Molecular Breeding

, 39:9 | Cite as

Evaluation of Japanese potatoes using single nucleotide polymorphisms (SNPs)

  • Toshiya Igarashi
  • Mutsuo Tsuyama
  • Keiichi Ogawa
  • Emiko Koizumi
  • Rena Sanetomo
  • Kazuyoshi HosakaEmail author


An understanding of the genetic diversity and structure of a breeding population is fundamental information for breeders to develop strategies for variety improvement. The genetic diversity of 250 diverse North American potatoes was previously characterized using an 8K single nucleotide polymorphism (SNP) array. In this study, using a 12K SNP array, 164 Japanese potatoes including 70 breeding clones for chip processing were characterized and compared with North American and European potatoes. A cluster analysis using 5972 polymorphic SNP loci grouped recently released Japanese chip processing varieties and breeding clones with North American and European chip processing varieties. The other Japanese potatoes, including those for starch processing, were not clearly differentiated to specific market types. A unique group of double-cropping varieties was identified, suggesting that strong selection pressure was applied to the cultivation system (spring-season product is used for fall-season cropping). The inter-populational distance between Japanese and foreign genotypes (mean Euclidean distance of 48.4) was significantly lower than the within-populational distance of foreign genotypes (49.3), indicating that the Japanese potatoes are not uniquely differentiated but are included within the genetic diversity of foreign genotypes. This study demonstrates the usefulness of SNP array technology for performing a cost-effective, robust and direct comparison of genetic diversity among different gene pools.


Potato Diversity Breeding population Single nucleotide polymorphism (SNP) 



This research was supported by Calbee Inc., Hokkaido Potato Growers Association, Kewpie Corp., KENKO Mayonnaise Co., Ltd., and Japan Snack Cereal Foods Association.

Authors’ contributions

TI, MT, and KH conceived and designed the experiments. TI, KO, EK, and RS performed the experiments and analyzed the data. TI, RS, and KH wrote the paper. All the authors have read and approved the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no competing interests.

Supplementary material

11032_2018_917_MOESM1_ESM.xlsx (23 kb)
Table S1 (XLSX 22 kb)
11032_2018_917_MOESM2_ESM.xlsx (4.3 mb)
Table S2 (XLSX 4408 kb)


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Copyright information

© Springer Nature B.V. 2018

Authors and Affiliations

  1. 1.Potato Research CenterCalbee Potato Inc.MemuroJapan
  2. 2.Potato Germplasm Enhancement LaboratoryObihiro University of Agriculture and Veterinary MedicineObihiroJapan

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