Global Patterns of Stage-Specific Alternative Polyadenylation in Rice Tillering Revealed by Nanopore Long Read Sequencing and Proteomics
Received date: 2025-12-04
Accepted date: 2026-03-06
Online published: 2026-06-02
Tiller number is a crucial agronomic trait that directly influences the grain yield per unit area of rice. Alternative polyadenylation (APA), an essential post-transcriptional regulatory mechanism, plays a significant role in rice growth and development by generating transcripts with varying 3ʹ untranslated region (3ʹUTR) lengths. However, the specific role of APA in rice tillering remains poorly understood. We employed nanopore cDNA sequencing and tandem mass tag proteomics to analyze tiller axillary buds at different developmental stages in rice. Our findings revealed that genes at the early stages of tillering (effective tillering) tend to utilize longer transcripts, whereas those at the later stages (ineffective tillering) favor shorter transcripts. APA-related genes at both the effective and ineffective tillering stages are enriched in known rice tillering-associated pathways, such as the terpenoid backbone biosynthesis pathway and the carotenoid biosynthesis pathway. Additionally, APA-related genes at the ineffective tillering stage are further enriched in pathways such as leaf and organ senescence. The results demonstrate that APA-mediated gene length variation regulates rice tillering in a spatiotemporally specific pattern, and APA further impacts the protein abundance of genes involved in tillering. Genes that utilize the distal AAUAAA signal and produce longer transcripts exhibit stronger expression than those using the proximal signal, while genes using the proximal AAUAAA signal and generating shorter transcripts show stronger expression than those using the distal signal. This study clarifies the regulatory patterns of APA in rice tillering, laying a molecular foundation for the potential breeding of rice with ideal plant architecture.
Li Xinyi, Huang Junying, Zhou Dahu, Cai Yicong, Chen Xiaorong, Hu Lifang, Ouyang Linjuan, Fu Junru, Li Qingshun, He Haohua, Fu Haihui . Global Patterns of Stage-Specific Alternative Polyadenylation in Rice Tillering Revealed by Nanopore Long Read Sequencing and Proteomics[J]. Rice Science, 2026 , 33(3) : 392 -410 . DOI: 10.1016/j.rsci.2026.03.002
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