BAC-end sequence-based SNPs and Bin mapping for rapid integration of physical and genetic maps in apple.
A genome-wide BAC physical map of the apple, Malus x 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 approximately 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.
Han
Yuepeng
Y
Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, IL 61801, USA.
Chagné
David
D
Gasic
Ksenija
K
Rikkerink
Erik H A
EH
Beever
Jonathan E
JE
Gardiner
Susan E
SE
Korban
Schuyler S
SS
D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D022202:Chromosomes, Artificial, Bacterial; D019295:Computational Biology / Q000379:methods*; D018745:Genome, Plant / Q000235:genetics*; D027845:Malus / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA
D010940:Plant Proteins