Assessment of the genetic structure and diversity of arracacha (Arracacia xanthorrhiza) using genotyping-by-sequencing
Arracacha, also known as “Peruvian carrot”, is a native crop from the Andean region, and is considered an unexplored root. To date, studies on this crop were mainly focused at the morphological and agronomic level. However, its genetics remains unclear. Today it is feasible to study the genetic comp...
| Autores principales: | , , , , , , , , |
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| Formato: | info:eu-repo/semantics/conferenceObject |
| Lenguaje: | Inglés |
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International Society for Horticultural Science
2024
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/20.500.12955/2483 https://doi.org/10.17660/actahortic.2024.1393.27 |
| _version_ | 1855028442060292096 |
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| author | Arbizu Berrocal, Carlos Irvin Saldaña Serrano, Carla Lizet Lazo, E. Suca Damiano, Esther Stefany Santa Cruz Padilla, Angel Esteban Chávez Cabrera, Alexander Cabrera Hoyos, Héctor Antonio Guerrero Abad, Juan Carlos Maicelo Quintana, Jorge Luis |
| author_browse | Arbizu Berrocal, Carlos Irvin Cabrera Hoyos, Héctor Antonio Chávez Cabrera, Alexander Guerrero Abad, Juan Carlos Lazo, E. Maicelo Quintana, Jorge Luis Saldaña Serrano, Carla Lizet Santa Cruz Padilla, Angel Esteban Suca Damiano, Esther Stefany |
| author_facet | Arbizu Berrocal, Carlos Irvin Saldaña Serrano, Carla Lizet Lazo, E. Suca Damiano, Esther Stefany Santa Cruz Padilla, Angel Esteban Chávez Cabrera, Alexander Cabrera Hoyos, Héctor Antonio Guerrero Abad, Juan Carlos Maicelo Quintana, Jorge Luis |
| author_sort | Arbizu Berrocal, Carlos Irvin |
| collection | Repositorio INIA |
| description | Arracacha, also known as “Peruvian carrot”, is a native crop from the Andean region, and is considered an unexplored root. To date, studies on this crop were mainly focused at the morphological and agronomic level. However, its genetics remains unclear. Today it is feasible to study the genetic composition of this Andean root by next-generation sequencing techniques such as genotyping-by-sequencing (GBS). We here for the first time employed 183 accessions of arracacha from six Andean localities of Peru and identified 8976 SNP markers. STRUCTURE analysis revealed this Andean crop is clustered into four populations, and with few accessions intermingled. A dendrogram was generated using the UPGMA clustering algorithm, and, similar to the principal coordinate analysis (PCoA), it showed four groups. Genetic diversity estimation was conducted considering the four populations identified, revealing very high expected heterozygosity (0.432). AMOVA revealed the greatest variation within populations (89.66%) and indicated that variability between populations is 10.34%. Population divergence (Fst) ranged from 0.02 (cluster 1 vs. cluster 3) to 0.036 (cluster 1 vs. cluster 4). Negative Fis values were also detected for all populations of arracacha, indicating it depends on cross-pollination. We hope this work stimulates the development of additional molecular tools for this orphan crop in order to establish a modern breeding program and conservation strategies of this important Andean crop. |
| format | info:eu-repo/semantics/conferenceObject |
| id | INIA2483 |
| institution | Institucional Nacional de Innovación Agraria |
| language | Inglés |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | International Society for Horticultural Science |
| publisherStr | International Society for Horticultural Science |
| record_format | dspace |
| spelling | INIA24832024-04-30T21:29:42Z Assessment of the genetic structure and diversity of arracacha (Arracacia xanthorrhiza) using genotyping-by-sequencing Arbizu Berrocal, Carlos Irvin Saldaña Serrano, Carla Lizet Lazo, E. Suca Damiano, Esther Stefany Santa Cruz Padilla, Angel Esteban Chávez Cabrera, Alexander Cabrera Hoyos, Héctor Antonio Guerrero Abad, Juan Carlos Maicelo Quintana, Jorge Luis Peruvian carrot Neglected crop NGS Apiaceae Molecular markers https://purl.org/pe-repo/ocde/ford#4.01.06 Arracacia xanthorrhiza Apiaceae Genetic markers Marcadores genéticos Arracacha, also known as “Peruvian carrot”, is a native crop from the Andean region, and is considered an unexplored root. To date, studies on this crop were mainly focused at the morphological and agronomic level. However, its genetics remains unclear. Today it is feasible to study the genetic composition of this Andean root by next-generation sequencing techniques such as genotyping-by-sequencing (GBS). We here for the first time employed 183 accessions of arracacha from six Andean localities of Peru and identified 8976 SNP markers. STRUCTURE analysis revealed this Andean crop is clustered into four populations, and with few accessions intermingled. A dendrogram was generated using the UPGMA clustering algorithm, and, similar to the principal coordinate analysis (PCoA), it showed four groups. Genetic diversity estimation was conducted considering the four populations identified, revealing very high expected heterozygosity (0.432). AMOVA revealed the greatest variation within populations (89.66%) and indicated that variability between populations is 10.34%. Population divergence (Fst) ranged from 0.02 (cluster 1 vs. cluster 3) to 0.036 (cluster 1 vs. cluster 4). Negative Fis values were also detected for all populations of arracacha, indicating it depends on cross-pollination. We hope this work stimulates the development of additional molecular tools for this orphan crop in order to establish a modern breeding program and conservation strategies of this important Andean crop. 2024-04-30T21:29:41Z 2024-04-30T21:29:41Z 2024-04-13 info:eu-repo/semantics/conferenceObject Suca, E.; Arbizu, C.; Saldaña, C.; Lazo, E.; Santa-Cruz, A.; Chávez, A.; Cabrera, H.; Guerrero, J.; & Maicelo, J. (2023). Assessment of the genetic structure and diversity of arracacha (Arracacia xanthorrhiza) using genotyping-by-sequencing. In III International Symposium on Carrot and Other Apiaceae. Acta Horticulturae, 1393, 209-216 p. doi: 10.17660/ActaHortic.2024.1393.27 0567-7572 https://hdl.handle.net/20.500.12955/2483 https://doi.org/10.17660/actahortic.2024.1393.27 eng urn:issn:0567-7572 Acta Horticulturae info:eu-repo/semantics/restrictedAccess application/pdf International Society for Horticultural Science BE Instituto Nacional de Innovación Agraria Repositorio Institucional - INIA |
| spellingShingle | Peruvian carrot Neglected crop NGS Apiaceae Molecular markers https://purl.org/pe-repo/ocde/ford#4.01.06 Arracacia xanthorrhiza Apiaceae Genetic markers Marcadores genéticos Arbizu Berrocal, Carlos Irvin Saldaña Serrano, Carla Lizet Lazo, E. Suca Damiano, Esther Stefany Santa Cruz Padilla, Angel Esteban Chávez Cabrera, Alexander Cabrera Hoyos, Héctor Antonio Guerrero Abad, Juan Carlos Maicelo Quintana, Jorge Luis Assessment of the genetic structure and diversity of arracacha (Arracacia xanthorrhiza) using genotyping-by-sequencing |
| title | Assessment of the genetic structure and diversity of arracacha (Arracacia xanthorrhiza) using genotyping-by-sequencing |
| title_full | Assessment of the genetic structure and diversity of arracacha (Arracacia xanthorrhiza) using genotyping-by-sequencing |
| title_fullStr | Assessment of the genetic structure and diversity of arracacha (Arracacia xanthorrhiza) using genotyping-by-sequencing |
| title_full_unstemmed | Assessment of the genetic structure and diversity of arracacha (Arracacia xanthorrhiza) using genotyping-by-sequencing |
| title_short | Assessment of the genetic structure and diversity of arracacha (Arracacia xanthorrhiza) using genotyping-by-sequencing |
| title_sort | assessment of the genetic structure and diversity of arracacha arracacia xanthorrhiza using genotyping by sequencing |
| topic | Peruvian carrot Neglected crop NGS Apiaceae Molecular markers https://purl.org/pe-repo/ocde/ford#4.01.06 Arracacia xanthorrhiza Apiaceae Genetic markers Marcadores genéticos |
| url | https://hdl.handle.net/20.500.12955/2483 https://doi.org/10.17660/actahortic.2024.1393.27 |
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