Background: In order to clarify the the molecular mechanism of anthocyanin accumulation in green and purple fruits of pepper using metabolomics and transcriptomics,to identify different anthocyanin metabolites,and to analyze the differentially expressed genes involved in anthocyanin biosynthesis.. Results: We analyzed the anthocyanin metabolome and transcriptome data of the fruits of 2 purple pepper and 1 green pepper. A total of 5 anthocyanin metabolites and 2224 differentially expressed genes were identified between the green and purple fruits of pepper. Among the 5 anthocyanin metabolites,delphin chloride was unique to purple pepper fruits,which is the mainly responsible for the purple fruit color of pepper. A total of 59 unigenes encoding 7 enzymes were identified as candidate genes involved in anthocyanin biosynthesis in pepper fruit. The six enzymes (PAL,C4H,CHI,DFR,ANS,UFGT) had higher expression levels except the F3H gene in purple compared with green fruits. In addition,seven transcription factors were also found in this study. These transcription factors may contribute to anthocyanin metabolite biosynthesis in the fruits of pepper. One of differentially expressed gene novel.2098 was founded. It was not annotated in NCBI. Though blast analysis we preliminarily considered that this gene related to MYB transcription factor and was involved in anthocyanin biosynthesis in pepper fruit. Conclusions: Overall, the results of this study provide useful information for understanding anthocyanin accumulation and the molecular mechanism of anthocyanin biosynthesis in peppers.

Utilizing Single Nucleotide Polymorphism (SNP) marker technology, a phylogenetic and agronomic trait network analysis was conducted on the collected hot pepper and sweet pepper germplasm resources, providing a theoretical basis for parental selection and new varieties. Specific-locus amplified fragment sequencing (SLAF-seq) technology was employed for a genome-wide association study (GWAS) on 197 hot pepper and sweet pepper germplasm resources, generating 1404.88 Mb clean reads data with an average Q30 of 91.5% and mean GC content of 37.96%. Through sequencing data analysis, a total of 639,815 SLAF tags were obtained with an average sequencing depth of 12.16x, among which 86,381 were polymorphic SLAF tags, leading to the development of 18,145,155 SNP markers. The identified SNP markers were used for cluster analysis of the genetic structure and phylogenetic relationships of hot pepper and sweet pepper germplasm resources, dividing the 197 hot pepper and sweet pepper germplasm resources into 9 clusters. Additionally, a genome-wide association analysis was conducted on 25 agronomic traits of the 197 hot pepper and sweet pepper materials, yielding a substantial number of significantly associated SNP loci with agronomic traits. A correlation network analysis diagram was drawn among the various agronomic traits, preliminarily determining the relationships between the 25 agronomic characteristics of hot pepper and sweet pepper and the positions of 15 agronomic traits (p < 1.707 × 10−8) on the chromosomes were annotated, forming multi-trait aggregation regions. Our research reveals the genetic diversity, phylogenetic relationships, and population structure of 197 hot pepper and sweet pepper germplasm resources, providing a basis for germplasm identification, resource utilization, and breeding.

This study aims to enhance the coloration of pepper fruit by identifying valuable genetic resources through the analysis of single nucleotide polymorphism (SNP). markers and candidate genes associated with fruit pigmentation. Utilizing 197 natural populations of both hot and sweet peppers, we employed specific-locus amplified fragment sequencing (SLAF-seq) to examine 1496 high-quality SNP markers, thereby identifying significant loci contributing to fruit color variation. Our genome-wide association study pinpointed 30 significant SNP sites located on chromosome 6. Further analysis using kompetitive allele-specific PCR(KASP) and phenotypic correlation with fruit color led to the identification of the CA.PGAv.1.6.scaffold919.44 gene, which is implicated in anthocyanin synthesisregulation via the NAC domain, thereby influencing pepper fruit coloration. These findings offer a valuable reference for the advancement of molecular-assisted breeding strategies aimed at improving the fruit color of both sweet and hot peppers.To improve the fruit color of sweet peppers, this study aimed to identify single nucleotide polymorphism (SNP) loci and candidate genes significantly associated with fruit color. A natural population of 197 sweet pepper accessions was used as the material. SLAF-seq was conducted with 1496 high-quality SNP markers to mine excellent variant loci and predict candidate genes. Through Manhattan plot analysis and association analysis with the best linear unbiased prediction (BLUP) values of fruit color, 30 significant loci were detected on chromosome 6. Combining KASP genotyping technology with field phenotypes, the gene CAPGAv.1.6.scaffold919.44 was identified as a candidate gene regulating mature fruit color. It is related to the NAC domain and is hypothesized to alter fruit color by regulating anthocyanin biosynthesis. This study lays the foundation for molecular-assisted breeding of sweet peppers related to fruit color.

Background: This study investigates the molecular mechanisms underlying genic male sterility in sweet pepper by examining the correlation between differentially expressed genes during various stages of anther development and pollen sterility.Results: We collected anthers from both pure fertile and sterile plants of the F2 generation of the sweet pepper genic male sterility line AB91 at three distinct developmental stages for comprehensive transcriptome sequencing. By integrating KEGG enrichment analysis with weighted gene co-expression network analysis (WGCNA), we identified Starch and sucrose metabolism (ko00500) and Phenylpropanoid biosynthesis (ko00940) as key metabolic pathways regulating genic male sterility in sweet pepper AB91. Additionally, we uncovered two specific gene modules (blue and brown) associated with genic male sterility. A total of 320 genes, which exhibited significant differences (MM≥0.8) between these two modules, were found to be highly expressed after the formation of tetrads. This finding suggests that the period following tetrad formation is a critical juncture for changes in gene expression related to genic male sterility in sweet pepper AB91. By comparing these genes with their homologs, we identified six differentially expressed genes that can serve as core genes related to genic male sterility and play essential roles during microspore development.Conclusions: This research provides a theoretical foundation for elucidating the molecular mechanisms of genic male sterility in sweet pepper and lays the groundwork for expanding fertility gene resources and advancing hybrid breeding efforts in this important crop.

Background: Breeding hybrids with nuclear male sterile lines is an important method for the cross breeding of sweet peppers. To date, few reports have been published on the nuclear male sterility gene of sweet pepper. Yet, there are approximately 20 pepper nuclear male sterility lines in the world. Results: Using the self-developed testing material, sweet pepper nuclear male sterile dual-purpose line AB91, the genome-wide resequencing technique was applied to firstly find that the mutation site causing the abortion of sweet pepper nuclear male sterility AB91 is on chromosome #5. The mutation gene Capana05g000747 was filtered out and validated by the flight mass spectrometry genotyping method and determined to be the gene causing the abortion of sweet pepper nuclear male sterility AB91. The gene Capana05g000747 contains eight exons and seven introns, and its mutation site is a non-synonymous mutation site located at the 6th exon; the base C mutated into A, and the amino acid changed from alanine to serine. Sequence alignment analysis showed that the gene Capana05g000747 has a similar function to gene At2g02148. Conclusion: The gene At2g02148 contains a pentatricopeptide repeat protein which has important physiological functions in the gene expression process of organelles and is closely related to the performance of male sterility genes. Therefore, Capana05g000747 was selected as an important candidate gene for sweet pepper nuclear male sterile testing material AB91.

Breeding hybrids with nuclear male sterile lines is an important method for the cross breeding of sweet peppers. To date, few reports have been published on the nuclear male sterility gene of sweet pepper. Yet, there are approximately 20 pepper nuclear male sterility lines in the world. Using the self-developed testing material, sweet pepper nuclear male sterile dual-purpose line AB91, the genome-wide resequencing technique was applied to firstly find that the mutation site causing the abortion of sweet pepper nuclear male sterility AB91 is on chromosome #5. The mutation gene Capana05g000747 was filtered out and validated by the flight mass spectrometry genotyping method and determined to be the gene causing the abortion of sweet pepper nuclear male sterility AB91. The gene Capana05g000747 contains eight exons and seven introns, and its mutation site is a non-synonymous mutation site located at the 6th exon; the base C mutated into A, and the amino acid changed from alanine to serine. Sequence alignment analysis showed that the gene Capana05g000747 has a similar function to gene At2g02148. The gene At2g02148 contains a pentatricopeptide repeat protein which has important physiological functions in the gene expression process of organelles and is closely related to the performance of male sterility genes. Therefore, Capana05g000747 was selected as an important candidate gene for sweet pepper nuclear male sterile testing material AB91.