New single nucleotide polymorphisms in Alectoris identified using chicken genome information allow Alectoris introgression detection

Abstract

Using the chicken genome, 114 polymorphisms (109 SNPs and 5 INDELs) were identified in the Alectoris genus by polymerase chain reaction–single strand conformation polymorphism. Using these, a panel of SNPs is described, which allows easy detection of introgression of Alectoris chukar in wild Alectoris rufa populations, when used with a primer extension protocol. The selected polymorphisms were genotyped and their allelic frequencies estimated on 98 A. rufa partridges sampled from nonrestocking Spanish areas, and 63 A. chukar partridges from Greek and Spanish farms. Power calculations to determine an optimum subset of markers for a given significance level were performed.