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Molecular Breeding

, 25:67 | Cite as

Application of high-resolution DNA melting for genotyping and variant scanning of diploid and autotetraploid potato

  • David De KoeyerEmail author
  • Katheryn Douglass
  • Agnes Murphy
  • Sean Whitney
  • Lana Nolan
  • Yong Song
  • Walter De Jong
Article

Abstract

The ideal marker system for tetraploid potato would be dosage-sensitive and have the ability to distinguish heterozygous genotypes with multiple haplotypes within the genomic region targeted by the marker. The objective of this study was to evaluate the utility of high-resolution DNA melting (HRM) for genotyping and polymorphism detection in diploid and tetraploid potato. Amplicon scanning, unlabelled probe, and short amplicon assays were developed for four candidate genes affecting tuber skin and flesh colour, and starch, and a marker linked to nematode resistance. Genotyping a set of 95 potato clones revealed several examples of clones with three distinct haplotypes. Combined probe and amplicon analysis identified between 29 and 44 unique genotypes for the same assays. Assays developed for four of the five target genes are suitable for marker-assisted selection in potato breeding programs. This study illustrates the use of HRM in potato genetics. Further advances in the technology and associated data analysis should make HRM a useful tool for basic and applied studies of potato.

Keywords

Potato High-resolution DNA melting Haplotype dosage Autotetraploid genetics Marker-assisted selection Variant scanning 

Notes

Acknowledgments

We thank Valerie Burns and Stephen Allaby for maintaining the plants and for providing trait descriptions. This work was supported, in part, with funds from the New Brunswick Department of Agriculture and Aquaculture Embracing Innovation in Agriculture program.

Supplementary material

11032_2009_9309_MOESM1_ESM.doc (794 kb)
(DOC 795 kb)

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Copyright information

© Springer Science+Business Media B.V. 2009

Authors and Affiliations

  • David De Koeyer
    • 1
    Email author
  • Katheryn Douglass
    • 1
  • Agnes Murphy
    • 1
  • Sean Whitney
    • 1
  • Lana Nolan
    • 1
    • 2
  • Yong Song
    • 1
    • 3
  • Walter De Jong
    • 4
  1. 1.Potato Research CentreAgriculture and Agri-Food CanadaFrederictonCanada
  2. 2.Faculty of Forestry and Environmental ManagementUniversity of New BrunswickFrederictonCanada
  3. 3.Hunan Provincial Key Laboratory of Crop Germplasm Innovation and UtilizationHunan Agricultural UniversityChangshaPeoples Republic of China
  4. 4.Department of Plant Breeding and GeneticsCornell UniversityIthacaUSA

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