Light quality and intensity can have a significant impact on plant health and crop productivity. Chlorophylls and carotenoids are classes of plant pigments that are responsible for harvesting light energy and protecting plants from the damaging effects of intense light. Our understanding of the role played by plant pigments in light sensitivity has been aided by light-sensitive mutants that change colors upon exposure to light of variable intensity. In this study, we conducted transcriptomic, metabolomic, and hormone analyses on a novel yellowing mutant of pepper (yl1) to shed light on the molecular mechanism that regulates the transition from green to yellow leaves in this mutant upon exposure to high-intensity light. Our results revealed greater accumulation of the carotenoid precursor phytoene and the carotenoids phytofluene, antheraxanthin, and zeaxanthin in yl1 compared with wild-type plants under high light intensity. A transcriptomic analysis confirmed that enzymes involved in zeaxanthin and antheraxanthin biosynthesis were upregulated in yl1 upon exposure to high-intensity light. We also identified a single bHLH transcription factor, bHLH71-like, that was differentially expressed and positively correlated with light intensity in yl1. Silencing of bHLH71-like in pepper plants suppressed the yellowing phenotype and led to reduced accumulation of zeaxanthin and antheraxanthin. We propose that the yellow phenotype of yl1 induced by high light intensity could be caused by an increase in yellow carotenoid pigments, concurrent with a decrease in chlorophyll accumulation. Our results also suggest that bHLH71-like functions as a positive regulator of carotenoid biosynthesis in pepper.

Cytoplasmic male sterility (CMS) is pivotal in plant breeding and widely employed in various crop hybrids, including pepper. However, the functional validation of the restorer of fertility (Rf) gene in pepper has been lacking until now. This study identifies and characterizes CaRf, a single dominant locus crucial for restoring CMS in the pepper strong recovery inbred line Zhangshugang. The CaRf gene encodes a mitochondria-targeted pentatricopeptide repeat protein, validated through the induction of male sterility upon its silencing in hybrid F₁ plants. To enhance pepper breeding efficiency, 176 important pepper breeding parent materials were resequenced, and a PepperSNP50K liquid-phase breeding chip was developed, comprising 51 172 markers. Integration of CaRf functional characterization and PepperSNP50K facilitated the development of a high-quality red pepper hybrid. These findings provide significant insights and practical strategies for advancing molecular-designed breeding in peppers.

AT-hook motif nuclear-localized (AHL) genes play critical roles in chromatin remodeling and gene transcription regulation, profoundly influencing plant growth, development, and stress responses. While AHL genes have been extensively characterized in multiple plant species, their biological functions in pepper (Capsicum annuum L.) remain largely uncharacterized. In this study, we identified 45 CaAHL genes in the pepper genome through bioinformatics approaches. Comprehensive analyses were conducted to examine their chromosomal distribution, phylogenetic relationships, and the structural and functional features of their encoded proteins. Phylogenetic clustering classified the CaAHL proteins into six distinct subgroups. Transcriptome profiling revealed widespread expression of CaAHL genes across diverse tissues—including roots, stems, leaves, flowers, seeds, pericarp, placenta, and fruits—at various developmental stages. Quantitative real-time PCR further demonstrated that CaAHL1, CaAHL33, and CaAHL23 exhibited consistently high expression throughout flower bud development, whereas CaAHL36 showed preferential upregulation at early bud development stages. Expression profiling under hormone treatments and abiotic stresses indicated that CaAHL36 and CaAHL23 are auxin-inducible but are repressed by ABA, cold, heat, salt, and drought stress. Subcellular localization assays in Nicotiana benthamiana leaf epidermal cells showed that both CaAHL36 and CaAHL23 were predominantly localized in the nucleus, with faint expression also detected in the cytoplasm. Collectively, this study provides foundational insights into the CaAHL gene family, laying the groundwork for future functional investigations of these genes in pepper.

SUMMARY: Stem strength is a key agronomic trait that influences planting adaptability and mechanical harvesting efficiency. Pepper is the most widely cultivated vegetable crop in China, and full mechanization of its production is crucial for enhancing quality and productivity. In the preliminary stage of this study, transcriptomic analysis was performed on pepper accessions exhibiting substantial differences in stem strength at various developmental stages. Through weighted gene co‐expression network analysis focused on genes involved in cell wall biosynthesis and transport, a candidate gene potentially regulating stem strength, designated CaDUF642.01, was identified. The CaDUF642.01 protein contains two DUF642 domains and localizes to the cell wall, plasma membrane, and nucleus. Silencing CaDUF642.01 led to a 42.17% decrease in soluble pectin content, a 1.63% reduction in water content, a 43.18% shortening of internode length, and more compact cell arrangement. Furthermore, CaDUF642.01 was shown to directly interact with pectin methylesterase 2 (CaPME2), forming a protein complex that modulates pectin methylation levels via regulation of random PME demethylesterification, thereby influencing stem strength. Our results demonstrate that the CaDUF642.01‐CaPME2 complex attenuates stem strength by altering pectin composition through PME activity, which also increases stem water content and promotes looser parenchyma cell packing. This study reveals a novel regulatory mechanism of stem strength in pepper, providing a theoretical basis for manipulating plant architecture and breeding mechanization‐adapted pepper varieties.

Background: Cell division plays a crucial role in plant growth and development. Cyclin-dependent kinase inhibitors (ICK/KRP) negatively regulate the cell cycle, thereby affecting cell elongation and organ development. This study aimed to systematically identify and characterize the ICK/KRP gene family in pepper, and to explore their roles in growth, development, and stress responses. Methods: Bioinformatics approaches were used for genome-wide identification, chromosomal localization, collinearity analysis, sequence characterization, promoter element prediction, and tissue-specific expression profiling of pepper ICK genes. Phylogenetic analysis was performed with homologs from Arabidopsis, tomato, maize, and rice. Quantitative real-time PCR and virus-induced gene silencing (VIGS) were applied to validate gene expression patterns and gene function, respectively. Subcellular localization assays were also conducted. Results: A total of six ICK genes were identified in pepper. They were classified into three subfamilies and distributed on different chromosomes, with one pair showing evidence of duplication. All ICK/KRPs contain the conserved Motif 1 (amino acid sequence: KIPTTREIEEFFATAEKQQQRRFIEKYNFDPVNEKPL) and were predicted to localize to the nucleus. Promoter analysis revealed cis-acting elements associated with plant development, stress responses, and hormone signaling. Expression pattern analysis indicated tissue-specific divergence and significant induction/repression under temperature stress. qRT-PCR results were consistent with transcriptome data, and expression differences were observed in materials with different stigma lengths. Subcellular localization confirmed that Caz03g38750.1 and Caz12g03790.1 proteins localize to both the nucleus and plasma membrane. Silencing of CazICK1 significantly repressed stigma elongation and altered stigma morphogenesis. Conclusions: The six pepper ICK/KRP genes display distinct diversity in distribution, structure and expression, and function in plant growth, development and stress adaptation. This work not only lays a solid basis for exploring the cell cycle regulatory network of pepper and contributes to relevant theoretical research, but it also identifies key gene resources for improving stigma traits. It has great potential for application in molecular breeding to promote high yield and efficient hybrid seed production in pepper.

The AT-hook motif nuclear-localized (AHL) genes play crucial roles in chromatin remodeling and regulation of gene transcription, significantly influencing biological processes such as plant growth, development, and stress responses. Although AHL genes have been extensively studied in various plants, their biological roles in pepper (Capsicum annuum L.) remain unknown. In this study, 45 AHL genes were identified in the pepper genome through bioinformatics approaches. These genes were analyzed for their chromosomal distribution, phylogenetic relationships, and the structural and functional characteristics of their encoded proteins. Phylogenetic analysis categorized the CaAHL proteins into four subgroups. Transcriptome data revealed that CaAHL genes are expressed across various tissues, including roots, stems, flowers, seeds, and fruits, at different growth stages. Subcellular localization experiments confirmed that CaAHL23 predominantly localizes to the cell nucleus, consistent with the localization of its homolog TEK in Arabidopsis thaliana. A yeast two-hybrid assay revealed that CaAHL23 binds to the promoter of CaCYP703A2, which is the homolog of the genic male sterility gene SlCYP703A2 in tomato. These findings indicate a potential link between CaAHL23 and genic male fertility in pepper. In summary, this study provides valuable insights that establish a foundation for future functional studies of CaAHL genes in pepper.