title: Genome-wide QTL mapping of nine body composition and bone mineral density traits in pigs.
abstract: BACKGROUND
  Since the pig is one of the most important livestock animals worldwide, mapping loci that are associated with economically important traits and/or traits that influence animal welfare is extremely relevant for efficient future pig breeding. Therefore, the purpose of this study was a genome-wide mapping of quantitative trait loci (QTL) associated with nine body composition and bone mineral traits: absolute (Fat, Lean) and percentage (FatPC, LeanPC) fat and lean mass, live weight (Weight), soft tissue X-ray attenuation coefficient (R), absolute (BMC) and percentage (BMCPC) bone mineral content and bone mineral density (BMD).
  
  
  METHODS
  Data on the nine traits investigated were obtained by Dual-energy X-ray absorptiometry for 551 pigs that were between 160 and 200 days old. In addition, all pigs were genotyped using Illumina's PorcineSNP60 Genotyping BeadChip. Based on these data, a genome-wide combined linkage and linkage disequilibrium analysis was conducted. Thus, we used 44 611 sliding windows that each consisted of 20 adjacent single nucleotide polymorphisms (SNPs). For the middle of each sliding window a variance component analysis was carried out using ASReml. The underlying mixed linear model included random QTL and polygenic effects, with fixed effects of sex, housing, season and age.
  
  
  RESULTS
  Using a Bonferroni-corrected genome-wide significance threshold of P < 0.001, significant peaks were identified for all traits except BMCPC. Overall, we identified 72 QTL on 16 chromosomes, of which 24 were significantly associated with one trait only and the remaining with more than one trait. For example, a QTL on chromosome 2 included the highest peak across the genome for four traits (Fat, FatPC, LeanPC and R). The nearby gene, ZNF608, is known to be associated with body mass index in humans and involved in starvation in Drosophila, which makes it an extremely good candidate gene for this QTL.
  
  
  CONCLUSIONS
  Our QTL mapping approach identified 72 QTL, some of which confirmed results of previous studies in pigs. However, we also detected significant associations that have not been published before and were able to identify a number of new and promising candidate genes, such as ZNF608.
authors.forename: Sophie
authors.initials: S
authors.lastname: Rothammer
authors.forename: Prisca V
authors.initials: PV
authors.lastname: Kremer
authors.forename: Maren
authors.initials: M
authors.lastname: Bernau
authors.forename: Ignacio
authors.initials: I
authors.lastname: Fernandez-Figares
authors.forename: Jennifer
authors.initials: J
authors.lastname: Pfister-Schär
authors.affiliation: Chair of Animal Genetics and Husbandry, Ludwig-Maximilians-University Munich, Veterinärstrasse 13, Munich, 80539, Germany. ivica.medjugorac@gen.vetmed.uni-muenchen.de.
authors.forename: Ivica
authors.initials: I
authors.lastname: Medugorac
authors.forename: Armin M
authors.initials: AM
authors.lastname: Scholz
mesh_terms: D000818:Animals; D017849:Animals, Inbred Strains; D001823:Body Composition / Q000235:genetics*; D015519:Bone Density / Q000235:genetics*; D002874:Chromosome Mapping; D003433:Crosses, Genetic; D008040:Genetic Linkage; D055106:Genome-Wide Association Study; D020412:Multifactorial Inheritance; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D034421:Sus scrofa / Q000235:genetics*