A High Resolution Melting Analysis-Based Genotyping Toolkit for the Peach (<i>Prunus persica</i>) Chilling Requirement
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...
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doaj-62d7ac1388744bd18ff5871444dd3d3d2020-11-25T01:40:48ZengMDPI AGInternational Journal of Molecular Sciences1422-00672020-02-01214154310.3390/ijms21041543ijms21041543A High Resolution Melting Analysis-Based Genotyping Toolkit for the Peach (<i>Prunus persica</i>) Chilling RequirementLin Chou0Shih-Jie Huang1Chen Hsieh2Ming-Te Lu3Chia-Wei Song4Fu-Chiun Hsu5Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei 10617, TaiwanDepartment of Horticulture and Landscape Architecture, National Taiwan University, Taipei 10617, TaiwanDepartment of Horticulture and Landscape Architecture, National Taiwan University, Taipei 10617, TaiwanCrop Science Division and Guansi Experiment Station, Taiwan Agricultural Research Institute, Council of Agriculture, Taichung 41301, TaiwanCrop Science Division and Guansi Experiment Station, Taiwan Agricultural Research Institute, Council of Agriculture, Taichung 41301, TaiwanDepartment of Horticulture and Landscape Architecture, National Taiwan University, Taipei 10617, TaiwanThe 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 <i>Prunus persica</i> 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.https://www.mdpi.com/1422-0067/21/4/1543chilling requirement (cr)genotypinghigh-resolution melting (hrm) analysismarker-assisted selection (mas)principal component analysis (pca)quantitative trait loci (qtls)single nucleotide polymorphisms (snps) |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Lin Chou Shih-Jie Huang Chen Hsieh Ming-Te Lu Chia-Wei Song Fu-Chiun Hsu |
spellingShingle |
Lin Chou Shih-Jie Huang Chen Hsieh Ming-Te Lu Chia-Wei Song Fu-Chiun Hsu A High Resolution Melting Analysis-Based Genotyping Toolkit for the Peach (<i>Prunus persica</i>) Chilling Requirement International Journal of Molecular Sciences chilling requirement (cr) genotyping high-resolution melting (hrm) analysis marker-assisted selection (mas) principal component analysis (pca) quantitative trait loci (qtls) single nucleotide polymorphisms (snps) |
author_facet |
Lin Chou Shih-Jie Huang Chen Hsieh Ming-Te Lu Chia-Wei Song Fu-Chiun Hsu |
author_sort |
Lin Chou |
title |
A High Resolution Melting Analysis-Based Genotyping Toolkit for the Peach (<i>Prunus persica</i>) Chilling Requirement |
title_short |
A High Resolution Melting Analysis-Based Genotyping Toolkit for the Peach (<i>Prunus persica</i>) Chilling Requirement |
title_full |
A High Resolution Melting Analysis-Based Genotyping Toolkit for the Peach (<i>Prunus persica</i>) Chilling Requirement |
title_fullStr |
A High Resolution Melting Analysis-Based Genotyping Toolkit for the Peach (<i>Prunus persica</i>) Chilling Requirement |
title_full_unstemmed |
A High Resolution Melting Analysis-Based Genotyping Toolkit for the Peach (<i>Prunus persica</i>) Chilling Requirement |
title_sort |
high resolution melting analysis-based genotyping toolkit for the peach (<i>prunus persica</i>) chilling requirement |
publisher |
MDPI AG |
series |
International Journal of Molecular Sciences |
issn |
1422-0067 |
publishDate |
2020-02-01 |
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 <i>Prunus persica</i> 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. |
topic |
chilling requirement (cr) genotyping high-resolution melting (hrm) analysis marker-assisted selection (mas) principal component analysis (pca) quantitative trait loci (qtls) single nucleotide polymorphisms (snps) |
url |
https://www.mdpi.com/1422-0067/21/4/1543 |
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