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

Abstract

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.

MAEL gene contributes to bovine testicular development through the m5C-mediated splicing

“…The analysis of AS events contributes to a better understanding of gene functions in the developmental process of animal species. 28 , 62 , 63 In the current study, the most abundant splicing events within the hub genes were the SE type, accounting for 23.63% of total AS events. Chacko and Ranganathan 64 also found that the majority of SE events were present in the bovine genome.…”

“… 26 DRS plays a vital role in dissecting the genotype-phenotype relationships that could reflect all aspects of testicular growth and development. To date, DRS technology has been adopted in identifying full-length splice isoforms, 27 exploring post-transcriptional events, 28 characterizing poly(A) tail lengths of transcripts, 29 improving the existing genome assembly, 30 and detecting RNA modifications. 31 Nevertheless, the DRS technology adopted for clarifying the transcriptome complexity has still not been widely applied in farm animal species, which delays the characterization and application of true transcriptomics in livestock industry.…”

Nuclear OsFKBP20‐1b maintains SR34 stability and promotes the splicing of retained introns upon ABA exposure in rice

“…We observed all four AS patterns: IR, ES, Alt 5′ss, and Alt 3′ss (Reddy et al ., 2013). This finding is consistent with the results of previous AS studies conducted in rice (Wei et al ., 2017; H. Li et al ., 2021). Intron retention events were more prevalent, closely followed by Alt 5′ss and Alt 3′ss, with a small percentage of transcripts affected by ES.…”

OsGRF4AA compromises heat tolerance of developing pollen grains in rice

“…In fact, some clues can be obtained from recent studies. A great number of genes encoding splicing factors, miRNAs, long noncoding RNAs (lncRNAs), and transcription factors were found to undergo AS in young panicles and florets of rice (Li et al, 2021). The same genes from different rice genotypes carried out differential AS regulations in response to salt stress stimulation (Jian et al, 2022).…”