Abstract
Knowing how genetic diversity is partitioned among and within wild potato species populations is important for efficient sampling for collection, preservation and evaluation. We sought to evaluate the effectiveness of SNPs for assessing germplasm by using the exact set of four model species previously evaluated by RAPDs. To avoid large numbers of SNP samples, population bulks of 25 plants were used, and original RAPD data was adjusted to match SNP genotype data. It was noted that especially for SNPs, it was necessary to examine only loci polymorphic within species to get a realistic view of genetic partitioning within species. This resulted in only a few hundred useful loci for some species. When considering among-population versus within-population partitioning of diversity, both SNPs and RAPDs distinguished the species as expected according to their known breeding system. Primitive wild species were confirmed as very heterogeneous within their populations. Both SNP and RAPD markers can be used to help breeders and genebank managers understand patterns and use in potato germplasm diversity.
Resumen
Conocer como la diversidad genética es particionada dentro y entre poblaciones de especies silvestres de papa es importante para lograr muestreos eficientes en colección, preservación y evaluación. Nuestro trabajo fue diseñado para evaluar la efectividad de SNPs en el análisis de germoplasma usando el mismo grupo de especies silvestres usados como modelos para evaluar RAPDs en un trabajo previo. Para evitar el uso de un gran número de muestras individuales en la generación de SNPs, en este trabajo cada muestra representó una composición de 25 plantas y los datos originales previos usando RAPDs tuvieron que ajustarse para coincidir con los genotipos producidos con SNPs. Se observó que en SNPs, especialmente, fue necesario examinar únicamente loci polimórficos dentro de cada especie para tener una visión clara de la partición de diversidad genética dentro de especies. Como resultado solo unos cuantos cientos de loci fueron útiles para analizar algunas especies. Cuando la partición de diversidad genética entre poblaciones fue comparada con la observada dentro de poblaciones, tanto SNPs como RAPDs fueron capaces de distinguir las especies como era esperado de acuerdo a sus sistemas reproductivos conocidos. Las especies silvestres primitivas confirmaron ser muy heterogéneas dentro de sus poblaciones. Ambos marcadores, SNPs y RAPDs, pueden ser usados para ayudar a los mejoradores, y a quienes manejan los bancos de germoplasma, a entender los patrones de diversidad en germoplasma de papa y su uso.
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Abbreviations
- RAPD:
-
Random Amplified Polymorphic DNA
- SNP:
-
Single Nucleotide Polymorphisms
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Acknowledgments
The authors thank Mrs. Adele Douglass for technical assistance, Nick Garrity and Matt Zuehlke for SNP technical assistance and the Peninsular Agricultural Research Station program and staff for their support.
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Bamberg, J., del Rio, A., Coombs, J. et al. Assessing SNPs Versus RAPDs for Predicting Heterogeneity and Screening Efficiency in Wild Potato (Solanum) Species. Am. J. Potato Res. 92, 276–283 (2015). https://doi.org/10.1007/s12230-014-9428-2
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DOI: https://doi.org/10.1007/s12230-014-9428-2