BAC-end sequence-based SNPs and Bin mapping for rapid integration of physical and genetic maps in apple

Yuepeng Han, David Chagné, Ksenija Gasic, Erik H.A. Rikkerink, Jonathan Edward Beever, Susan E. Gardiner, Schuyler S. Korban

Research output: Contribution to journalArticlepeer-review

Abstract

A genome-wide BAC physical map of the apple, Malus × domestica Borkh., has been recently developed. Here, we report on integrating the physical and genetic maps of the apple using a SNP-based approach in conjunction with bin mapping. Briefly, BAC clones located at ends of BAC contigs were selected, and sequenced at both ends. The BAC end sequences (BESs) were used to identify candidate SNPs. Subsequently, these candidate SNPs were genetically mapped using a bin mapping strategy for the purpose of mapping the physical onto the genetic map. Using this approach, 52 (23%) out of 228 BESs tested were successfully exploited to develop SNPs. These SNPs anchored 51 contigs, spanning ∼ 37 Mb in cumulative physical length, onto 14 linkage groups. The reliability of the integration of the physical and genetic maps using this SNP-based strategy is described, and the results confirm the feasibility of this approach to construct an integrated physical and genetic maps for apple.

Original languageEnglish (US)
Pages (from-to)282-288
Number of pages7
JournalGenomics
Volume93
Issue number3
DOIs
StatePublished - Mar 2009
Externally publishedYes

Keywords

  • Apple
  • Bin mapping
  • Genetic map
  • Physical map
  • Single nucleotide polymorphisms

ASJC Scopus subject areas

  • Genetics

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