A Core Subset of the ex situ  Collection of S. demissum at the US Potato Genebank

Abstract

Useful genetic diversity found in wild potato germplasm is important for progress in potato breeding and science. An effective way to maximize its utilization is through characterization of ex situ collections. For example, marker-based core subsets from large collections are an effective strategy to accelerate evaluation, utilize germplasm, and enhance cost-effectiveness. This project used AFLP markers to create a core subset for the US Potato Genebank’s collection of S. demissum. This species from Mexico and Guatemala is known for excellent levels of late blight resistance and frost tolerance. A total of 149 accessions with diverse geographic origin were characterized with 1403 AFLP markers; these markers were effective on determining genetic associations among the accessions. For the core subset, the AFLP loci were considered as traits, with the presence of the marker as the required state to include in a core. The results of the analyses identified that 10 of the accessions of S. demissum captured 83% of all the markers detected in the whole collection. The inclusion of 28 additional accessions, which had between 1 to 5 unique markers, resulted in a core set of 38 accessions that captured 96% of all the marker diversity. We expect this can benefit the genebank and the potato community by opening opportunities for research, trait screenings, and marker association studies.

Resumen

La diversidad genética útil que se encuentra en el germoplasma de la papa silvestre es importante para el progreso en el mejoramiento de la papa y de la ciencia. Una manera efectiva de maximizar su utilización es a través de la caracterización de las colecciones ex situ. Por ejemplo, sub grupos o core subsets de colecciones grandes, basados en marcadores moleculares, son una estrategia efectiva para acelerar la evaluación, uso del germoplásma, y mejorar costo-efectividad. Este proyecto utilizó marcadores AFLP para crear un sub grupo para la colección de S. demissum del banco de germoplasma de papa de los Estados Unidos . Esta especie de México y Guatemala es conocida por sus excelentes niveles de resistencia al tizón tardío y tolerancia al frío. Se caracterizaron un total de 149 accesiones de diverso origen geográfico con 1403 marcadores AFLP; estos marcadores fueron efectivos en la determinación de asociaciones genéticas entre las accesiones. Para el sub grupo o core, los loci AFLP se consideraron como los caracteres utiles, con la presencia del marcador como el estado requerido para incluirse en un grupo. Los resultados de estos análisis identificaron que 10 de las accesiones de Sdemissum capturaron 83% de todos los marcadores detectados en la colección completa. La inclusión de 28 accesiones adicionales, que tenían de 1 a 5 marcadores únicos, resultaron en un sub grupo final de 38 accesiones que capturaron 96% de toda la diversidad encontrada en los marcadores. Esperamos que esto pueda beneficiar al banco de germoplasma y a la comunidad de la papa mediante la apertura de oportunidades para investigación, detección de caracteres, y de estudios de asociación s a marcadores.

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Abbreviations

AFLP:

Amplified Fragment Length Polymorphism

GS:

Genetic Similarity

USPG:

US Potato Genebank

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Acknowledgments

The authors wish to express their thanks to the staff of the US Potato Genebank for their support and technical assistance.

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Correspondence to Alfonso del Rio.

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del Rio, A., Bamberg, J. A Core Subset of the ex situ  Collection of S. demissum at the US Potato Genebank. Am. J. Potato Res. 97, 505–512 (2020). https://doi.org/10.1007/s12230-020-09799-9

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Keywords

  • AFLP markers
  • Core Subsets
  • Solanum demissum
  • Germplasm organization