Amomum villosum Lour., a perennial medicinal plant in the Zingiber genus, usually requires approximately 3–4 years of vegetative growth from seed germination to first fruiting, resulting in high initial investment costs and a prolonged revenue cycle, which pose significant challenges to the industry’s sustainable development. Our research team observed a distinct premature fruiting phenomenon in A. villosum. We investigated the regulatory mechanisms underlying premature fruiting in A. villosum by identifying the key differentially expressed genes (DEGs) and metabolic pathways governing the premature fruiting (Precocious) and typical plants (CK) of the ‘Yunsha No.8’ cultivar. Transcriptomic sequencing (RNA-seq) and bioinformatic analyses were performed using the DNBSEQ^TM platform. The sequencing generated 29.0 gigabases (Gb) of clean data, and 115,965 unigenes were identified, with an average length of 1368 bp. Based on the sequencing results, 1545 DEGs were identified. Gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were annotated for these DEGs. This study identifies phytohormone signaling, carbohydrate and lipid metabolism, and polysaccharide degradation as critical pathways controlling premature fruiting in A. villosum. Six randomly selected DEGs were validated using real-time fluorescence quantitative polymerase chain reaction (RT-qPCR), and the results corroborated the transcriptome data, confirming their reliability. This study lays the foundation for the elucidation of the molecular mechanisms and metabolic pathways driving premature fruiting in A. villosum.

As a perennial medicinal plant in the Zingiber genus, Amomum villosum Lour. faces agricultural challenges due to its prolonged vegetative and reproductive growth phases, which hinder efficient pollination and delay fruiting. To address this limitation, the present study aimed to identify the FD gene involved in regulating flowering in A. villosum to provide a basis for research on the molecular mechanisms of early fruiting cultivars. Based on the differentially expressed gene AvFD1 obtained from the transcriptome database of early fruiting plants and controls, specific primers were designed for PCR to clone the full-length sequence of AvFD1. The characteristics of the cloned AvFD1 gene were analyzed using online bioinformatics software. The expression profiles of AvFD1 in various tissues and in 1- and 2-year bearing A. villosum varieties were investigated by quantitative real-time PCR. This study successfully cloned the FD1 gene sequence of A. villosum, marking the first reported characterization of this gene in the species. Tissue-specific expression analysis revealed significantly elevated AvFD1 expression levels in stolon tips and flower buds compared to tender leaves, suggesting its potential role as a positive regulator of flowering initiation. The obtained sequence establishes essential molecular data for subsequent functional validation of AvFD1 in A. villosum.

Precocious-fruiting Amomum villosum Lour. is characterized by early fruit set, rapid yield formation, and shortened economic return cycles, indicating strong cultivation potential. However, the molecular mechanisms underlying its flowering transition remain unclear. To elucidate the flowering mechanism of A. villosum, we used the Illumina NovaSeq X Plus platform to compare gene expression profiles in three tissues (Rhizomes, R; Stems, S; Leaves, L) during the vegetative stage and three tissues (Rhizomes and Inflorescences, R&I; Stems, S; Leaves, L) during the flowering stage of individual plants: VS-R vs. FS-R&I, VS-S vs. FS-S, and VS-L vs. FS-L. We obtained 52.5 Gb clean data and 789 million reads, and identified 2963 novel genes. The 3061 differentially expressed genes (DEGs, FDR ≤ 0.05 and |log2FC| ≥ 1) identified in the three comparison groups included six overlapping genes. The DEGs were enriched primarily in GO terms related to cellular process, metabolic process, binding, catalytic activity, and cellular anatomical entity, as well as multiple terms associated with development and reproduction. KEGG enrichment analysis revealed enrichment primarily in metabolic pathways, including global and overview maps, energy metabolism, and carbohydrate metabolism. Moreover, the most significantly enriched core pathways included metabolic pathways, photosynthesis, and carbon assimilation. Among all alternative splicing (AS) events, skipped exons (SEs) accounted for the largest proportion (59.5%), followed by retained introns (RI, 19.4%), alternative 3′ splice sites (A3SS, 10.7%), alternative 5′ splice sites (A5SS, 6.8%), and mutually exclusive exons (MXE, 3.6%). A preliminary set of 43 key DEGs was predicted, displaying spatiotemporal expression specificity and strong interactions among certain genes. Nine genes were further selected for RT-qPCR validation to confirm the reliability of the RNA-seq results. This study established a foundational framework for elucidating the flowering mechanism of precocious-fruiting A. villosum.