Comprehensive Evaluation of <i>Nanhaia speciosa</i> Germplasm Resources Using Agronomic Traits, Molecular Markers, and Metabolomics
<i>Nanhaia speciosa</i> is a valuable industrial crop known for its significant edible and medicinal properties, attributed to its abundance of secondary metabolites. This study aims to elucidate the genetic relationships among <i>N. speciosa</i>, enhance species identificati...
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2025-02-01
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| author | Jing Yang Nanchen Lai Yiqin Zheng Ruifeng Ji Ping Wang Wei Dai Gantao Cheng Xin He |
| author_facet | Jing Yang Nanchen Lai Yiqin Zheng Ruifeng Ji Ping Wang Wei Dai Gantao Cheng Xin He |
| author_sort | Jing Yang |
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| description | <i>Nanhaia speciosa</i> is a valuable industrial crop known for its significant edible and medicinal properties, attributed to its abundance of secondary metabolites. This study aims to elucidate the genetic relationships among <i>N. speciosa</i>, enhance species identification accuracy, and select genetically stable, high-quality germplasms of <i>N. speciosa</i>. To achieve this, we conducted chloroplast gene amplification and sequencing, alongside an analysis of the agronomic traits of 19 <i>N. speciosa</i> germplasms. Additionally, non-targeted metabolomic profiling using UPLC-Q-Orbitrap/MS and chemometric methods was employed to assess their metabolic diversity and genetic relationships. The results revealed notable differences in DNA barcodes and secondary structures across the germplasms, with the <i>atp</i>F-<i>atp</i>H sequence successfully distinguishing all 19 germplasms into distinct varieties. Multivariate statistical analyses, including principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA), and hierarchical clustering, identified 12 key marker metabolites that effectively differentiated the germplasms, consistent with the observed phenotypic diversity. A clustering analysis integrating genetic, phenotypic, and metabolomic data further validated the utility of DNA barcoding for species identification. The results of the comprehensive analysis showed that NDL-2 and NDL-18 exhibited relatively good edible and medicinal properties, while NDL-1 and NDL-19 exhibited relatively poor edible and medicinal properties. This study provides crucial insights for the breeding and genetic improvement of <i>N. speciosa</i> and related species, offering a valuable reference for the identification, conservation, and utilization of germplasm resources within the <i>N. speciosa</i>. |
| format | Article |
| id | doaj-art-69ad056a4c684d0cb8e9ec2fddb34d76 |
| institution | Kabale University |
| issn | 2073-4395 |
| language | English |
| publishDate | 2025-02-01 |
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| record_format | Article |
| series | Agronomy |
| spelling | doaj-art-69ad056a4c684d0cb8e9ec2fddb34d762025-08-20T03:40:42ZengMDPI AGAgronomy2073-43952025-02-0115350810.3390/agronomy15030508Comprehensive Evaluation of <i>Nanhaia speciosa</i> Germplasm Resources Using Agronomic Traits, Molecular Markers, and MetabolomicsJing Yang0Nanchen Lai1Yiqin Zheng2Ruifeng Ji3Ping Wang4Wei Dai5Gantao Cheng6Xin He7School of Chinese Materia Medica, Guangdong Pharmaceutical University, Guangzhou 510006, ChinaSchool of Chinese Materia Medica, Guangdong Pharmaceutical University, Guangzhou 510006, ChinaSchool of Chinese Materia Medica, Guangdong Pharmaceutical University, Guangzhou 510006, ChinaSchool of Chinese Materia Medica, Guangdong Pharmaceutical University, Guangzhou 510006, ChinaTeaching and Experimental Center, Guangdong Pharmaceutical University, Guangzhou 510006, ChinaTeaching and Experimental Center, Guangdong Pharmaceutical University, Guangzhou 510006, ChinaGuangdong Xiaoyang Ecological Agriculture Co., Ltd., Yunfu 527500, ChinaSchool of Chinese Materia Medica, Guangdong Pharmaceutical University, Guangzhou 510006, China<i>Nanhaia speciosa</i> is a valuable industrial crop known for its significant edible and medicinal properties, attributed to its abundance of secondary metabolites. This study aims to elucidate the genetic relationships among <i>N. speciosa</i>, enhance species identification accuracy, and select genetically stable, high-quality germplasms of <i>N. speciosa</i>. To achieve this, we conducted chloroplast gene amplification and sequencing, alongside an analysis of the agronomic traits of 19 <i>N. speciosa</i> germplasms. Additionally, non-targeted metabolomic profiling using UPLC-Q-Orbitrap/MS and chemometric methods was employed to assess their metabolic diversity and genetic relationships. The results revealed notable differences in DNA barcodes and secondary structures across the germplasms, with the <i>atp</i>F-<i>atp</i>H sequence successfully distinguishing all 19 germplasms into distinct varieties. Multivariate statistical analyses, including principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA), and hierarchical clustering, identified 12 key marker metabolites that effectively differentiated the germplasms, consistent with the observed phenotypic diversity. A clustering analysis integrating genetic, phenotypic, and metabolomic data further validated the utility of DNA barcoding for species identification. The results of the comprehensive analysis showed that NDL-2 and NDL-18 exhibited relatively good edible and medicinal properties, while NDL-1 and NDL-19 exhibited relatively poor edible and medicinal properties. This study provides crucial insights for the breeding and genetic improvement of <i>N. speciosa</i> and related species, offering a valuable reference for the identification, conservation, and utilization of germplasm resources within the <i>N. speciosa</i>.https://www.mdpi.com/2073-4395/15/3/508<i>Nanhaia speciosa</i>genetic diversityDNA barcodingUPLC-Q-Orbitrap/MSnontargeted metabonomicgermplasm resources |
| spellingShingle | Jing Yang Nanchen Lai Yiqin Zheng Ruifeng Ji Ping Wang Wei Dai Gantao Cheng Xin He Comprehensive Evaluation of <i>Nanhaia speciosa</i> Germplasm Resources Using Agronomic Traits, Molecular Markers, and Metabolomics Agronomy <i>Nanhaia speciosa</i> genetic diversity DNA barcoding UPLC-Q-Orbitrap/MS nontargeted metabonomic germplasm resources |
| title | Comprehensive Evaluation of <i>Nanhaia speciosa</i> Germplasm Resources Using Agronomic Traits, Molecular Markers, and Metabolomics |
| title_full | Comprehensive Evaluation of <i>Nanhaia speciosa</i> Germplasm Resources Using Agronomic Traits, Molecular Markers, and Metabolomics |
| title_fullStr | Comprehensive Evaluation of <i>Nanhaia speciosa</i> Germplasm Resources Using Agronomic Traits, Molecular Markers, and Metabolomics |
| title_full_unstemmed | Comprehensive Evaluation of <i>Nanhaia speciosa</i> Germplasm Resources Using Agronomic Traits, Molecular Markers, and Metabolomics |
| title_short | Comprehensive Evaluation of <i>Nanhaia speciosa</i> Germplasm Resources Using Agronomic Traits, Molecular Markers, and Metabolomics |
| title_sort | comprehensive evaluation of i nanhaia speciosa i germplasm resources using agronomic traits molecular markers and metabolomics |
| topic | <i>Nanhaia speciosa</i> genetic diversity DNA barcoding UPLC-Q-Orbitrap/MS nontargeted metabonomic germplasm resources |
| url | https://www.mdpi.com/2073-4395/15/3/508 |
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