A high-throughput apple SNP genotyping platform using the GoldenGate™ assay

M. Awais Khan, Yuepeng Han, Youfu Frank Zhao, Schuyler S. Korban

Research output: Contribution to journalArticlepeer-review


EST data generated from 14 apple genotypes were downloaded from NCBI and mapped against a reference EST assembly to identify Single Nucleotide Polymorphisms (SNPs). Mapping of these SNPs was undertaken using 90% of sequence similarity and minimum coverage of four reads at each SNP position. In total, 37,807 SNPs were identified with an average of one SNP every 187. bp from a total of 6888 unique EST contigs. Identified SNPs were checked for flanking sequences of ≥ 60 bp along both sides of SNP alleles for reliable design of a custom high-throughput genotyping assay. A total of 12,299 SNPs, representing 6525 contigs, fit the selected criterion of ≥ 60 bp sequences flanking a SNP position. Of these, 1411 SNPs were validated using four apple genotypes. Based on genotyping assays, it was estimated that 60% of SNPs were valid SNPs, while 26% of SNPs might be derived from paralogous regions.

Original languageEnglish (US)
Pages (from-to)196-201
Number of pages6
Issue number2
StatePublished - Feb 25 2012


  • Expressed sequence tags (ESTs)
  • Genotyping
  • Malus
  • Single Nucleotide Polymorphisms (SNPs)

ASJC Scopus subject areas

  • Genetics


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