Abstract
AFLP markers were used to build a core subset in 144 accessions of the United States Potato Genebank (USPG) ex situ collection of the species formerly known as Solanum phureja (now reclassified as Solanum tuberosum L. subsp. andigenum). A core subset aims to sample the minimum number possible of non-redundant germplasm units capturing the maximum diversity of the entire collection. Characterization and trait evaluation of a core subset is expected to be easier and more effective when compared to the entire germplasm collection. In this study 1534 polymorphic AFLP markers were generated and demonstrated to be useful to determine genetic relationships in the materials used. All the accessions were clearly discriminated from each other with genetic similarity levels ranging from 62 to 89%, and no duplicate germplasm samples were detected. To create the core subset, the presence of the AFLP marker was considered as the genetic trait to retain and the selection of accessions was determined by their rankings on the number of most markers added to the core. The results of this selection process revealed that the 9 top-ranked accessions of phureja, when combined, achieved the benchmark of capturing 85% of the markers detected in the complete collection. Further selection to increase the percentage of marker capture added 17 accessions with unique marker contributions which resulted in a final core subset of 26 accessions capturing 96% of the marker diversity. A Principal Component analysis determined that spatial distribution of diversity in the core was a proportional sampling of the entire diversity of the collection validating the selecting approach used. A review of the public database for valuable traits for the USPG phureja germplasm revealed that the core subset also included accessions with desirable pest/disease resistances and stress tolerances (in 25 out of the 30 traits reported in the database). The USPG expects this core subset would create opportunities for facilitating evaluation and research by using a reduced set of germplasm units with nearly all the diversity of the entire set.
Resumen
Marcadores AFLP fueron usados en 144 accesiones para construir un sub-grupo (core subset) de la colección ex situ de la especie conocida anteriormente como Solanum phureja (reclasificada ahora como Solanum tuberosum L. subsp. andigenum) del Banco de Germoplasma de Papa de los Estados Unidos (USPG). Un sub-grupo tiene como objetivo muestrear el número mínimo posible de unidades de germoplasma, no redundantes, que capturen la máxima diversidad genetica encontrada en toda la colección. Se esperaría asi que la caracterización y evaluación de caracteres de interes sea más fácil y eficiente usando el sub-grupo que usando la colección completa de germoplasma. En este estudio se generaron 1534 marcadores polimórficos de AFLP que demostraron ser útiles para establecer relaciones genéticas entre los materiales utilizados. Todas las accesiones fueron claramente diferenciadas entre sí, con niveles de similaridad genética entre 62% y 89%, además no se detectaron unidades de germoplasma duplicadas. Para la creación del sub-grupo, la presencia del marcador AFLP fue considerada como el caracter genético a retener. La selección de accesiones para incluir en el sub-grupo fue determinada por el mayor número de marcadores que cada accessión contribuyó al sub-grupo. Los resultados de este proceso revelaron que las 9 accesiones de phureja con mayor contribución, cuando combinadas, capturaron 85% de los marcadores detectados en toda la colección. Una selección adicional para elevar el porcentaje de captura de diversidad identificó 17 accesiones mas, las cuales contribuyeron con marcadores únicos, para producir un sub-grupo final de 26 accesiones que combinadas capturaron 96% de la diversidad. Un análisis de Componentes Principales (PC) determinó que la distribución espacial de la diversidad en el sub-grupo fue proporcional a la diversidad encontrada en la colección entera, validando asi la metodologia de selección usada. Una revisión de la base de datos públicos de caracteres importantes encontrados para el germoplasma de phureja conservado en USPG reveló que el sub grupo también incluyó accesiones con resistencias deseables a plagas / enfermedades asi como tolerancias a estreses abioticos (en 25 de los 30 caracteres reportados en la base de datos). USPG espera que este sub grupo pueda crear oportunidades para facilitar la evaluación y la investigación mediante el uso de un grupo reducido de germoplasma que incluye casi toda la diversidad de la colección completa.
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Abbreviations
- AFLP:
-
Amplified Fragment Length Polymorphism
- USPG:
-
US Potato Genebank
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Acknowledgements
The authors express their thanks to the US Potato Genebank and staff for their support and technical assistance. We also thank the technical help in fragment analyses given by the staff at the University of Wisconsin-Madison Biotech Center, Ms. Laura McCulley for her technical help in the generation of AFLPs, and Ms. Natalia del Rio for her constructive comments and assistance in appropriate editing of the manuscript.
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del Rio, A., Bamberg, J. An AFLP Marker Core Subset for the Cultivated Potato Species Solanum phureja ( Solanum tuberosum L. subsp. andigenum). Am. J. Potato Res. 98, 374–383 (2021). https://doi.org/10.1007/s12230-021-09849-w
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DOI: https://doi.org/10.1007/s12230-021-09849-w