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Genetic Fingerprinting of Potato Varieties from the Northwest Potato Variety Development Program

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Abstract

The Northwest Potato Variety Development (NWPVD) Program has released 45 improved potato varieties since 1985. Thirty-four potato varieties, four breeding clones and two advanced selections from NWPVD Program, and six commonly-grown potato varieties were fingerprinted using 32 simple sequence repeat (SSR) markers and 12,808 single nucleotide polymorphism (SNP) markers. Of 32 SSR markers, 29 exhibited significant polymorphism across all the 46 potato clones studied. A total of 143 alleles were observed with an average of 4.6 alleles per SSR marker. These markers span all 12 chromosomes of potato, with a maximum of five markers from chromosome VIII and minimum of one marker from chromosome VI. The polymorphic information content (PIC) and expected heterozygosity (He) of the SSR markers ranges between 0.18 to 0.75 and 0.20 to 0.78, respectively. Based on PIC, He, and ease of scoring, we recommend a set of eight SSR markers: STG0016, STI0004, STI0012, STI0023, STI0030, STI0033, STM1016 and STM1104 for fingerprinting NWPVD varieties. Out of 12,808 SNPs, 88.8% resulted in reliable three cluster diploid calling of which 87.8% were polymorphic. Tetraploid calling resulted in 44.2% of SNPs of which 94.5% were polymorphic. Our study provided fingerprinting resources for the NWPVD varieties and can be used in issues related to intellectual property rights, ownership, trademark and diversity analysis.

Resumen

El Programa de Desarrollo de Variedades de Papa Noroccidental (NWPVD, por sus siglas en inglés), ha liberado 45 variedades mejoradas de papa desde 1985. Se le obtuvo la huella digital molecular a 34 variedades de papa, cuatro clones para mejoramiento, y a dos selecciones avanzadas del Programa NWPVD, así como a seis variedades de papa de cultivo común, utilizando 32 marcadores de repeticiones de secuencias simples (SSR en inglés) y 12,808 marcadores de polimorfismo de nucleótidos simples (SNP). De los 32 marcadores SSR, 29 exhibieron polimorfismo significativo en todos los 46 clones de papa estudiados. Se observó un total de 143 alelos, con un promedio de 4.6 alelos por marcador SSR. Estos marcadores abarcaron los 12 cromosomas de la papa, con un máximo de cinco marcadores del cromosoma VIII y un mínimo de un marcador del cromosoma VI. El contenido de información polimórfica (PIC) y la heterocigocidad esperada (He) de los marcadores SSR fluctúa entre 0.18 a 0.75 y 0.20 a 0.78 respectivamente. Con base en el PIC, He, y las calificaciones, recomendamos un juego de ocho marcadores SSR: STG0016, STI0004, STI0012, STI0023, STI0030, STI0033, STM1016 y STM1104 para obtener la huella molecular digital de las variedades del NWPVD. De 12,808 SNPs, el 88.8% resultó en tres agrupamientos confiables de diploides identificados, de los cuales 87.8% fueron polimórficos. La identificación de tetraploides resultó en 44.2% de SNPs, de los cuales 94.5% fueron polimórficos. Nuestro estudio proporciona recursos de huellas moleculares para las variedades de NWPVD, y puede usarse en temas relacionados con derechos de propiedad intelectual, pertenencia, marcas registradas y análisis de diversidad.

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Acknowledgments

This study was supported by Potato Variety Management Institute, Northwest Potato Research Consortium and startup funds from Oregon State University to Dr. Vidyasagar Sathuvalli.

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Authors and Affiliations

  1. Hermiston Agricultural R&E Center, Oregon State University, Hermiston, OR, 97838, USA

    Sapinder Bali & Vidyasagar Sathuvalli

  2. Department of Crop and Soil Sciences, Oregon State University, Corvallis, OR, 97331, USA

    Vidyasagar Sathuvalli, Brian Charlton, Solomon Yilma & Clinton Shock

  3. USDA-ARS Yakima Agricultural Research Laboratory, Prosser, WA, 99350, USA

    Chuck Brown & Duroy Navarre

  4. USDA-ARS Aberdeen R&E Center, Aberdeen, ID, 83210, USA

    Rich Novy & Jonathan Whitworth

  5. Potato Tissue Culture Lab, University of Idaho, Moscow, ID, 83843, USA

    Lorie Ewing

  6. Potato Variety Management Institute, 60380 Chickasaw Way, Bend, OR, 97702, USA

    Jeanne Debons

  7. Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA

    David Douches & Joseph Coombs

  8. Idaho Falls R&E Center, University of Idaho, Idaho Falls, ID, 83402, USA

    Jeff Stark

  9. Department of Horticulture, Washington State University, Pullman, WA, 99164, USA

    Mark Pavek & N. Richard Knowles

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  1. Sapinder Bali
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  2. Vidyasagar Sathuvalli
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  3. Chuck Brown
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  7. David Douches
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  10. Jonathan Whitworth
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  12. Solomon Yilma
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  16. N. Richard Knowles
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Correspondence to Vidyasagar Sathuvalli.

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Bali, S., Sathuvalli, V., Brown, C. et al. Genetic Fingerprinting of Potato Varieties from the Northwest Potato Variety Development Program. Am. J. Potato Res. 94, 54–63 (2017). https://doi.org/10.1007/s12230-016-9547-z

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