American Journal of Potato Research

, Volume 94, Issue 2, pp 184–190

Pedigree Reconstruction with Genome-Wide Markers in Potato

  • Jeffrey B. Endelman
  • Cari A. Schmitz Carley
  • David S. Douches
  • Joseph J. Coombs
  • Benoit Bizimungu
  • Walter S. De Jong
  • Kathleen G. Haynes
  • David G. Holm
  • J. Creighton MillerJr
  • Richard G. Novy
  • Jiwan P. Palta
  • David L. Parish
  • Gregory A. Porter
  • Vidyasagar R. Sathuvalli
  • Asunta L. Thompson
  • G. Craig Yencho
Short Communication
  • 420 Downloads

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.

Keywords

Pedigrees SNPs Solanum tuberosum 

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.

Supplementary material

12230_2016_9556_MOESM1_ESM.csv (6 kb)
ESM 1(CSV 5 kb)
12230_2016_9556_MOESM2_ESM.csv (3.2 mb)
ESM 2(CSV 3241 kb)

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Copyright information

© The Potato Association of America 2017

Authors and Affiliations

  • Jeffrey B. Endelman
    • 1
  • Cari A. Schmitz Carley
    • 1
  • David S. Douches
    • 2
  • Joseph J. Coombs
    • 2
  • Benoit Bizimungu
    • 3
  • Walter S. De Jong
    • 4
  • Kathleen G. Haynes
    • 5
  • David G. Holm
    • 6
  • J. Creighton MillerJr
    • 7
  • Richard G. Novy
    • 8
  • Jiwan P. Palta
    • 1
  • David L. Parish
    • 9
  • Gregory A. Porter
    • 10
  • Vidyasagar R. Sathuvalli
    • 11
  • Asunta L. Thompson
    • 12
  • G. Craig Yencho
    • 13
  1. 1.Department of HorticultureUniversity of WisconsinMadisonUSA
  2. 2.Department of Plant, Soil and Microbial SciencesMichigan State UniversityEast LansingUSA
  3. 3.Fredericton Research and Development CentreAgriculture and Agri-Food CanadaFrederictonCanada
  4. 4.School of Integrative Plant ScienceCornell UniversityIthacaUSA
  5. 5.USDA-ARS, Genetic Improvement of Fruits and Vegetables LabBeltsvilleUSA
  6. 6.San Luis Valley Research Center, Department of Horticulture and Landscape ArchitectureColorado State UniversityCenterUSA
  7. 7.Department of Horticultural SciencesTexas A&M UniversityCollege StationUSA
  8. 8.USDA–ARS Small Grains and Potato Germplasm Research UnitAberdeenUSA
  9. 9.AIS Consulting LLCAllenUSA
  10. 10.School of Food and AgricultureUniversity of MaineOronoUSA
  11. 11.Department of Crop and Soil ScienceOregon State UniversityHermistonUSA
  12. 12.Department of Plant SciencesNorth Dakota State UniversityFargoUSA
  13. 13.Department of Horticultural ScienceNorth Carolina State UniversityRaleighUSA

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