title: Association, effects and validation of polymorphisms within the NCAPG - LCORL locus located on BTA6 with feed intake, gain, meat and carcass traits in beef cattle.
abstract: BACKGROUND
  In a previously reported genome-wide association study based on a high-density bovine SNP genotyping array, 8 SNP were nominally associated (P ≤ 0.003) with average daily gain (ADG) and 3 of these were also associated (P ≤ 0.002) with average daily feed intake (ADFI) in a population of crossbred beef cattle. The SNP were clustered in a 570 kb region around 38 Mb on the draft sequence of bovine chromosome 6 (BTA6), an interval containing several positional and functional candidate genes including the bovine LAP3, NCAPG, and LCORL genes. The goal of the present study was to develop and examine additional markers in this region to optimize the ability to distinguish favorable alleles, with potential to identify functional variation.
  
  
  RESULTS
  Animals from the original study were genotyped for 47 SNP within or near the gene boundaries of the three candidate genes. Sixteen markers in the NCAPG-LCORL locus displayed significant association with both ADFI and ADG even after stringent correction for multiple testing (P ≤ 005). These markers were evaluated for their effects on meat and carcass traits. The alleles associated with higher ADFI and ADG were also associated with higher hot carcass weight (HCW) and ribeye area (REA), and lower adjusted fat thickness (AFT). A reduced set of markers was genotyped on a separate, crossbred population including genetic contributions from 14 beef cattle breeds. Two of the markers located within the LCORL gene locus remained significant for ADG (P ≤ 0.04).
  
  
  CONCLUSIONS
  Several markers within the NCAPG-LCORL locus were significantly associated with feed intake and body weight gain phenotypes. These markers were also associated with HCW, REA and AFT suggesting that they are involved with lean growth and reduced fat deposition. Additionally, the two markers significant for ADG in the validation population of animals may be more robust for the prediction of ADG and possibly the correlated trait ADFI, across multiple breeds and populations of cattle.
authors.affiliation: United States Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center,Clay Center, NE 68933, USA. Amanda.Lindholm@ars.usda.gov
authors.forename: Amanda K
authors.initials: AK
authors.lastname: Lindholm-Perry
authors.forename: Andrea K
authors.initials: AK
authors.lastname: Sexten
authors.forename: Larry A
authors.initials: LA
authors.lastname: Kuehn
authors.forename: Timothy P L
authors.initials: TP
authors.lastname: Smith
authors.forename: D Andy
authors.initials: DA
authors.lastname: King
authors.forename: Steven D
authors.initials: SD
authors.lastname: Shackelford
authors.forename: Tommy L
authors.initials: TL
authors.lastname: Wheeler
authors.forename: Calvin L
authors.initials: CL
authors.lastname: Ferrell
authors.forename: Thomas G
authors.initials: TG
authors.lastname: Jenkins
authors.forename: Warren M
authors.initials: WM
authors.lastname: Snelling
authors.forename: Harvey C
authors.initials: HC
authors.lastname: Freetly
mesh_terms: D000818:Animals; D001823:Body Composition / Q000235:genetics*; D002417:Cattle / Q000235:genetics*; D018797:Cell Cycle Proteins / Q000235:genetics*; D002874:Chromosome Mapping; D005819:Genetic Markers; D008460:Meat; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D015430:Weight Gain / Q000235:genetics
chemical_list: D018797:Cell Cycle Proteins; D005819:Genetic Markers