Abstract
The development and application of single nucleotide polymorphisms (SNPs) is in its infancy for pepper. Here, a set of 15,000 SNPs were chosen from the resequencing data to develop an array for pepper with 12,720 loci being ultimately synthesized. Of these, 8,199 (~64.46%) SNPs were found to be scorable and covered ~81.18% of the whole genome. With this array, a high-density interspecific genetic map with 5,569 SNPs was constructed using 297 F2 individuals, and genetic diversity of a panel of 399 pepper elite/landrace lines was successfully characterized. Based on the genetic map, one major QTL, named Up12.1, was detected for the fruit orientation trait. A total of 65 protein-coding genes were predicted within this QTL region based on the current annotation of the Zunla-1 genome. In summary, the thousands of well-validated SNP markers, high-density genetic map and genetic diversity information will be useful for molecular genetics and innovative breeding in pepper. Furthermore, the mapping results lay foundation for isolating the genes underlying variation in fruit orientation of Capsicum.
Highlights
The development and application of single nucleotide polymorphisms (SNPs) is in its infancy for pepper
8,199 (~64.46%) SNP loci were scored with normal signals among all 1,019 investigated samples (Table 1), and the detailed genomic coordinates, variation types and flanking sequences of these scorable SNP loci were given in Supplementary Table S1
These scorable SNPs anchored a total of 5,107 scaffolds, which covered 2,719,081,414bp of physical length and accounted for approximately 81.18% of the Zunla-1 genome assembly (Table 1)
Summary
The development and application of single nucleotide polymorphisms (SNPs) is in its infancy for pepper. 8,199 (~64.46%) SNPs were found to be scorable and covered ~81.18% of the whole genome With this array, a high-density interspecific genetic map with 5,569 SNPs was constructed using 297 F2 individuals, and genetic diversity of a panel of 399 pepper elite/landrace lines was successfully characterized. The thousands of well-validated SNP markers, high-density genetic map and genetic diversity information will be useful for molecular genetics and innovative breeding in pepper. Various marker systems, including restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNA (RAPD), amplified fragment length polymorphisms (AFLPs) and simple sequence repeats (SSRs), have been developed and utilized to assess diversity[5,6,7], construct genetic maps[8,9,10] and perform marker assisted selection (MAS)[11,12] in pepper. The validation of these in silico SNPs through laboratory experiments and practical breeding in pepper merits further study
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