Genetic diversity plays an essential role in plant breeding and utilization. Pepper is an important vegetable and spice crop worldwide. The genetic diversity of 1 904 accessions of pepper conserved at the National Mid-term Genebank for Vegetables, Beijing, China was analyzed based on 29 simple sequence repeat (SSR) markers, which were evenly distributed over 12 pepper chromosomes. The pepper accessions were divided into two groups in a genetic structure analysis, and the two groups showed obvious differences in fruit type and geographical distribution. We finally selected 248 accessions capturing 75.6% of the SSR alleles as the core collection for further research. Insights into the genetic structure of pepper provide the basis for population-level gene mining and genetic improvement.

Background: Colletotrichum species are the causal agents of anthracnose, a major disease affecting the yield and quality of pepper (Capsicum spp.). Colletotrichum scovillei is widespread in China, has strong pathogenicity and drug resistance, and causes anthracnose disease in pepper fruits that severely reduces production. Previously, an anti-anthracnose locus AnR_GO5 was mapped to the P5 chromosome on the basis of analyses of fruit at the green mature stage. The aim of this study was to narrow down the interval of this locus and identify the gene responsible for conferring resistance. Results: On the basis of results of re-sequencing of Capsicum chinense ‘PBC932’ and C. annuum ‘77013’, we developed Kompetitive allele-specific PCR (KASPar) markers and insertion–deletion (InDel) markers linked to AnR_GO5 at the green mature fruit stage and used them to construct a genetic linkage map (42 markers, 24.4 cM in length). Using data obtained in phenotypic and genotypic analyses of BC₄S₁, BC₄S₂, and BC₄S₃ populations, AnR_GO5 was located between the markers P5in-2266-404 and P5in-2268-978 within a physical distance of 164 kb. This region contained five genes, including CA05g17730. CA05g17730 encodes ‘R1C-3-like’ putative late blight resistance protein homologs. The transcript level of CA05g17730 differed between ‘PBC932’ and ‘77013’. The structure of the CA05g17730 gene also differed between ‘PBC932’ and ‘77013’. Conclusions: We narrowed down the QTL interval to a region containing five genes. These results will be useful for further research on the mechanisms of resistance to anthracnose, and for marker assisted selection for anthracnose-resistant capsicum lines.

Capsicum annuum L. is extensively cultivated in subtropical and temperate regions globally, respectively, when grown in a medium with 8 holding significant economic importance. Despite the availability of genome sequences and editing tools, gene editing in peppers is limited by the lack of a stable regeneration and transformation method. This study assessed regeneration and transformation protocols in seven chili pepper varieties, including CM334, Zunla-1, Zhongjiao6 (ZJ6), 0818, 0819, 297, and 348, in order to enhance genetic improvement efforts. Several explants, media compositions, and hormonal combinations were systematically evaluated to optimize the in vitro regeneration process across different chili pepper varieties. The optimal concentrations for shoot formation, shoot elongation, and rooting in regeneration experiments were determined as 5 mg/L of 6-Benzylaminopurine (BAP) with 5 mg/L of silver nitrate (AgNO₃), 0.5 mg/L of Gibberellic acid (GA₃), and 1 mg/L of Indole-3-butyric acid (IBA), respectively. The highest regeneration rate of 41% was observed from CM334 cotyledon explants. Transformation optimization established 300 mg/L of cefotaxime for bacterial control, with a 72-h co-cultivation period at OD₆₀₀ = 0.1. This study optimizes the protocols for chili pepper regeneration and transformation, thereby contributing to genetic improvement efforts.

Fruit weight is an important agronomic trait in pepper production and is closely related to yield. At present, many quantitative trait loci (QTL) related to fruit weight have been found in pepper; however, the genes affecting fruit weight remain unknown. We analyzed the fruit weight-related quantitative traits in an intraspecific Capsicum annuum cross between the cultivated species blocky-type pepper, cv. Qiemen, and the bird pepper accession, “129−1” (Capsicum annuum var. glatriusculum), which was the wild progenitor of C. annuum. Using the QTL-seq combined with the linkage-based QTL mapping approach, QTL detection was performed; and two major effects of QTL related to fruit weight, qFW2.1 and qFW3.1, were identified on chromosomes 2 and 3. The qFW2.1 maximum explained 12.28% of the phenotypic variance observed in two F₂ generations, with the maximum LOD value of 11.02, respectively; meanwhile, the qFW3.1 maximum explained 15.50% of the observed phenotypic variance in the two F₂ generations, with the maximum LOD value of 11.36, respectively. qFW2.1 was narrowed down to the 1.22 Mb region using homozygous recombinant screening from BC₂S₂ and BC₂S₃ populations, while qFW3.1 was narrowed down to the 4.61Mb region. According to the transcriptome results, a total of 47 and 86 differentially expressed genes (DEGs) in the candidate regions of qFW2.1 and qFW3.1 were identified. Further, 19 genes were selected for a qRT-PCR analysis based on sequence difference combined with the gene annotation. Finally, Capana02g002938 and Capana02g003021 are the most likely candidate genes for qFW2.1, and Capana03g000903 may be a candidate gene for qFW3.1. Taken together, our results identified and fine-mapped two major QTL for fruit weight in pepper that will facilitate marker-assistant breeding for the manipulation of yield in pepper.

Background/Objectives: Pepper (Capsicum annuum L.) is a widely grown vegetable and spice crop worldwide. This study aims to reveal the differences of metabolites among pepper accessions from different regions and explore candidate genes related to metabolites of pepper. Methods: The metabolome and transcriptome of 36 pepper accessions were determined by widely targeted metabolomics analysis and RNA sequencing technology, and the differential metabolites and differential genes among C. annuum from four important pepper production and consumption provinces of China, Hunan, Guizhou, Yunnan and Sichuan, were analyzed. Results: Flavonoids are the main characteristic metabolites that distinguish pepper accessions from Yun_Gui_Chuan Group and Hunan Group. The aglycones of characteristic flavonoids in each group are different; in Yun_Gui_Chuan Group mainly are luteolin, quercetin, chrysoeriol and isorhamnetin; in Hunan Group mainly are apigenin. Transcriptome data showed that two genes related to flavonoid 3′-monooxygenase differed significantly between the two groups of chili peppers, and we speculated that they may be the core enzymes regulating their flavonoid profile. And an SNP mutation located in gene Cgla06g001871 showed a strong correlation with pepper accessions from Yun_Gui_Chuan Group, which can be used as a DNA marker to identify pepper accessions from Yun_Gui_Chuan Group, and provide strong support for regional specialty variety conservation. In addition, we also analyzed the metabolites related to the taste and nutrition of pepper accessions in the four provinces, and the results showed that the sugar content of pepper accessions from Guizhou was low and the capsaicinoids content of pepper accessions from Sichuan was low, while no significant difference was found in acid and vitamin contents among pepper accessions from the four provinces. Conclusions: The metabolome and transcriptome of 36 pepper accessions from four important pepper production and consumption provinces of China were determined, and the characteristic metabolites and expressed genes of pepper accessions from each province were analyzed.

Capsicum frutescens (C. frutescens) has rich germplasm resources, but there have been no reports on its genetic diversity analysis alone using simplified genome sequencing technology (GBS). To provide a basis for the breeding of new pepper varieties and the later development of C. frutescens SNP molecular markers, this study used GBS technology to sequence 65 collected pepper germplasm resources. A total of 1,399,391 SNP sites were obtained by GBS simplified genome sequencing, and there were 1,465,897 SNP variant sites. Through population genetic structure analysis, the population structure and phylogenetic tree of 65 C. frutescens germplasms were constructed. The GBS method is also suitable for the genetic relationship analysis of C. frutescens, and it also shows that there is an obvious separation of materials from different origins, and there is also a certain degree of genetic exchange. Most of C. frutescens varieties from Fujian Province and its surrounding areas are clustered together; C. frutescens varieties from western China are also clustered together. We selected T62 and T60 with a genetic distance of 0.2796 and a spiciness level of nine as the female and male parent combinations, respectively, and bred a new high-yield C. frutescens combination, ‘Mingjiao 308’. C. frutescens varieties from the same geographical origin are usually clustered together. These germplasms may contain the ancestry of multiple varieties. This result can also provide basic data for the later construction of an SNP fingerprint database.