Tree Genetics & Genomes

, Volume 10, Issue 4, pp 853–863 | Cite as

Transcriptome-based single nucleotide polymorphism markers for genome mapping in Japanese pear (Pyrus pyrifolia Nakai)

  • Shingo Terakami
  • Chikako Nishitani
  • Miyuki Kunihisa
  • Kenta Shirasawa
  • Shusei Sato
  • Satoshi Tabata
  • Kanako Kurita
  • Hiroyuki Kanamori
  • Yuichi Katayose
  • Norio Takada
  • Toshihiro Saito
  • Toshiya Yamamoto
Original Paper


The development of single nucleotide polymorphism (SNP) markers in Japanese pear (Pyrus pyrifolia Nakai) offers the opportunity to use DNA markers for marker-assisted selection in breeding programs because of their high abundance, codominant inheritance, and potential for automated high-throughput analysis. We developed a 1,536-SNP bead array without a reference genome sequence from more than 44,000 base changes on the basis of a large-scale expressed sequence tag (EST) analysis combined with 454 genome sequencing data of Japanese pear ‘Housui’. Among the 1,536 SNPs on the array, 756 SNPs were genotyped, and 609 SNP loci were mapped to linkage groups on a genetic linkage map of ‘Housui’, based on progeny of an interspecific cross between European pear (Pyrus communis L.) ‘Bartlett’ and ‘Housui’. The newly constructed genetic linkage map consists of 951 loci, comprising 609 new SNPs, 110 pear genomic simple sequence repeats (SSRs), 25 pear EST–SSRs, 127 apple SSRs, 61 pear SNPs identified by the “potential intron polymorphism” method, and 19 other loci. The map covers 22 linkage groups spanning 1341.9 cM with an average distance of 1.41 cM between markers and is anchored to reference genetic linkage maps of European pears and apples. A total of 514 contigs containing mapped SNP loci showed significant similarity to known proteins by functional annotation analysis.


Genetic linkage map Genome-wide SNPs GoldenGate Housui Linkage map 



We thank Ms. F. Hosaka, N. Shigeta, and N. Yagihashi for their technical help. This work was partially supported by a grant from the Ministry of Agriculture, Forestry and Fisheries of Japan (Genomics for Agricultural Innovation, SGE-1003).

Supplementary material

11295_2014_726_MOESM1_ESM.xlsx (217 kb)
ESM 1 (XLSX 216 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Shingo Terakami
    • 1
  • Chikako Nishitani
    • 1
  • Miyuki Kunihisa
    • 1
  • Kenta Shirasawa
    • 2
  • Shusei Sato
    • 2
  • Satoshi Tabata
    • 2
  • Kanako Kurita
    • 3
  • Hiroyuki Kanamori
    • 3
  • Yuichi Katayose
    • 3
  • Norio Takada
    • 1
  • Toshihiro Saito
    • 1
  • Toshiya Yamamoto
    • 1
  1. 1.NARO Institute of Fruit Tree ScienceTsukubaJapan
  2. 2.Kazusa DNA Research InstituteKisarazuJapan
  3. 3.National Institute of Agrobiological SciencesTsukubaJapan

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