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Pedigree Reconstruction with Genome-Wide Markers in Potato

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Abstract

Reliable pedigree information facilitates a scientific approach to breeding, but errors can be introduced in many stages of a breeding program. Our objective was to use single nucleotide polymorphisms (SNPs) to check the pedigree records of elite North American potato germplasm. A population of 719 tetraploids was genotyped with an Infinium SNP array, yielding 5063 high-quality markers. Based on pedigree records, the dataset contained 198 parent-offspring trios, of which 182 were consistent with the marker data. For 13 of the 16 trios with a pedigree error, the true parent was identified in the population. By comparing the additive relationship matrix calculated from pedigree with the genetic distance calculated from markers, an additional 24 pedigree modifications were proposed, including the paternity of several varieties developed with bulk pollen. To ensure accurate pedigree records are published in the future, we recommend that new varieties be SNP genotyped and checked against this dataset.

Resumen

La información confiable sobre el pedigree facilita un enfoque científico para el mejoramiento genético, pero se pueden introducir errores en muchas etapas de un programa de mejoramiento. Nuestro objetivo fue usar polimorfismos de un solo nucleótido (SNPs) para cotejar los archivos de pedigree de germoplasma élite de papa de Norteamérica. Una población de 719 tetraploides fue genotipada con una colección de SNPs en una plataforma Infinium, obteniendo 5063 marcadores de alta calidad. Con base a los records del pedigree, la hoja de datos contenía 198 tríos de descendientes con sus padres, de los cuales 182 fueron consistentes con los datos de marcadores. Para 13 de 16 tríos con error de pedigree, se identificó al progenitor verdadero en la población. Al comparar la matriz de relación aditiva calculada del pedigree con la distancia genética calculada de los marcadores, se propusieron 24 modificaciones adicionales al pedigree, incluyendo la paternidad de varias variedades desarrolladas con polen masivo. Para asegurar que a futuro sean publicados registros precisos de pedigree, recomendamos que las nuevas variedades sean genotipadas utilizando SNPs y se cotejen con esta hoja de datos.

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Acknowledgments

Financial support for this research was provided by Potatoes USA (formerly the U.S. Potato Board), state potato industry boards, the National Chip and Fry Processing Trial consortia, and USDA-NIFA-Hatch Project Number 1002731. The authors thank Felix Navarro and Horia Groza for contributing pedigree records.

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Authors and Affiliations

  1. Department of Horticulture, University of Wisconsin, Madison, WI, 53706, USA

    Jeffrey B. Endelman, Cari A. Schmitz Carley & Jiwan P. Palta

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

    David S. Douches & Joseph J. Coombs

  3. Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB, E3B 4Z7, Canada

    Benoit Bizimungu

  4. School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA

    Walter S. De Jong

  5. USDA-ARS, Genetic Improvement of Fruits and Vegetables Lab, Beltsville, MD, 20705, USA

    Kathleen G. Haynes

  6. San Luis Valley Research Center, Department of Horticulture and Landscape Architecture, Colorado State University, Center, CO, 81125, USA

    David G. Holm

  7. Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA

    J. Creighton Miller Jr

  8. USDA–ARS Small Grains and Potato Germplasm Research Unit, Aberdeen, ID, 83210, USA

    Richard G. Novy

  9. AIS Consulting LLC, Allen, TX, 75013, USA

    David L. Parish

  10. School of Food and Agriculture, University of Maine, Orono, ME, 04469, USA

    Gregory A. Porter

  11. Department of Crop and Soil Science, Oregon State University, Hermiston, OR, 97838, USA

    Vidyasagar R. Sathuvalli

  12. Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA

    Asunta L. Thompson

  13. Department of Horticultural Science, North Carolina State University, Raleigh, NC, 27695, USA

    G. Craig Yencho

Authors
  1. Jeffrey B. Endelman
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  2. Cari A. Schmitz Carley
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  3. David S. Douches
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  4. Joseph J. Coombs
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  5. Benoit Bizimungu
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  6. Walter S. De Jong
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  7. Kathleen G. Haynes
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  8. David G. Holm
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  9. J. Creighton Miller Jr
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  10. Richard G. Novy
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  11. Jiwan P. Palta
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  12. David L. Parish
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  13. Gregory A. Porter
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  14. Vidyasagar R. Sathuvalli
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  15. Asunta L. Thompson
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  16. G. Craig Yencho
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Corresponding author

Correspondence to Jeffrey B. Endelman.

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The authors declare that they have no conflict of interest.

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Endelman, J.B., Schmitz Carley, C.A., Douches, D.S. et al. Pedigree Reconstruction with Genome-Wide Markers in Potato. Am. J. Potato Res. 94, 184–190 (2017). https://doi.org/10.1007/s12230-016-9556-y

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  • DOI: https://doi.org/10.1007/s12230-016-9556-y

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