Global Survey of Alternative Splicing in Rice by Direct RNA Sequencing During Reproductive Development: Landscape and Genetic Regulation

Haoxuan Li, Aixuan Li, Wei Shen, Nenghui Ye , Guanqun Wang*, Jianhua Zhang*

*Corresponding author for this work

Research output: Contribution to journalJournal articlepeer-review

11 Citations (Scopus)


Alternative splicing is a widespread phenomenon, which generates multiple isoforms of the gene product. Reproductive development is the key process for crop production. Although numerous forms of alternative splicing have been identified in model plants, large-scale study of alternative splicing dynamics during reproductive development in rice has not been conducted. Here, we investigated alternative splicing of reproductive development of young panicles (YP), unfertilized florets (UF) and fertilized florets (F) in rice using direct RNA sequencing, small RNA sequencing, and degradome sequencing. We identified a total of 35,317 alternative splicing (AS) events, among which 67.2% splicing events were identified as novel alternative splicing events. Intron retention (IR) was the most abundant alternative splicing subtype. Splicing factors that differentially expressed and alternatively spliced could result in global alternative splicing. Global analysis of miRNAs-targets prediction revealed that alternative spliced transcripts affected miRNAs’ targets during development. Degradome sequencing detected only 6.8% of the differentially alternative splicing transcripts, suggesting a productive transcripts generation during development. In addition, alternative splicing isoforms of Co-like, a transcription factor, interacted with Casein kinase 1-like protein HD1 (CKI) examined in luciferase assay, which could modulate normal male-floral organs development and flowering time. These results reveal that alternative splicing is intensely associated with developmental stages, and a high complexity of gene regulation.
Original languageEnglish
Article number75
Issue number1
Early online date12 Aug 2021
Publication statusPublished - Dec 2021

User-Defined Keywords

  • Oryza sativa
  • Direct RNA sequencing
  • Alternative splicing
  • Small RNA targets
  • Transcription factors
  • Reproductive development


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