Pepper is a major horticultural crop cultivated extensively worldwide. Among its various agronomic characteristics, fruit length is a key trait influencing both yield and visual quality. Despite its importance, the genetic mechanisms regulating fruit length in Capsicum remain insufficiently characterized, hindering the development of high-yielding and aesthetically desirable cultivars. In this study, fruits at three developmental stages (0, 15, and 30 days after flowering) were sampled from the long-fruit mutant fe1 and its wild-type progenitor LY0. Phenotypic characterization and transcriptomic sequencing were conducted to identify candidate genes associated with fruit length regulation. Morphological analysis revealed that the most pronounced difference in fruit length occurred at 30 days after flowering. RNA-seq analysis identified 41,194 genes, including 13,512 differentially expressed genes (DEGs). Enrichment analysis highlighted key pathways, such as plant–pathogen interaction, plant hormone signal transduction, and the MAPK signaling pathway. DEG classification suggested that several downregulated genes related to early auxin responses may contribute to the regulation of fruit elongation. Notably, the gibberellin signaling gene SCL13 (Caz12g26660), transcription factors MYB48 (Caz11g07190) and ERF3-like (Caz10g00810), and the cell-wall-modifying gene XTH15-like (Caz07g19100) showed significantly elevated expression in 30-day-old fruits of fe1. Weighted gene co-expression network analysis (WGCNA) further revealed a strong positive correlation among these genes. Quantitative RT-PCR analysis of eight selected DEGs confirmed the RNA-seq results. This study provides a foundational framework for dissecting the molecular regulatory network of fruit length in Capsicum, offering valuable insights for breeding programs.

The germination rate of pepper (Capsicum annuum L.) seeds is a key indicator of their vitality, which is complexly regulated by genetic and environmental factors. This study aims to elucidate the physiological and molecular mechanisms underlying the differences in germination rates among different pepper germplasm resources and identify the key genes regulating this trait. Three representative pepper materials (‘22HL6’, ‘22HL14’, ‘22HL2’) with significantly different germination rates were selected for this study. Key physiological and biochemical parameters during their germination process were systematically evaluated, including germination rate, vigor index, water absorption characteristics, amylase activity, antioxidant enzyme activity, and soluble sugar and protein content. Based on this, candidate genes related to germination rate were screened through transcriptome sequencing, and core candidate genes were preliminarily functionally validated using the Arabidopsis thaliana heterologous overexpression system. Materials with fast germination rates (‘22HL6’, ‘22HL14’) exhibited higher water absorption efficiency, amylase activity, antioxidant protection (such as lower MDA content and higher POD activity), and more active material metabolism (soluble sugar and protein) during the critical 72-h period. Transcriptome analysis successfully identified seven candidate genes closely related to germination rate. Among them, gene Capann_59V1aChr03g048850 had extremely high expression levels in fast-germinating materials but was almost not expressed in slow-germinating materials, and was identified as a core candidate gene. Heterologous overexpression of Capann_59V1aChr03g048850 in A. thaliana significantly promoted seed germination, with transgenic lines exhibiting earlier germination initiation, more developed taproot and lateral root systems, larger rosette diameter, and earlier bolting and flowering compared to wild-type plants. This study reveals the basis for the differences in germination rates of pepper seeds from the physiological and biochemical to molecular mechanism levels, and for the first time links the function of Capann_59V1aChr03g048850 gene to promoting seed germination and early seedling development. This gene provides valuable genetic resources for improving the germination uniformity and seedling vitality of pepper and even other crops through molecular breeding in the future.