title: Large-scale association study for structural soundness and leg locomotion traits in the pig.
abstract: BACKGROUND
  Identification and culling of replacement gilts with poor skeletal conformation and feet and leg (FL) unsoundness is an approach used to reduce sow culling and mortality rates in breeding stock. Few candidate genes related to soundness traits have been identified in the pig.
  
  
  METHODS
  In this study, 2066 commercial females were scored for 17 traits describing body conformation and FL structure, and were used for association analyses. Genotyping of 121 SNPs derived from 95 genes was implemented using Sequenom's MassARRAY system.
  
  
  RESULTS
  Based on the association results from single trait and principal components using mixed linear model analyses and false discovery rate testing, it was observed that APOE, BMP8, CALCR, COL1A2, COL9A1, DKFZ, FBN1 and VDBP were very highly significantly (P < 0.001) associated with body conformation traits. The genes ALOX5, BMP8, CALCR, OPG, OXTR and WNT16 were very highly significantly (P < 0.001) associated with FL structures, and APOE, CALCR, COL1A2, GNRHR, IHH, MTHFR and WNT16 were highly significantly (P < 0.01) associated with overall leg action. Strong linkage disequilibrium between CALCR and COL1A2 on SSC9 was detected, and haplotype -ACGACC- was highly significantly (P < 0.01) associated with overall leg action and several important FL soundness traits.
  
  
  CONCLUSIONS
  The present findings provide a comprehensive list of candidate genes for further use in fine mapping and biological functional analyses.
authors.affiliation: Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, IA 50011, USA. bfan@iastate.edu
authors.forename: Bin
authors.initials: B
authors.lastname: Fan
authors.forename: Suneel K
authors.initials: SK
authors.lastname: Onteru
authors.forename: Benny E
authors.initials: BE
authors.lastname: Mote
authors.forename: Timo
authors.initials: T
authors.lastname: Serenius
authors.forename: Kenneth J
authors.initials: KJ
authors.lastname: Stalder
authors.forename: Max F
authors.initials: MF
authors.lastname: Rothschild
mesh_terms: D000818:Animals; D005260:Female; D055106:Genome-Wide Association Study; D005838:Genotype; D006614:Hindlimb / Q000502:physiology*; D015810:Linkage Disequilibrium; D008124:Locomotion; D008297:Male; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D019655:Quantitative Trait, Heritable; D013552:Swine / Q000235:genetics* / Q000502:physiology