ArticleBMC genomics2025
SLAF-seq technology-based genome-wide association and population structure analyses of hot pepper and sweet pepper.
Article in BMC genomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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Who cites it
2 citing papers in PubMed.
- Effects of Biochar Combined with Nitrogen Fertilizer Application on Pepper Yield, Quality and Rhizosphere Soil Microbial Community Diversity.Plants (Basel, Switzerland) · 2025Article
- Pangenomic and Phenotypic Characterization of ColombianInternational journal of molecular sciences · 2025Article
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Authors and funding
7 authors.
Funding
Abstract
backgroundUtilizing 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.
resultsSpecific-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
conclusionsOur 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.
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