Simple Sequence Repeat Fingerprint Identification of Essential-Oil-Bearing <i>Rosa rugosa</i> via High-Resolution Melting (HRM) Analysis
Oil-bearing <i>Rosa rugosa</i> are popular in the essential oil and perfume markets. The similar botanical characteristics between high-oil-yield or low-oil-yield cultivars are confusing and it is hard for farmers or breeders to identify the high-oil-yield cultivar by phenotype differenc...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-09-01
|
| Series: | Biomolecules |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2218-273X/13/10/1468 |
| _version_ | 1797574506198335488 |
|---|---|
| author | Xiaoyu Xu Nan Wang Liguo Feng Jianwen Wang |
| author_facet | Xiaoyu Xu Nan Wang Liguo Feng Jianwen Wang |
| author_sort | Xiaoyu Xu |
| collection | DOAJ |
| description | Oil-bearing <i>Rosa rugosa</i> are popular in the essential oil and perfume markets. The similar botanical characteristics between high-oil-yield or low-oil-yield cultivars are confusing and it is hard for farmers or breeders to identify the high-oil-yield cultivar by phenotype difference. High-resolution melting (HRM) analysis of simple sequence repeats (SSRs) can construct accurate DNA fingerprints quickly, which was shown to be effective for identification of closely related cultivars of <i>R. rugosa</i>. Optimization of HRM-SSR indicated that the 10 µL HRM reaction mixture containing 20 ng of genomic DNA of <i>R. rugosa</i> and 0.75 µL of 10 µmol/L of each primer with an annealing temperature of 64 °C was a robust SSR genotyping protocol. Using this protocol, 9 polymorphic SSR markers with 3–9 genotypes among the 19 <i>R. rugosa</i> cultivars were identified. The top three polymorphic makers SSR9, SSR12 and SSR19 constructed a fingerprint of all cultivars, and the rare insertion in the flanking sequences of the repeat motif of SSR19 generated three characteristic genotypes of three high-oil-yield cultivars. These results may be economical and practical for the identification of high-oil-yield <i>R. rugosa</i> and be helpful for the selection and breeding of oil-bearing roses. |
| first_indexed | 2024-03-10T21:24:28Z |
| format | Article |
| id | doaj.art-642ac8afb4f84aa28276ab2ef6536d13 |
| institution | Directory Open Access Journal |
| issn | 2218-273X |
| language | English |
| last_indexed | 2024-03-10T21:24:28Z |
| publishDate | 2023-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biomolecules |
| spelling | doaj.art-642ac8afb4f84aa28276ab2ef6536d132023-11-19T15:49:41ZengMDPI AGBiomolecules2218-273X2023-09-011310146810.3390/biom13101468Simple Sequence Repeat Fingerprint Identification of Essential-Oil-Bearing <i>Rosa rugosa</i> via High-Resolution Melting (HRM) AnalysisXiaoyu Xu0Nan Wang1Liguo Feng2Jianwen Wang3College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, ChinaCollege of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, ChinaCollege of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, ChinaCollege of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, ChinaOil-bearing <i>Rosa rugosa</i> are popular in the essential oil and perfume markets. The similar botanical characteristics between high-oil-yield or low-oil-yield cultivars are confusing and it is hard for farmers or breeders to identify the high-oil-yield cultivar by phenotype difference. High-resolution melting (HRM) analysis of simple sequence repeats (SSRs) can construct accurate DNA fingerprints quickly, which was shown to be effective for identification of closely related cultivars of <i>R. rugosa</i>. Optimization of HRM-SSR indicated that the 10 µL HRM reaction mixture containing 20 ng of genomic DNA of <i>R. rugosa</i> and 0.75 µL of 10 µmol/L of each primer with an annealing temperature of 64 °C was a robust SSR genotyping protocol. Using this protocol, 9 polymorphic SSR markers with 3–9 genotypes among the 19 <i>R. rugosa</i> cultivars were identified. The top three polymorphic makers SSR9, SSR12 and SSR19 constructed a fingerprint of all cultivars, and the rare insertion in the flanking sequences of the repeat motif of SSR19 generated three characteristic genotypes of three high-oil-yield cultivars. These results may be economical and practical for the identification of high-oil-yield <i>R. rugosa</i> and be helpful for the selection and breeding of oil-bearing roses.https://www.mdpi.com/2218-273X/13/10/1468SSRhigh-resolution melting<i>Rosa rugosa</i>fingerprintessential oil |
| spellingShingle | Xiaoyu Xu Nan Wang Liguo Feng Jianwen Wang Simple Sequence Repeat Fingerprint Identification of Essential-Oil-Bearing <i>Rosa rugosa</i> via High-Resolution Melting (HRM) Analysis Biomolecules SSR high-resolution melting <i>Rosa rugosa</i> fingerprint essential oil |
| title | Simple Sequence Repeat Fingerprint Identification of Essential-Oil-Bearing <i>Rosa rugosa</i> via High-Resolution Melting (HRM) Analysis |
| title_full | Simple Sequence Repeat Fingerprint Identification of Essential-Oil-Bearing <i>Rosa rugosa</i> via High-Resolution Melting (HRM) Analysis |
| title_fullStr | Simple Sequence Repeat Fingerprint Identification of Essential-Oil-Bearing <i>Rosa rugosa</i> via High-Resolution Melting (HRM) Analysis |
| title_full_unstemmed | Simple Sequence Repeat Fingerprint Identification of Essential-Oil-Bearing <i>Rosa rugosa</i> via High-Resolution Melting (HRM) Analysis |
| title_short | Simple Sequence Repeat Fingerprint Identification of Essential-Oil-Bearing <i>Rosa rugosa</i> via High-Resolution Melting (HRM) Analysis |
| title_sort | simple sequence repeat fingerprint identification of essential oil bearing i rosa rugosa i via high resolution melting hrm analysis |
| topic | SSR high-resolution melting <i>Rosa rugosa</i> fingerprint essential oil |
| url | https://www.mdpi.com/2218-273X/13/10/1468 |
| work_keys_str_mv | AT xiaoyuxu simplesequencerepeatfingerprintidentificationofessentialoilbearingirosarugosaiviahighresolutionmeltinghrmanalysis AT nanwang simplesequencerepeatfingerprintidentificationofessentialoilbearingirosarugosaiviahighresolutionmeltinghrmanalysis AT liguofeng simplesequencerepeatfingerprintidentificationofessentialoilbearingirosarugosaiviahighresolutionmeltinghrmanalysis AT jianwenwang simplesequencerepeatfingerprintidentificationofessentialoilbearingirosarugosaiviahighresolutionmeltinghrmanalysis |