Development of a SNP array and its application to genetic mapping and diversity assessment in pepper (Capsicum spp.)

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.

Figure 1. The high-density interspecific genetic map (BY-SNP) of pepper.

This genetic map comprises 12 linkage groups (LG1-LG12) with 5,569 SNP markers. The corresponding chromosome numbers are shown in brackets, and the pseudo-linkage between P1 and P8 is shown with a dashed red line.

Figure 2. Extent and orientation of the distorted segregation of SNP markers in the BA3 × YNXML interspecific population.

This analysis was performed on 4,879 SNP markers with a missing rate less than 0.1 among the 297 F₂ progenies, and those with a chi-square test P value smaller than 0.01 were regarded as distorted markers. The skewed orientation towards BA3, YNXML and F₁ is shown in red, blue and green, respectively, and 4 SNPs skewed to YNXML and F₁ are shown in orange. All undistorted markers are presented in black.

Figure 3. Likelihood profile of QTL mapping with phenotypic datasets from EP and ELV methods.

Blue and red solid lines depict the EP and ELV methods, respectively. The genome-wide threshold LOD values for EP and ELV are shown as blue (LOD = 5.3) and red (LOD = 5.1) dashed lines, respectively.

Figure 4. Phylogenetic tree of 399 pepper lines inferred from 5,149 SNP markers.

The erect lines are labelled with solid red triangles.

Figure 5. Representation of genetic structure of 398 C. annuum lines.

(A) Estimated LnP (D) and ΔK values for different numbers of populations assumed (K, from 1 to 10) based on 833 SNPs; (B) Two population stratifications (P1 in red and P2 in green) based on the optimal K = 2; (C) PCA plot of the 398 C. annuum lines based on 6,470 SNPs (P1 in red and P2 in green).