In-depth genetic diversity and population structure of endangered Peruvian Amazon rosewood germplasm using Genotyping by Sequencing (GBS) technology
Research studies on conservative genetics of endangered plants are very important to establish the management plans for the conservation of biodiversity. Rosewood is an evergreen tree of the Amazon region and its essential oil has great acceptance in the medical and cosmetic industry. The present st...
| Autores principales: | , , , , , , , , , , , , , , , , |
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| Formato: | Artículo |
| Lenguaje: | Inglés |
| Publicado: |
MDPI
2023
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/20.500.12955/2244 https://doi.org/10.3390/f12020197 |
| _version_ | 1855490159138570240 |
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| author | Azhar Nadeem, Muhammad Vasquez Guizado, Stalin Juan Qasim Shahid, Muhammad Amjad Nawaz, Muhammad Habyarimana, Ephrem Ercişli, Sezai Ali, Fawad Karaköy, Tolga Aasim, Muhammad Hatipoğlu, Rüştü Castro Gómez, Juan Carlos Marapara Del Aguila, Jorge Luis Adrianzén Julca, Pedro Marcelino Torres Canales, Esperanza Hwan Yang, Seung Chung, Gyuhwa Shehzad Baloch, Faheem |
| author_browse | Aasim, Muhammad Adrianzén Julca, Pedro Marcelino Ali, Fawad Amjad Nawaz, Muhammad Azhar Nadeem, Muhammad Castro Gómez, Juan Carlos Chung, Gyuhwa Ercişli, Sezai Habyarimana, Ephrem Hatipoğlu, Rüştü Hwan Yang, Seung Karaköy, Tolga Marapara Del Aguila, Jorge Luis Qasim Shahid, Muhammad Shehzad Baloch, Faheem Torres Canales, Esperanza Vasquez Guizado, Stalin Juan |
| author_facet | Azhar Nadeem, Muhammad Vasquez Guizado, Stalin Juan Qasim Shahid, Muhammad Amjad Nawaz, Muhammad Habyarimana, Ephrem Ercişli, Sezai Ali, Fawad Karaköy, Tolga Aasim, Muhammad Hatipoğlu, Rüştü Castro Gómez, Juan Carlos Marapara Del Aguila, Jorge Luis Adrianzén Julca, Pedro Marcelino Torres Canales, Esperanza Hwan Yang, Seung Chung, Gyuhwa Shehzad Baloch, Faheem |
| author_sort | Azhar Nadeem, Muhammad |
| collection | Repositorio INIA |
| description | Research studies on conservative genetics of endangered plants are very important to establish the management plans for the conservation of biodiversity. Rosewood is an evergreen tree of the Amazon region and its essential oil has great acceptance in the medical and cosmetic industry. The present study aimed to explore the genetic diversity and population structure of 90 rosewood accessions collected from eight localities of Peruvian Amazon territory through DArTseq markers. A total of 7485 informative markers resulted from genotyping by sequencing (GBS) analysis were used for the molecular characterization of rosewood germplasm. Mean values of various calculated diversity parameters like observed number of alleles (1.962), the effective number of alleles (1.669), unbiased expected heterozygosity (0.411), and percent polymorphism (93.51%) over the entire germplasm showed the existence of a good level of genetic variations. Our results showed that the Mairiricay population was more diverse compared to the rest of the populations. Tamshiyacu-2 and Mairiricay-15 accessions were found genetically distinct accessions. The analysis of molecular variance (AMOVA) reflected maximum variations (75%) are due to differences within populations. The implemented clustering algorithms, i.e.; STRUCTURE, neighbor-joining analysis and principal coordinate analysis (PCoA) separated the studied germplasm on the basis of their geographical locations. Diversity indices for STRUCTURE-based populations showed that subpopulation A is more diverse population than the rest of the populations, for such reason, individuals belonging to this subpopulation should be used for reintroduction or reinforcement plans of rosewood conservation. We envisage that molecular characterization of Peruvian rosewood germplasm with DArTseq markers will provide a platform for the conservation, management and restoration of endangered rosewood in upcoming years. |
| format | Artículo |
| id | INIA2244 |
| institution | Institucional Nacional de Innovación Agraria |
| language | Inglés |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | MDPI |
| publisherStr | MDPI |
| record_format | dspace |
| spelling | INIA22442023-12-15T22:33:24Z In-depth genetic diversity and population structure of endangered Peruvian Amazon rosewood germplasm using Genotyping by Sequencing (GBS) technology Azhar Nadeem, Muhammad Vasquez Guizado, Stalin Juan Qasim Shahid, Muhammad Amjad Nawaz, Muhammad Habyarimana, Ephrem Ercişli, Sezai Ali, Fawad Karaköy, Tolga Aasim, Muhammad Hatipoğlu, Rüştü Castro Gómez, Juan Carlos Marapara Del Aguila, Jorge Luis Adrianzén Julca, Pedro Marcelino Torres Canales, Esperanza Hwan Yang, Seung Chung, Gyuhwa Shehzad Baloch, Faheem Aniba rosaeodora DArTseq Germplasm characterization Molecular markers Population genetics https://purl.org/pe-repo/ocde/ford#4.01.02 Aniba rosaeodora Aniba Genetic markers Marcadores genéticos Population genetics Genética de poblaciones Genotyping-by-sequencing Genotipado mediante secuenciación Research studies on conservative genetics of endangered plants are very important to establish the management plans for the conservation of biodiversity. Rosewood is an evergreen tree of the Amazon region and its essential oil has great acceptance in the medical and cosmetic industry. The present study aimed to explore the genetic diversity and population structure of 90 rosewood accessions collected from eight localities of Peruvian Amazon territory through DArTseq markers. A total of 7485 informative markers resulted from genotyping by sequencing (GBS) analysis were used for the molecular characterization of rosewood germplasm. Mean values of various calculated diversity parameters like observed number of alleles (1.962), the effective number of alleles (1.669), unbiased expected heterozygosity (0.411), and percent polymorphism (93.51%) over the entire germplasm showed the existence of a good level of genetic variations. Our results showed that the Mairiricay population was more diverse compared to the rest of the populations. Tamshiyacu-2 and Mairiricay-15 accessions were found genetically distinct accessions. The analysis of molecular variance (AMOVA) reflected maximum variations (75%) are due to differences within populations. The implemented clustering algorithms, i.e.; STRUCTURE, neighbor-joining analysis and principal coordinate analysis (PCoA) separated the studied germplasm on the basis of their geographical locations. Diversity indices for STRUCTURE-based populations showed that subpopulation A is more diverse population than the rest of the populations, for such reason, individuals belonging to this subpopulation should be used for reintroduction or reinforcement plans of rosewood conservation. We envisage that molecular characterization of Peruvian rosewood germplasm with DArTseq markers will provide a platform for the conservation, management and restoration of endangered rosewood in upcoming years. Authors are very grateful to Servicio Nacional Forestal y de Fauna Silvestre (SERFOR), Peru for providing the financial support for the collection of germplasm (1360-2018-MINAGRI-SERFOR-CAF). Authors also pay their gratitude to Programa Nacional de Innovación Agraria (PNIA), Peru for providing a scientific internship to Stalin Juan Vasquez Guizado (156-2018-INIA-PNIA), at the Bolu Abant Izzet Baysal University, Bolu, Turkey. 2023-08-11T14:38:16Z 2023-08-11T14:38:16Z 2021-02-08 info:eu-repo/semantics/article Nadeem, M. A.; Guizado, S. J. V.; Shahid, M. Q.; Nawaz, M. A.; Habyarimana, E.; Ercişli, S.; ... & Baloch, F. S. (2021). In-depth genetic diversity and population structure of endangered Peruvian Amazon rosewood germplasm using Genotyping by Sequencing (GBS) technology. Forests, 12(2), 197. doi: 10.3390/f12020197 1999-4907 https://hdl.handle.net/20.500.12955/2244 https://doi.org/10.3390/f12020197 eng urn:issn:1999-4907 Forests info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/ application/pdf application/pdf MDPI CH Instituto Nacional de Innovación Agraria Repositorio Institucional - INIA |
| spellingShingle | Aniba rosaeodora DArTseq Germplasm characterization Molecular markers Population genetics https://purl.org/pe-repo/ocde/ford#4.01.02 Aniba rosaeodora Aniba Genetic markers Marcadores genéticos Population genetics Genética de poblaciones Genotyping-by-sequencing Genotipado mediante secuenciación Azhar Nadeem, Muhammad Vasquez Guizado, Stalin Juan Qasim Shahid, Muhammad Amjad Nawaz, Muhammad Habyarimana, Ephrem Ercişli, Sezai Ali, Fawad Karaköy, Tolga Aasim, Muhammad Hatipoğlu, Rüştü Castro Gómez, Juan Carlos Marapara Del Aguila, Jorge Luis Adrianzén Julca, Pedro Marcelino Torres Canales, Esperanza Hwan Yang, Seung Chung, Gyuhwa Shehzad Baloch, Faheem In-depth genetic diversity and population structure of endangered Peruvian Amazon rosewood germplasm using Genotyping by Sequencing (GBS) technology |
| title | In-depth genetic diversity and population structure of endangered Peruvian Amazon rosewood germplasm using Genotyping by Sequencing (GBS) technology |
| title_full | In-depth genetic diversity and population structure of endangered Peruvian Amazon rosewood germplasm using Genotyping by Sequencing (GBS) technology |
| title_fullStr | In-depth genetic diversity and population structure of endangered Peruvian Amazon rosewood germplasm using Genotyping by Sequencing (GBS) technology |
| title_full_unstemmed | In-depth genetic diversity and population structure of endangered Peruvian Amazon rosewood germplasm using Genotyping by Sequencing (GBS) technology |
| title_short | In-depth genetic diversity and population structure of endangered Peruvian Amazon rosewood germplasm using Genotyping by Sequencing (GBS) technology |
| title_sort | in depth genetic diversity and population structure of endangered peruvian amazon rosewood germplasm using genotyping by sequencing gbs technology |
| topic | Aniba rosaeodora DArTseq Germplasm characterization Molecular markers Population genetics https://purl.org/pe-repo/ocde/ford#4.01.02 Aniba rosaeodora Aniba Genetic markers Marcadores genéticos Population genetics Genética de poblaciones Genotyping-by-sequencing Genotipado mediante secuenciación |
| url | https://hdl.handle.net/20.500.12955/2244 https://doi.org/10.3390/f12020197 |
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