SNP fingerprint database and makers screening for current Phalaenopsis cultivars
The Moth orchid is globally recognized as one of the most popular and important ornamental species. However, due to the complicated history of hybridization, long growth cycles, and industrial vegetative propagation, there are huge challenges in cultivar identification and protection leading to mark...
Saved in:
| Main Authors: | , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Maximum Academic Press
2025-01-01
|
| Series: | Ornamental Plant Research |
| Subjects: | |
| Online Access: | https://www.maxapress.com/article/doi/10.48130/opr-0025-0005 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849699403094294528 |
|---|---|
| author | Xiuming Chen Qin Wang Fei Wang Xiaopei Wu Yun Pan Luyu Xue Yanru Duan Shunshun Wang Yunxiao Guan Kai Zhao Yuzhen Zhou Donghui Peng |
| author_facet | Xiuming Chen Qin Wang Fei Wang Xiaopei Wu Yun Pan Luyu Xue Yanru Duan Shunshun Wang Yunxiao Guan Kai Zhao Yuzhen Zhou Donghui Peng |
| author_sort | Xiuming Chen |
| collection | DOAJ |
| description | The Moth orchid is globally recognized as one of the most popular and important ornamental species. However, due to the complicated history of hybridization, long growth cycles, and industrial vegetative propagation, there are huge challenges in cultivar identification and protection leading to market issues. Consequently, it is important to develop effective and stable markers to identify and preserve core Phalaenopsis cultivar resources. In this study, we collected 53 commercially prevalent Phalaenopsis cultivars in China. Through detailed phenotypic observations, morphological genetic diversity was measured in 19 quantitative and 15 qualitative traits. By genome skimming and the subsequent SNP calling pipeline, we discovered 5,984 high-quality single nucleotide polymorphisms (SNPs) and constructed a comprehensive Phalaenopsis SNP database of cultivars. These SNPs got a high correlation with variation for quantitative traits ranging from 16.09% to 154.60%, while those for qualitative traits spanned from 20.54% to 130.81%. This database demonstrated a high degree of genetic diversity and a robust capacity for identifying polymorphisms and distinguishing among current varieties. These discovered SNPs consist of 12 types, C/T (23.86%), G/A (22.31%), A/G (8.89%), and T/C (7.84%). The ratio of transition to transversion was approximately 1.70. 70.91% of the SNP loci were in intergenic regions, 9.61% in upstream regions, and 9.37% within intronic regions. Fifty three cultivar PCAs could serve as three groups, which was matched with trait clusters. Based on 5,984 SNP sites, we conducted secondary screening and screened out 14 core sites. The clustering results of the NJ tree based on 14 core SNP loci and the NJ tree based on 5,984 whole genome SNP loci were consistent among 53 Phalaenopsis cultivars. Besides, each variety was then encoded with a unique barcode by 14 core SNP markers. This preliminary approach offers a putative and effective tool for variety identification, genetic analysis, and further development of Phalaenopsis germplasm resources. |
| format | Article |
| id | doaj-art-01f2b36de8664b0b9701c792ed9547b4 |
| institution | DOAJ |
| issn | 2769-2094 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Maximum Academic Press |
| record_format | Article |
| series | Ornamental Plant Research |
| spelling | doaj-art-01f2b36de8664b0b9701c792ed9547b42025-08-20T03:18:35ZengMaximum Academic PressOrnamental Plant Research2769-20942025-01-015111010.48130/opr-0025-0005opr-0025-0005SNP fingerprint database and makers screening for current Phalaenopsis cultivarsXiuming Chen0Qin Wang1Fei Wang2Xiaopei Wu3Yun Pan4Luyu Xue5Yanru Duan6Shunshun Wang7Yunxiao Guan8Kai Zhao9Yuzhen Zhou10Donghui Peng11The Cross-Strait Scientific and Technological Innovation Hub of Flower Industry, Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaThe Cross-Strait Scientific and Technological Innovation Hub of Flower Industry, Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaThe Cross-Strait Scientific and Technological Innovation Hub of Flower Industry, Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaThe Cross-Strait Scientific and Technological Innovation Hub of Flower Industry, Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaThe Cross-Strait Scientific and Technological Innovation Hub of Flower Industry, Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaThe Cross-Strait Scientific and Technological Innovation Hub of Flower Industry, Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaThe Cross-Strait Scientific and Technological Innovation Hub of Flower Industry, Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaThe Cross-Strait Scientific and Technological Innovation Hub of Flower Industry, Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaThe Cross-Strait Scientific and Technological Innovation Hub of Flower Industry, Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaCollege of Life Sciences, Fujian Normal University, Fuzhou 350117, ChinaThe Cross-Strait Scientific and Technological Innovation Hub of Flower Industry, Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaThe Cross-Strait Scientific and Technological Innovation Hub of Flower Industry, Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaThe Moth orchid is globally recognized as one of the most popular and important ornamental species. However, due to the complicated history of hybridization, long growth cycles, and industrial vegetative propagation, there are huge challenges in cultivar identification and protection leading to market issues. Consequently, it is important to develop effective and stable markers to identify and preserve core Phalaenopsis cultivar resources. In this study, we collected 53 commercially prevalent Phalaenopsis cultivars in China. Through detailed phenotypic observations, morphological genetic diversity was measured in 19 quantitative and 15 qualitative traits. By genome skimming and the subsequent SNP calling pipeline, we discovered 5,984 high-quality single nucleotide polymorphisms (SNPs) and constructed a comprehensive Phalaenopsis SNP database of cultivars. These SNPs got a high correlation with variation for quantitative traits ranging from 16.09% to 154.60%, while those for qualitative traits spanned from 20.54% to 130.81%. This database demonstrated a high degree of genetic diversity and a robust capacity for identifying polymorphisms and distinguishing among current varieties. These discovered SNPs consist of 12 types, C/T (23.86%), G/A (22.31%), A/G (8.89%), and T/C (7.84%). The ratio of transition to transversion was approximately 1.70. 70.91% of the SNP loci were in intergenic regions, 9.61% in upstream regions, and 9.37% within intronic regions. Fifty three cultivar PCAs could serve as three groups, which was matched with trait clusters. Based on 5,984 SNP sites, we conducted secondary screening and screened out 14 core sites. The clustering results of the NJ tree based on 14 core SNP loci and the NJ tree based on 5,984 whole genome SNP loci were consistent among 53 Phalaenopsis cultivars. Besides, each variety was then encoded with a unique barcode by 14 core SNP markers. This preliminary approach offers a putative and effective tool for variety identification, genetic analysis, and further development of Phalaenopsis germplasm resources.https://www.maxapress.com/article/doi/10.48130/opr-0025-0005phalaenopsissnp markergenetic diversityfingerprinting |
| spellingShingle | Xiuming Chen Qin Wang Fei Wang Xiaopei Wu Yun Pan Luyu Xue Yanru Duan Shunshun Wang Yunxiao Guan Kai Zhao Yuzhen Zhou Donghui Peng SNP fingerprint database and makers screening for current Phalaenopsis cultivars Ornamental Plant Research phalaenopsis snp marker genetic diversity fingerprinting |
| title | SNP fingerprint database and makers screening for current Phalaenopsis cultivars |
| title_full | SNP fingerprint database and makers screening for current Phalaenopsis cultivars |
| title_fullStr | SNP fingerprint database and makers screening for current Phalaenopsis cultivars |
| title_full_unstemmed | SNP fingerprint database and makers screening for current Phalaenopsis cultivars |
| title_short | SNP fingerprint database and makers screening for current Phalaenopsis cultivars |
| title_sort | snp fingerprint database and makers screening for current phalaenopsis cultivars |
| topic | phalaenopsis snp marker genetic diversity fingerprinting |
| url | https://www.maxapress.com/article/doi/10.48130/opr-0025-0005 |
| work_keys_str_mv | AT xiumingchen snpfingerprintdatabaseandmakersscreeningforcurrentphalaenopsiscultivars AT qinwang snpfingerprintdatabaseandmakersscreeningforcurrentphalaenopsiscultivars AT feiwang snpfingerprintdatabaseandmakersscreeningforcurrentphalaenopsiscultivars AT xiaopeiwu snpfingerprintdatabaseandmakersscreeningforcurrentphalaenopsiscultivars AT yunpan snpfingerprintdatabaseandmakersscreeningforcurrentphalaenopsiscultivars AT luyuxue snpfingerprintdatabaseandmakersscreeningforcurrentphalaenopsiscultivars AT yanruduan snpfingerprintdatabaseandmakersscreeningforcurrentphalaenopsiscultivars AT shunshunwang snpfingerprintdatabaseandmakersscreeningforcurrentphalaenopsiscultivars AT yunxiaoguan snpfingerprintdatabaseandmakersscreeningforcurrentphalaenopsiscultivars AT kaizhao snpfingerprintdatabaseandmakersscreeningforcurrentphalaenopsiscultivars AT yuzhenzhou snpfingerprintdatabaseandmakersscreeningforcurrentphalaenopsiscultivars AT donghuipeng snpfingerprintdatabaseandmakersscreeningforcurrentphalaenopsiscultivars |