Assessing genetic redundancy and diversity in Colombian cacao germplasm banks using SNP fingerprinting
Cacao germplasm is the cornerstone of sustainable cacao production, underpinning efforts to develop high-yielding, quality-rich, and climate-resilient varieties. This study aimed to evaluate the mislabeling, the genetic redundancy, and diversity of two cacao germplasm banks maintained at the Palmira...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2025-07-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2025.1632888/full |
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| author | Jaime A. Osorio-Guarín Jhon A. Berdugo-Cely Gina A. Garzón-Martínez Deisy Lisseth Toloza-Moreno Paola Delgadillo-Duran Eliana Y. Báez-Daza Lyndel W. Meinhardt Sunchung Park Dapeng Zhang Roxana Yockteng Roxana Yockteng |
| author_facet | Jaime A. Osorio-Guarín Jhon A. Berdugo-Cely Gina A. Garzón-Martínez Deisy Lisseth Toloza-Moreno Paola Delgadillo-Duran Eliana Y. Báez-Daza Lyndel W. Meinhardt Sunchung Park Dapeng Zhang Roxana Yockteng Roxana Yockteng |
| author_sort | Jaime A. Osorio-Guarín |
| collection | DOAJ |
| description | Cacao germplasm is the cornerstone of sustainable cacao production, underpinning efforts to develop high-yielding, quality-rich, and climate-resilient varieties. This study aimed to evaluate the mislabeling, the genetic redundancy, and diversity of two cacao germplasm banks maintained at the Palmira and La Suiza research centers of the Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), from Colombia. We genotyped 4,653 cacao trees from these collections, and after applying quality control filters, a final set of 77 SNP markers was used for all subsequent analyses. Our results revealed that both collections exhibit a similar pattern of genetic diversity. However, a medium rate of mislabeling (12.4%) and high genetic redundancy (53.1%) were detected, likely due to errors in collecting, introduction, pre-planting labeling, and the use of rootstocks. To optimize the evaluation conserved cacao germplasm, we defined core collections independently, which comprise 246 and 190 samples for Palmira and La Suiza, respectively. This research demonstrates the importance of maintaining a well-classified cacao collection with minimal genetic redundancy, thereby improving accuracy and reducing maintenance costs. This will not only enhance conservation efforts but also enrich the genetic diversity of the collection. |
| format | Article |
| id | doaj-art-ee3666e16e0d475fa98bb7afd8ab1c45 |
| institution | DOAJ |
| issn | 1664-462X |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj-art-ee3666e16e0d475fa98bb7afd8ab1c452025-08-20T03:16:10ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2025-07-011610.3389/fpls.2025.16328881632888Assessing genetic redundancy and diversity in Colombian cacao germplasm banks using SNP fingerprintingJaime A. Osorio-Guarín0Jhon A. Berdugo-Cely1Gina A. Garzón-Martínez2Deisy Lisseth Toloza-Moreno3Paola Delgadillo-Duran4Eliana Y. Báez-Daza5Lyndel W. Meinhardt6Sunchung Park7Dapeng Zhang8Roxana Yockteng9Roxana Yockteng10Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Mosquera, ColombiaCentro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Mosquera, ColombiaCentro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Mosquera, ColombiaCentro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Mosquera, ColombiaCentro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Mosquera, ColombiaCentro de Investigación La Suiza, Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Rionegro, ColombiaDepartment of Agriculture, United States Department of Agriculture - Agricultural Research Service (USDA ARS) Sustainable Perennial Crops Laboratory, Beltsville, MD, United StatesDepartment of Agriculture, United States Department of Agriculture - Agricultural Research Service (USDA ARS) Sustainable Perennial Crops Laboratory, Beltsville, MD, United StatesDepartment of Agriculture, United States Department of Agriculture - Agricultural Research Service (USDA ARS) Sustainable Perennial Crops Laboratory, Beltsville, MD, United StatesCentro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Mosquera, ColombiaInstitut de Systématique, Evolution, Biodiversité-UMR-CNRS 7205, Muséum National d´Histoire Naturelle, Paris, FranceCacao germplasm is the cornerstone of sustainable cacao production, underpinning efforts to develop high-yielding, quality-rich, and climate-resilient varieties. This study aimed to evaluate the mislabeling, the genetic redundancy, and diversity of two cacao germplasm banks maintained at the Palmira and La Suiza research centers of the Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), from Colombia. We genotyped 4,653 cacao trees from these collections, and after applying quality control filters, a final set of 77 SNP markers was used for all subsequent analyses. Our results revealed that both collections exhibit a similar pattern of genetic diversity. However, a medium rate of mislabeling (12.4%) and high genetic redundancy (53.1%) were detected, likely due to errors in collecting, introduction, pre-planting labeling, and the use of rootstocks. To optimize the evaluation conserved cacao germplasm, we defined core collections independently, which comprise 246 and 190 samples for Palmira and La Suiza, respectively. This research demonstrates the importance of maintaining a well-classified cacao collection with minimal genetic redundancy, thereby improving accuracy and reducing maintenance costs. This will not only enhance conservation efforts but also enrich the genetic diversity of the collection.https://www.frontiersin.org/articles/10.3389/fpls.2025.1632888/fullbreedingcacaoduplicategermplasm banksKASPmislabeling |
| spellingShingle | Jaime A. Osorio-Guarín Jhon A. Berdugo-Cely Gina A. Garzón-Martínez Deisy Lisseth Toloza-Moreno Paola Delgadillo-Duran Eliana Y. Báez-Daza Lyndel W. Meinhardt Sunchung Park Dapeng Zhang Roxana Yockteng Roxana Yockteng Assessing genetic redundancy and diversity in Colombian cacao germplasm banks using SNP fingerprinting Frontiers in Plant Science breeding cacao duplicate germplasm banks KASP mislabeling |
| title | Assessing genetic redundancy and diversity in Colombian cacao germplasm banks using SNP fingerprinting |
| title_full | Assessing genetic redundancy and diversity in Colombian cacao germplasm banks using SNP fingerprinting |
| title_fullStr | Assessing genetic redundancy and diversity in Colombian cacao germplasm banks using SNP fingerprinting |
| title_full_unstemmed | Assessing genetic redundancy and diversity in Colombian cacao germplasm banks using SNP fingerprinting |
| title_short | Assessing genetic redundancy and diversity in Colombian cacao germplasm banks using SNP fingerprinting |
| title_sort | assessing genetic redundancy and diversity in colombian cacao germplasm banks using snp fingerprinting |
| topic | breeding cacao duplicate germplasm banks KASP mislabeling |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2025.1632888/full |
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