34 DES were predicted to target 176 transcripts, of which 112 encoded 94 transcription factors. Further analysis showed that 67.6% of DES expression levels were negatively correlated with their target mRNAs either in flag leaves or panicles. The target genes of DES were significantly enriched in some important biological processes, including the auxin signalling pathway, in which existed a regulatory network mediated by DES and their targets, closely associated with plant growth and development. Overall, 20.8% of DES and their target genes were significantly enriched in quantitative trait loci of small intervals related to important rice agronomic traits including growth vigour, grain yield, and plant architecture, suggesting that the interaction between sRNAs and their targets contributes to the heterotic phenotypes of hybrid rice. Our findings revealed that sRNAs might play important roles in hybrid vigour of super-hybrid rice by regulating their target genes, especially in controlling the auxin signalling pathway. The above finding provides a novel insight into the molecular mechanism of heterosis.
authors.affiliation: State Key Laboratory of Plant Genomics and National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, PR China.
authors.forename: Lei
authors.initials: L
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Plant Genomics and National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, PR China.
authors.forename: Yonggang
authors.initials: Y
authors.lastname: Peng
authors.affiliation: State Key Laboratory of Plant Genomics and National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, PR China.
authors.forename: Xiaoli
authors.initials: X
authors.lastname: Wei
authors.affiliation: State Key Laboratory of Plant Genomics and National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, PR China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Dai
authors.affiliation: State Key Laboratory of Plant Genomics and National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, PR China.
authors.forename: Dawei
authors.initials: D
authors.lastname: Yuan
authors.affiliation: State Key Laboratory of Plant Genomics and National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, PR China.
authors.forename: Yufei
authors.initials: Y
authors.lastname: Lu
authors.affiliation: State Key Laboratory of Plant Genomics and National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, PR China.
authors.forename: Yangyang
authors.initials: Y
authors.lastname: Pan
authors.affiliation: State Key Laboratory of Plant Genomics and National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, PR China zzhu@genetics.ac.cn.
authors.forename: Zhen
authors.initials: Z
authors.lastname: Zhu
mesh_terms: D002874:Chromosome Mapping; D002523:Edible Grain / Q000235:genetics; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D006823:Hybrid Vigor / Q000235:genetics; D007210:Indoleacetic Acids / Q000378:metabolism; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics*; D012275:Oryza / Q000235:genetics*; D010641:Phenotype; D018515:Plant Leaves / Q000235:genetics; D040641:Quantitative Trait Loci / Q000235:genetics; D058727:RNA, Small Untranslated / Q000737:chemistry / Q000235:genetics*; D015398:Signal Transduction
chemical_list: D007210:Indoleacetic Acids; D035683:MicroRNAs; D058727:RNA, Small Untranslated
keywords: Auxin signalling pathway; QTL mapping; differentially expressed gene; heterosis; rice; small RNA; transcriptional profile.