Ppe.RPT/SSC-1: from QTL mapping to a predictive KASP test for ripening time and soluble solids concentration in peach
Abstract Genomic regions associated with ripening time (RPT) and soluble solids concentration (SSC) were mapped using a pedigreed population including multiple F1 and F2 families from the Clemson University peach breeding program (CUPBP). RPT and SSC QTLs were consistently identified in two seasons...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2024-01-01
|
| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-024-51599-2 |
| _version_ | 1797349988773134336 |
|---|---|
| author | Cassia da Silva Linge Wanfang Fu Alejandro Calle Zena Rawandoozi Lichun Cai David H. Byrne Margaret Worthington Ksenija Gasic |
| author_facet | Cassia da Silva Linge Wanfang Fu Alejandro Calle Zena Rawandoozi Lichun Cai David H. Byrne Margaret Worthington Ksenija Gasic |
| author_sort | Cassia da Silva Linge |
| collection | DOAJ |
| description | Abstract Genomic regions associated with ripening time (RPT) and soluble solids concentration (SSC) were mapped using a pedigreed population including multiple F1 and F2 families from the Clemson University peach breeding program (CUPBP). RPT and SSC QTLs were consistently identified in two seasons (2011 and 2012) and the average datasets (average of two seasons). A target region spanning 10,981,971–11,298,736 bp on chromosome 4 of peach reference genome used for haplotype analysis revealed four haplotypes with significant differences in trait values among different diplotype combinations. Favorable alleles at the target region for both RPT and SSC were determined and a DNA test for predicting RPT and SSC was developed. Two Kompetitive Allele Specific PCR (KASP) assays were validated on 84 peach cultivars and 163 seedlings from the CUPBP, with only one assay (Ppe.RPT/SSC-1) needed to predict between early and late-season ripening cultivars and low and high SSC. These results advance our understanding of the genetic basis of RPT and SSC and facilitate selection of new peach cultivars with the desired RPT and SSC. |
| first_indexed | 2024-03-08T12:38:18Z |
| format | Article |
| id | doaj.art-484e6615b08e41939f9af499932fecce |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-08T12:38:18Z |
| publishDate | 2024-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-484e6615b08e41939f9af499932fecce2024-01-21T12:17:44ZengNature PortfolioScientific Reports2045-23222024-01-0114111310.1038/s41598-024-51599-2Ppe.RPT/SSC-1: from QTL mapping to a predictive KASP test for ripening time and soluble solids concentration in peachCassia da Silva Linge0Wanfang Fu1Alejandro Calle2Zena Rawandoozi3Lichun Cai4David H. Byrne5Margaret Worthington6Ksenija Gasic7Department of Plant and Environmental Sciences, College of Agriculture, Forestry and Life Sciences, Clemson UniversityDepartment of Plant and Environmental Sciences, College of Agriculture, Forestry and Life Sciences, Clemson UniversityDepartment of Plant and Environmental Sciences, College of Agriculture, Forestry and Life Sciences, Clemson UniversityDepartment of Horticultural Sciences, Texas A&M UniversityDepartment of Plant and Environmental Sciences, College of Agriculture, Forestry and Life Sciences, Clemson UniversityDepartment of Horticultural Sciences, Texas A&M UniversityDepartment of Horticulture, University of Arkansas System Division of AgricultureDepartment of Plant and Environmental Sciences, College of Agriculture, Forestry and Life Sciences, Clemson UniversityAbstract Genomic regions associated with ripening time (RPT) and soluble solids concentration (SSC) were mapped using a pedigreed population including multiple F1 and F2 families from the Clemson University peach breeding program (CUPBP). RPT and SSC QTLs were consistently identified in two seasons (2011 and 2012) and the average datasets (average of two seasons). A target region spanning 10,981,971–11,298,736 bp on chromosome 4 of peach reference genome used for haplotype analysis revealed four haplotypes with significant differences in trait values among different diplotype combinations. Favorable alleles at the target region for both RPT and SSC were determined and a DNA test for predicting RPT and SSC was developed. Two Kompetitive Allele Specific PCR (KASP) assays were validated on 84 peach cultivars and 163 seedlings from the CUPBP, with only one assay (Ppe.RPT/SSC-1) needed to predict between early and late-season ripening cultivars and low and high SSC. These results advance our understanding of the genetic basis of RPT and SSC and facilitate selection of new peach cultivars with the desired RPT and SSC.https://doi.org/10.1038/s41598-024-51599-2 |
| spellingShingle | Cassia da Silva Linge Wanfang Fu Alejandro Calle Zena Rawandoozi Lichun Cai David H. Byrne Margaret Worthington Ksenija Gasic Ppe.RPT/SSC-1: from QTL mapping to a predictive KASP test for ripening time and soluble solids concentration in peach Scientific Reports |
| title | Ppe.RPT/SSC-1: from QTL mapping to a predictive KASP test for ripening time and soluble solids concentration in peach |
| title_full | Ppe.RPT/SSC-1: from QTL mapping to a predictive KASP test for ripening time and soluble solids concentration in peach |
| title_fullStr | Ppe.RPT/SSC-1: from QTL mapping to a predictive KASP test for ripening time and soluble solids concentration in peach |
| title_full_unstemmed | Ppe.RPT/SSC-1: from QTL mapping to a predictive KASP test for ripening time and soluble solids concentration in peach |
| title_short | Ppe.RPT/SSC-1: from QTL mapping to a predictive KASP test for ripening time and soluble solids concentration in peach |
| title_sort | ppe rpt ssc 1 from qtl mapping to a predictive kasp test for ripening time and soluble solids concentration in peach |
| url | https://doi.org/10.1038/s41598-024-51599-2 |
| work_keys_str_mv | AT cassiadasilvalinge pperptssc1fromqtlmappingtoapredictivekasptestforripeningtimeandsolublesolidsconcentrationinpeach AT wanfangfu pperptssc1fromqtlmappingtoapredictivekasptestforripeningtimeandsolublesolidsconcentrationinpeach AT alejandrocalle pperptssc1fromqtlmappingtoapredictivekasptestforripeningtimeandsolublesolidsconcentrationinpeach AT zenarawandoozi pperptssc1fromqtlmappingtoapredictivekasptestforripeningtimeandsolublesolidsconcentrationinpeach AT lichuncai pperptssc1fromqtlmappingtoapredictivekasptestforripeningtimeandsolublesolidsconcentrationinpeach AT davidhbyrne pperptssc1fromqtlmappingtoapredictivekasptestforripeningtimeandsolublesolidsconcentrationinpeach AT margaretworthington pperptssc1fromqtlmappingtoapredictivekasptestforripeningtimeandsolublesolidsconcentrationinpeach AT ksenijagasic pperptssc1fromqtlmappingtoapredictivekasptestforripeningtimeandsolublesolidsconcentrationinpeach |