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A high resolution melting analysis-based genotyping toolkit for the Peach (Prunus persica) chilling requirement

International Journal of Molecular Sciences, ISSN: 1422-0067, Vol: 21, Issue: 4
2020
  • 10
    Citations
  • 0
    Usage
  • 33
    Captures
  • 0
    Mentions
  • 13
    Social Media
Metric Options:   Counts1 Year3 Year

Metrics Details

  • Citations
    10
  • Captures
    33
  • Social Media
    13
    • Shares, Likes & Comments
      13
      • Facebook
        13

Article Description

The chilling requirement (CR) is the main factor controlling the peach floral bud break and subsequent reproductive growth. To date, several peach CR quantitative trait loci (QTLs) have been identified. To improve the accessibility and convenience of this genetic information for peach breeders, the aim of this study was to establish an easy-to-use genotype screening system using peach CR molecular markers as a toolkit for marker-assisted selection. Here, we integrated 22 CR-associated markers from three published QTLs and positioned them on the Prunus persica physical map. Then, we built a PCR-based genotyping platform by using high-resolution melting (HRM) analysis with specific primers and trained this platform with 27 peach cultivars. Due to ambiguous variant calls from a commercial HRM software, we developed an R-based pipeline using principal component analysis (PCA) to accurately differentiate genotypes. Based on the PCA results, this toolkit was able to determine the genotypes at the CR-related single nucleotide polymorphisms (SNPs) in all tested peach cultivars. In this study, we showed that this HRM-PCA pipeline served as a low-cost, high-throughput, and non-gel genotyping solution. This system has great potential to accelerate CR-focused peach breeding.

Bibliographic Details

Chou, Lin; Huang, Shih-Jie; Hsieh, Chen; Lu, Ming-Te; Song, Chia-Wei; Hsu, Fu-Chiun

MDPI AG

Chemical Engineering; Biochemistry, Genetics and Molecular Biology; Chemistry; Computer Science

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