title: Genome-wide genetic diversity of 'Nici', the DNA source for the CHORI-260 turkey BAC library and candidate for whole genome sequencing.
abstract: Vertebrate whole genome sequence assembly can benefit from a priori knowledge of variability in the target genome, with researchers often selecting highly inbred individuals for sequencing. However, for most species highly inbred research lines are lacking, requiring the use of an outbred individual(s). Here we examined the source DNA [Nicholas inbred (Nici)] of the CHORI-260 turkey bacterial artificial chromosome (BAC) library through analysis of microsatellites and BAC sequences. Heterozygosity of Nici was compared with that of individuals from several breeder lines. Seventy-eight microsatellites were screened for polymorphism in a total of 43 birds, identifying an average individual heterozygosity of 0.39, with Nici at 0.35. Additional loci (total of 147) were examined on a subset of individuals to obtain better genome coverage. The mean heterozygosity for this subset was 0.33 with Nici at 0.31. Examination of approximately 200 kb of genome sequence identified SNPs in the order of one per 200 bp in Nici. These data suggest that the heterozygosity of Nici is comparable to other birds of selected breeder lines and that whole genome sequencing would result in an abundant resource of genome-wide polymorphisms.
authors.affiliation: Department of Veterinary and Biomedical Sciences, University of Minnesota, St Paul, MN 55108, USA. chave012@umn.edu
authors.forename: L D
authors.initials: LD
authors.lastname: Chaves
authors.forename: D E
authors.initials: DE
authors.lastname: Harry
authors.forename: K M
authors.initials: KM
authors.lastname: Reed
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics*; D004247:DNA / Q000737:chemistry / Q000235:genetics*; D005260:Female; D014644:Genetic Variation; D005838:Genotype; D008297:Male; D018895:Microsatellite Repeats; D020641:Polymorphism, Single Nucleotide; D014422:Turkeys / Q000235:genetics*
chemical_list: D004247:DNA