Plant cuticular wax serves as a critical component for defense against biotic and abiotic stresses, with its biosynthetic pathway regulated by the ECERIFERUM (CER) gene family. This study presents the first genome-wide identification of 79 CER genes (CalCERs) in pepper (Capsicum annuum L.), which are distributed across all 12 chromosomes. Phylogenetic analysis classified CalCERs into five clades, with clade-specific conservation of exon–intron architectures and protein motifs. Promoter cis-element analysis revealed enrichment of light-responsive elements, abscisic acid (ABA), jasmonic acid (JA), and stress-responsive regulatory motifs, indicating multi-pathway regulation. Transcriptomic data highlighted tissue-specific expression patterns, such as the root-predominant express gene CalCER1-2 and the flower-specific express gene CalCER3-1. Under abiotic stresses (drought, salt, heat, and cold), CalCER4-2 and CalCER6-6 responded rapidly, while most genes showed delayed differential expression. Under biotic stress, CalCER3-1 and CalCER5-3 were upregulated, whereas CalCER2-2 exhibited pathogen-specific suppression, suggesting roles in modulating wax-mediated pathogen resistance. Hormone treatments revealed dynamic responses: CalCER2-2 was persistently ABA-inducible, while CalCER3-1 specifically responded to JA. This study underscores evolutionary conservation and species-specific expansion of the pepper CER family, linking their expression to wax biosynthesis and stress adaptation. These insights provide a foundation for enhancing stress resilience in crops. Future work should employ gene editing and metabolomics to validate functional mechanisms and optimize breeding strategies.

Tomato chlorosis virus (ToCV) is an emerging plant virus that poses a substantial threat to the cultivation of economically vital vegetable crops, particularly tomato (Solanum lycopersicum). Despite its substantial impact on crop yield, resistant or tolerant tomato germplasms have not been well documented, and the genetic basis of resistance to ToCV remains poorly understood. In this study, two wild accessions that were immune to ToCV and five accessions that were highly resistant to ToCV were identified from 58 tomato accessions. Additionally, a novel method was developed for evaluating resistance to ToCV in tomatoes, and it was observed that tomatoes exhibited typical pathological features on days 15 and 30 after ToCV inoculation, referred to as Stage 1 and Stage 2, respectively. Using quantitative trait locus (QTL) sequencing in conjunction with classical QTL approaches, ToCV resistance loci were identified in two F2 populations derived from the crosses between SG11 (susceptible) and LA1028 (resistant) and between SP15 (susceptible) and LA0444 (resistant). Genetic analysis indicated that resistance to ToCV in the wild-type ToCV-resistant tomato accessions LA1028 and LA0444 was quantitative and mainly governed by four loci (Qtc1.1 and Qtc11.1 from LA1028 and Qtc7.1 and Qtc9.1 from LA0444). Subsequently, transcriptome analysis of three resistant accessions (LA2157, LA0444, and LA1028) and two susceptible accessions (SG11 and SP15) revealed unique differentially expressed genes and specific biological processes in the two stages of ToCV infection. This study provides new resistant germplasms and potential genetic resources for ToCV resistance, which can be valuable in tomato molecular breeding programs in obtaining resistant varieties.

Male sterility is an essential trait for minimizing costs and ensuring seed purity in the production of tomato hybrid seeds. However, its application in commercial breeding faces challenges such as instability, low stigma exsertion rates, and the lack of molecular markers to facilitate the efficient backcrossing of male sterile loci into elite tomato lines. This study characterized the male sterile-24 (ms-24) mutant, which demonstrated exserted stigmas and complete male sterility. Our histological examination revealed that ms-24 anthers displayed dysfunctional development of the tetrads and tapetum. The ms-24 locus was finely mapped to a 149 kb interval containing 22 putative genes. Among these, Solyc02g079810, also known as MS-10, encodes a basic helix–loop–helix (bHLH) transcription factor essential for tapetum and pollen development. A sequencing analysis revealed an approximately 4.9 kb retrotransposon insertion in the first exon of the MS-10 gene in ms-24. Allelism tests confirmed that ms-24 was allelic to ms-10, which is also allelic to ms-35 and ms-36. The same retrotransposon insertion was also identified in the ms-10 mutant, and a similar insertion of retrotransposon was detected in the second exon of the MS-10 gene in the ms-36 mutant. Based on these retrotransposon sequences, codominant insertion–deletion (InDel) markers, MS-24I and MS-35I, were developed for the precise identification of the ms-24, ms-10, ms-35, and ms-36 alleles. These findings establish a foundational basis for subsequent investigations into the molecular mechanisms underlying male sterility and enhance the selection process of male sterile lines in tomato hybrid breeding programs.