The domestication of chili peppers (Capsicum spp.) across diverse environments has generated a wide range of cultivars that constitute valuable reservoirs of allelic diversity. Single nucleotide polymorphism (SNPs) markers are particularly useful for characterizing this diversity due to their high abundance in plants and environmental stability. However, the latest methods such as multiplexed inter-simple sequence repeats genotyping by sequencing (MIG-seq) and genotyping by sequencing (GBS) face limitations in terms of efficiency and costs, respectively. To address these challenges, we applied the novel, cost-effective, degenerate oligonucleotide primer MIG-seq (dpMIG-seq) method to assess genetic diversity in 65 Capsicum accessions from South America and Asia, representing C. annuum, C. chinense, C. frutescens, and C. baccatum. Sequencing generated a total of 78,673 SNPs, of which 11,557 high-quality markers were retained. Principal component analysis and neighbor-joining phylogenetic method resolved two major genetic pools corresponding to C. annuum and C. baccatum complexes, further dividing the collection into four clusters. C. baccatum formed a distinct branch, while C. chinense and C. frutescens occupied intermediate positions, suggesting their potential role as genetic bridges between C. annuum and C. baccatum. Population structure analysis (K = 5) confirmed species-level clustering and revealed admixture among C. frutescens and C. chinense for unclassified Capsicum spp. accessions. Because of the overall low interspecific gene flow, it is necessary to incorporate novel alleles into breeding programs. Using dpMIG-seq for SNP discovery and genetic analysis in Capsicum expands the study of phylogenetic relationships, germplasm characterization, and breeding strategies for crop improvement and biodiversity conservation.
Morales et al. (Thu,) studied this question.
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