Abstract
BackgroundThe widely cultivated pepper (Capsicum spp.) is one of the most diverse vegetables; however, little research has focused on characterizing the genetic diversity and relatedness of commercial varieties grown in China. In this study, a panel of 92 perfect single-nucleotide polymorphisms (SNPs) was identified using re-sequencing data from 35 different C. annuum lines. Based on this panel, a Target SNP-seq genotyping method was designed, which combined multiplex amplification of perfect SNPs with Illumina sequencing, to detect polymorphisms across 271 commercial pepper varieties.ResultsThe perfect SNPs panel had a high discriminating capacity due to the average value of polymorphism information content, observed heterozygosity, expected heterozygosity, and minor allele frequency, which were 0.31, 0.28, 0.4, and 0.31, respectively. Notably, the studied pepper varieties were morphologically categorized based on fruit shape as blocky-, long horn-, short horn-, and linear-fruited. The long horn-fruited population exhibited the most genetic diversity followed by the short horn-, linear-, and blocky-fruited populations. A set of 35 core SNPs were then used as kompetitive allele-specific PCR (KASPar) markers, another robust genotyping technique for variety identification. Analysis of genetic relatedness using principal component analysis and phylogenetic tree construction indicated that the four fruit shape populations clustered separately with limited overlaps. Based on STRUCTURE clustering, it was possible to divide the varieties into five subpopulations, which correlated with fruit shape. Further, the subpopulations were statistically different according to a randomization test and Fst statistics. Nine loci, located on chromosomes 1, 2, 3, 4, 6, and 12, were identified to be significantly associated with the fruit shape index (p < 0.0001).ConclusionsTarget SNP-seq developed in this study appears as an efficient power tool to detect the genetic diversity, population relatedness and molecular breeding in pepper. Moreover, this study demonstrates that the genetic structure of Chinese pepper varieties is significantly influenced by breeding programs focused on fruit shape.
Highlights
The widely cultivated pepper (Capsicum spp.) is one of the most diverse vegetables; little research has focused on characterizing the genetic diversity and relatedness of commercial varieties grown in China
This study demonstrated that a novel Target Single-nucleotide polymorphism (SNP)-seq can be used as a rapid and efficient tool for genotyping peppers, and the genetic structure of these cultivated varieties have been strongly impacted by breeding programs that select for fruit shapes
Genome-wide perfect SNPs used for target SNP-seq Re-sequencing of the 31 pepper lines (C. annuum) in this study generated a total of 872 Gb of paired-end sequence data, at an average depth of ~ 8.4
Summary
The widely cultivated pepper (Capsicum spp.) is one of the most diverse vegetables; little research has focused on characterizing the genetic diversity and relatedness of commercial varieties grown in China. A panel of 92 perfect single-nucleotide polymorphisms (SNPs) was identified using resequencing data from 35 different C. annuum lines. Based on this panel, a Target SNP-seq genotyping method was designed, which combined multiplex amplification of perfect SNPs with Illumina sequencing, to detect polymorphisms across 271 commercial pepper varieties. The most predominant species is C. annuum, which has numerous commercial varieties varying greatly in size, shape, pungency, and color. Several PCR-based tools have been used to detect genetic diversity in peppers, including random amplified polymorphic (RAPD), restriction fragment length polymorphism (RFLP), and amplified fragment length polymorphism (AFLP) [9,10,11,12]
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