Transcriptomics

Dataset Information

297

Transcription profiling by high throughput sequencing of flag leaves and panicles of LYP9 hybrid rice and its parental lines


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. We constructed six sRNA sequencing libraries and six mRNA sequencing libraries of flag leaves and panicles of the super-hybrid rice Liangyou-pei9 (LYP9) combination at the grain-filling stage. The above hybrid rice combination includes F1 hybrid LYP9 and its parental lines including the male-sterile line Peiai64s (PA64s) and the restorer line 93-11.

ORGANISM(S): Oryza sativa  

SUBMITTER: Dawei Yuan   Yangyang Pan  Yufei Lu  Yonggang Peng  Zhen Zhu  Lei Zhang  Yan Dai  Xiaoli Wei 

PROVIDER: E-GEOD-51468 | ArrayExpress | 2014-08-17

SECONDARY ACCESSION(S): GSE51468SRP031623PRJNA223270

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Small RNAs as important regulators for the hybrid vigour of super-hybrid rice.

Zhang Lei L   Peng Yonggang Y   Wei Xiaoli X   Dai Yan Y   Yuan Dawei D   Lu Yufei Y   Pan Yangyang Y   Zhu Zhen Z  

Journal of experimental botany 20140816 20


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  ...[more]

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