Alternative polyadenylation and metabolic profiling in young panicle development of hybrid rice and its parents

Alternative polyadenylation (APA) is a widespread post-transcriptional regulatory mechanism in eukaryotes that modulates gene expression by generating transcript variants. The development of young panicles in rice is a critical stage that determines grain number and weight. However, the regulatory mechanisms and inheritance patterns of APA during this process remain poorly understood. In this study, full-length isoform sequencing (Iso-seq) and metabolome were employed to investigate APA dynamics in the young panicle of hybrid rice variety Wufengyou T025 and in parent lines, Wufeng B and Changhui T025. This analysis revealed that approximately 80% of genes possessed two or more polyadenylation (pA) sites. These APA genes were predominantly enriched in the pathways associated with rice spikelet development, including response to external photoperiod changes, energy production and transportation, protein signal exchange, and amino acid metabolism. Notably, transcripts with a shortened 3'-untranslated region (3'UTR) exhibited elevated expression levels of their corresponding genes, suggesting that APA plays an important role in modulating gene expression. Furthermore, the variable 3'UTR of the 25% differentially expressed APA genes contained numerous miRNA binding sites, including osa-miR1848 and osa-miR5075, which are known to influence spikelet development. In the offspring, the expression levels of core APA factors during young panicle development were generally downregulated compared to the parental lines. Additionally, metabolomic analysis identified 209 and 164 differentially abundant metabolites in the offspring relative to Wufeng B and Changhui T025, respectively. Intriguingly, some of the enriched metabolic pathways overlapped with those of differentially expressed APA genes, implying that APA may influence small-molecule metabolites in pathways related to spike development. Collectively, these findings are valuable for understanding the regulation of APA and its genetic basis in young panicle development, offering new insights into the molecular mechanisms underlying this critical development stage.