title: Linkage disequilibrium in crossbred and pure line chickens.
abstract: BACKGROUND
  Both genome-wide association (GWA) studies and genomic selection depend on the level of non-random association of alleles at different loci, i.e. linkage disequilibrium (LD), across the genome. Therefore, characterizing LD is of fundamental importance to implement both approaches. In this study, using a 60K single nucleotide polymorphism (SNP) panel, we estimated LD and haplotype structure in crossbred broiler chickens and their component pure lines (one male and two female lines) and calculated the consistency of LD between these populations.
  
  
  RESULTS
  The average level of LD (measured by r(2)) between adjacent SNPs across the chicken autosomes studied here ranged from 0.34 to 0.40 in the pure lines but was only 0.24 in the crossbred populations, with 28.4% of adjacent SNP pairs having an r(2) higher than 0.3. Compared with the pure lines, the crossbred populations consistently showed a lower level of LD, smaller haploblock sizes and lower haplotype homozygosity on macro-, intermediate and micro-chromosomes. Furthermore, correlations of LD between markers at short distances (0 to 10 kb) were high between crossbred and pure lines (0.83 to 0.94).
  
  
  CONCLUSIONS
  Our results suggest that using crossbred populations instead of pure lines can be advantageous for high-resolution QTL (quantitative trait loci) mapping in GWA studies and to achieve good persistence of accuracy of genomic breeding values over generations in genomic selection. These results also provide useful information for the design and implementation of GWA studies and genomic selection using crossbred populations.
authors.affiliation: Department of Animal and Food Sciences, University of Delaware, Newark, DE, 19716, USA. wfu@udel.edu.
authors.forename: Weixuan
authors.initials: W
authors.lastname: Fu
authors.affiliation: Department of Animal Science, Iowa State University, Ames, IA, 50011, USA. jdekkers@iastate.edu.
authors.forename: Jack C M
authors.initials: JC
authors.lastname: Dekkers
authors.affiliation: Heritage Breeders, LLC, Salisbury, MD, 21804, USA. bill.lee@perdue.com.
authors.forename: William R
authors.initials: WR
authors.lastname: Lee
authors.affiliation: Department of Animal and Food Sciences, University of Delaware, Newark, DE, 19716, USA. abasht@udel.edu.
authors.forename: Behnam
authors.initials: B
authors.lastname: Abasht
mesh_terms: D000483:Alleles; D000818:Animals; D001947:Breeding / Q000379:methods*; D002645:Chickens / Q000235:genetics*; D002874:Chromosome Mapping; D005260:Female; D005787:Gene Frequency; D005819:Genetic Markers; D016678:Genome; D055106:Genome-Wide Association Study; D005838:Genotype; D006824:Hybridization, Genetic; D015810:Linkage Disequilibrium; D008297:Male; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D012641:Selection, Genetic
chemical_list: D005819:Genetic Markers