As one of the most important vegetables globally, peppers have garnered significant attention from breeders due to their diverse agronomic traits, including plant type, leaf shape, and maturity. Understanding the genetic mechanisms underlying these traits is crucial for systematic advancements in sweet pepper breeding. In this study, leveraging the PepperSNP50K liquid breeding chip, we conducted a comprehensive analysis of horticultural traits and genetic diversity using sweet pepper germplasm samples. Initially, the sweet pepper populations were analyzed using SNP-based liquid chip technology. Subsequently, phenotypic surveys were performed on 217 sweet pepper samples, and the collected phenotypic data were integrated with SNP markers to conduct a genome-wide association study (GWAS) of key agronomic traits. Among the 25 horticultural traits evaluated, 11 exhibited significant associations with 54 SNP polymerization regions and 193 candidate genes. These findings provide a robust foundation for the utilization of sweet pepper germplasm resources and the development of new, improved varieties. Furthermore, in this study, we identified Caz06g05770 (Lycopene beta-cyclase) as a candidate gene responsible for the color of mature ripe fruits. This research not only enhances our understanding of the genetic basis of sweet pepper traits but also offers a practical roadmap for advancing breeding programs and boosting agricultural productivity. By bridging the gap between genetic research and practical breeding applications, this study paves the way for the development of high-yield, high-quality sweet pepper varieties tailored to meet the growing demands of global agriculture.

Background: Pepper (Capsicum annuum L.) is highly susceptible to various abiotic stresses during their growth and development, leading to severe reductions in both yield and quality. β-Glucosidase (BGLU) is widely involved in plant growth and development, as well as in the response to abiotic stress. Methods: We performed a genome-wide identification of pepper BGLU (CaBGLU) genes. Phylogenetic analysis included BGLU proteins from Arabidopsis, tomato, and pepper. Gene structures, conserved motifs, and promoter cis-elements were analyzed bioinformatically. Synteny within the pepper genome was assessed. Protein-protein interaction potential was predicted. Gene expression patterns were analyzed across tissues and under abiotic stresses using transcriptomic data and qRT-PCR. Subcellular localization of a key candidate protein CaBGLU21 was confirmed experimentally. Results: We identified 32 CaBGLU genes unevenly distributed across eight chromosomes. Phylogenetic classification of 99 BGLU proteins into 12 subfamilies revealed an uneven distribution of CaBGLUs across six subfamilies. Proteins within subfamilies shared conserved motifs and gene structures. CaBGLU promoters harbored abundant light-, hormone- (MeJA, ABA, SA, GA), and stress-responsive elements (including low temperature). A duplicated gene pair (CaBGLU19/CaBGLU24) was identified. 27 CaBGLU proteins showed potential for interactions. Expression analysis indicated CaBGLU5 and CaBGLU30 were mesophyll-specific, while CaBGLU21 was constitutively high in non-leaf tissues. CaBGLU21 was consistently upregulated by cold, heat, and ABA. Subcellular localization confirmed CaBGLU21 resides in the tonoplast. Conclusions: This comprehensive analysis characterizes the pepper BGLU gene family. CaBGLU21, exhibiting constitutive expression in non-leaf tissues, strong upregulation under multiple stresses, and tonoplast localization, emerges as a prime candidate gene for further investigation into abiotic stress tolerance mechanisms in pepper. The findings provide a foundation for future functional studies and stress-resistant pepper breeding.

The cation/H⁺ exchanger (CHX) gene family plays a vital role in maintaining K⁺/Na⁺ homeostasis in plants, yet its functional characterization in pepper (Capsicum annuum L.) remains largely unexplored. To elucidate the potential roles of CHX genes in stress adaptation and development in pepper, a genome-wide identification and systematic analysis of this gene family was performed. Using a combination of Hidden Markov Model (HMM) searches, phylogenetic reconstruction, conserved motif and promoter analysis, and expression profiling across tissues and under multiple stress conditions, a total of 23 CaCHX genes were identified, which are unevenly distributed across 10 chromosomes and classified into 6 phylogenetic subfamilies. Expression profiling revealed that most CaCHX genes were highly expressed in flowers, suggesting their potential involvement in reproductive development, while only CaCHX12 and CaCHX17 were detected in leaves. Under treatments such as abscisic acid (ABA), gibberellic acid (GA), NaCl, and jasmonic acid (JA), CaCHX1, CaCHX20, and CaCHX23 exhibited distinct temporal expression patterns, suggesting their involvement in hormone-mediated stress responses. This study provides the first comprehensive genomic and transcriptomic overview of the CHX family in pepper, offering novel insights into its regulatory roles in flower development and stress tolerance and, thus supplying valuable genetic resources for molecular breeding aimed at enhancing pepper resilience.

The ubiquitin-specific protease (UBP) family constitutes the largest group within the deubiquitinating enzymes (DUBs) and plays a crucial role in regulating the cell cycle, growth, and developmental processes in living organisms. By utilizing genomic and transcriptomic databases, we employed bioinformatics tools to identify UBP family members within pepper genomes and to analyze the expression profiles of CaUBP genes under various abiotic stresses, as well as in different tissues and organs. Our findings revealed the presence of 40 CaUBPs in peppers, exhibiting significant variation in their physicochemical properties. Subcellular localization studies indicated that all CaUBPs are localized in the nucleus. Phylogenetic analysis categorized the 40 CaUBPs into 11 distinct subfamilies (G1–G11), with the largest subfamily comprising seven members. Members within the same subfamily displayed similar domain and motif structures. The promoter regions of CaUBP genes were found to be enriched with elements responsive to light, stress, and hormones. Syntenic analysis revealed that 12 CaUBPs were mapped to the Arabidopsis thaliana genome, suggesting potential functional conservation. Additionally, tandem duplications were observed in the alignment of two sets of genes within the pepper genome. CaUBPs were implicated in the stress response and organ growth, with CaUBP17/34/35 showing significant changes in expression under heat stress. While most genes were not expressed in leaves, the expression of several genes (CaUBP3/17/27/32/35/38) in flowers was significantly altered. This study establishes a foundation for further exploration of the roles of CaUBPs in pepper growth, development, and stress response mechanisms.