Ppe.CR.1 DNA test for predicting chilling requirement in peach
Abstract Chilling requirement (CR) is an important agronomic trait controlling the floral bud break for proper flowering in peach. Even though it has been widely researched and several peach CR quantitative trait loci (QTLs) have been identified, no diagnostic DNA tests validated in the U.S. peach b...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-01-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-27475-w |
| _version_ | 1797945954455781376 |
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| author | Gizem Demirel Alejandro Calle John Mark Lawton Omer Atagul Wanfang Fu Ksenija Gasic |
| author_facet | Gizem Demirel Alejandro Calle John Mark Lawton Omer Atagul Wanfang Fu Ksenija Gasic |
| author_sort | Gizem Demirel |
| collection | DOAJ |
| description | Abstract Chilling requirement (CR) is an important agronomic trait controlling the floral bud break for proper flowering in peach. Even though it has been widely researched and several peach CR quantitative trait loci (QTLs) have been identified, no diagnostic DNA tests validated in the U.S. peach breeding germplasm are available for this trait. Breeders and growers need a simple DNA test to predict the CR of peach cultivars for their particular environment. Therefore, we developed a quick and reliable Kompetitive Allele Specific PCR (KASP) DNA test using haplotype information from 9K IPSC genotype data of the U.S. peach germplasm integrating four CR-associated SNP markers from the previously reported CR QTL region on linkage group 1. Four KASP assays (Ppe.CR.1-1 to -4) were developed and validated on 77 peach cultivars, and nine accessions from two F2 populations, with 96 and 74% accuracy in determining expected CR genotype (compared to SNP array) and predicting phenotype, respectively. Furthermore, the Ppe.CR.1 showed 80% accuracy in predicting the precise CR phenotype in the Clemson University peach breeding material. Only one Ppe.CR.1 KASP assay (Ppe.CR.1-1) is needed to distinguish between haplotypes with CR lower and higher than 800 chilling hours, and two Ppe.CR.1 assays (Pp.CR.1-1 and -4), are capable of distinguishing low, moderate, and high CR alleles. Coupled with the crude DNA extraction, the Ppe.CR.1 DNA test provides a low-cost option for breeders and growers to predict CR in peach material with more than 70% accuracy. |
| first_indexed | 2024-04-10T21:04:18Z |
| format | Article |
| id | doaj.art-6ef09b65330745b1a4778a5b05c6674b |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-04-10T21:04:18Z |
| publishDate | 2023-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-6ef09b65330745b1a4778a5b05c6674b2023-01-22T12:09:26ZengNature PortfolioScientific Reports2045-23222023-01-0113111110.1038/s41598-023-27475-wPpe.CR.1 DNA test for predicting chilling requirement in peachGizem Demirel0Alejandro Calle1John Mark Lawton2Omer Atagul3Wanfang Fu4Ksenija Gasic5Department of Plant and Environmental Sciences, Clemson UniversityDepartment of Plant and Environmental Sciences, Clemson UniversityDepartment of Plant and Environmental Sciences, Clemson UniversityDepartment of Plant and Environmental Sciences, Clemson UniversityDepartment of Plant and Environmental Sciences, Clemson UniversityDepartment of Plant and Environmental Sciences, Clemson UniversityAbstract Chilling requirement (CR) is an important agronomic trait controlling the floral bud break for proper flowering in peach. Even though it has been widely researched and several peach CR quantitative trait loci (QTLs) have been identified, no diagnostic DNA tests validated in the U.S. peach breeding germplasm are available for this trait. Breeders and growers need a simple DNA test to predict the CR of peach cultivars for their particular environment. Therefore, we developed a quick and reliable Kompetitive Allele Specific PCR (KASP) DNA test using haplotype information from 9K IPSC genotype data of the U.S. peach germplasm integrating four CR-associated SNP markers from the previously reported CR QTL region on linkage group 1. Four KASP assays (Ppe.CR.1-1 to -4) were developed and validated on 77 peach cultivars, and nine accessions from two F2 populations, with 96 and 74% accuracy in determining expected CR genotype (compared to SNP array) and predicting phenotype, respectively. Furthermore, the Ppe.CR.1 showed 80% accuracy in predicting the precise CR phenotype in the Clemson University peach breeding material. Only one Ppe.CR.1 KASP assay (Ppe.CR.1-1) is needed to distinguish between haplotypes with CR lower and higher than 800 chilling hours, and two Ppe.CR.1 assays (Pp.CR.1-1 and -4), are capable of distinguishing low, moderate, and high CR alleles. Coupled with the crude DNA extraction, the Ppe.CR.1 DNA test provides a low-cost option for breeders and growers to predict CR in peach material with more than 70% accuracy.https://doi.org/10.1038/s41598-023-27475-w |
| spellingShingle | Gizem Demirel Alejandro Calle John Mark Lawton Omer Atagul Wanfang Fu Ksenija Gasic Ppe.CR.1 DNA test for predicting chilling requirement in peach Scientific Reports |
| title | Ppe.CR.1 DNA test for predicting chilling requirement in peach |
| title_full | Ppe.CR.1 DNA test for predicting chilling requirement in peach |
| title_fullStr | Ppe.CR.1 DNA test for predicting chilling requirement in peach |
| title_full_unstemmed | Ppe.CR.1 DNA test for predicting chilling requirement in peach |
| title_short | Ppe.CR.1 DNA test for predicting chilling requirement in peach |
| title_sort | ppe cr 1 dna test for predicting chilling requirement in peach |
| url | https://doi.org/10.1038/s41598-023-27475-w |
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