title: Extent and consistency of linkage disequilibrium and identification of DNA markers for production and egg quality traits in commercial layer chicken populations.
abstract: BACKGROUND
  The genome sequence and a high-density SNP map are now available for the chicken and can be used to identify genetic markers for use in marker-assisted selection (MAS). Effective MAS requires high linkage disequilibrium (LD) between markers and quantitative trait loci (QTL), and sustained marker-QTL LD over generations. This study used data from a 3,000 SNP panel to assess the level and consistency of LD between single nucleotide polymorphisms (SNPs) over consecutive years in two egg-layer chicken lines, and analyzed one line by two methods (SNP-wise association and genome-wise Bayesian analysis) to identify markers associated with egg-quality and egg-production phenotypes.
  
  
  RESULTS
  The LD between markers pairs was high at short distances (r2 > 0.2 at < 2 Mb) and remained high after one generation (correlations of 0.80 to 0.92 at < 5 Mb) in both lines. Single- and 3-SNP regression analyses using a mixed model with SNP as fixed effect resulted in 159 and 76 significant tests (P < 0.01), respectively, across 12 traits. A Bayesian analysis called BayesB, that fits all SNPs simultaneously as random effects and uses model averaging procedures, identified 33 SNPs that were included in the model >20% of the time (phi > 0.2) and an additional ten 3-SNP windows that had a sum of phi greater than 0.35. Generally, SNPs included in the Bayesian model also had a small P-value in the 1-SNP analyses.
  
  
  CONCLUSIONS
  High LD correlations between markers at short distances across two generations indicate that such markers will retain high LD with linked QTL and be effective for MAS. The different association analysis methods used provided consistent results. Multiple single SNPs and 3-SNP windows were significantly associated with egg-related traits, providing genomic positions of QTL that can be useful for both MAS and to identify causal mutations.
authors.affiliation: Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, IA 50011, USA. abasht@iastate.edu
authors.forename: Behnam
authors.initials: B
authors.lastname: Abasht
authors.forename: Erin
authors.initials: E
authors.lastname: Sandford
authors.forename: Jesus
authors.initials: J
authors.lastname: Arango
authors.forename: Petek
authors.initials: P
authors.lastname: Settar
authors.forename: Janet E
authors.initials: JE
authors.lastname: Fulton
authors.forename: Neil P
authors.initials: NP
authors.lastname: O'Sullivan
authors.forename: Abebe
authors.initials: A
authors.lastname: Hassen
authors.forename: David
authors.initials: D
authors.lastname: Habier
authors.forename: Rohan L
authors.initials: RL
authors.lastname: Fernando
authors.forename: Jack C M
authors.initials: JC
authors.lastname: Dekkers
authors.forename: Susan J
authors.initials: SJ
authors.lastname: Lamont
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D001947:Breeding; D002645:Chickens / Q000235:genetics*; D004531:Eggs; D005819:Genetic Markers; D005828:Genetics, Population; D016678:Genome; D005838:Genotype; D015810:Linkage Disequilibrium; D008957:Models, Genetic; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D012044:Regression Analysis
chemical_list: D005819:Genetic Markers