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This article in JAS

  1. Vol. 91 No. 3, p. 1041-1050
     
    Received: July 12, 2012
    Accepted: Nov 29, 2012
    Published: December 2, 2014


    2 Corresponding author(s): goutam.sahana@agrsci.dk
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doi:10.2527/jas.2012-5643

A genome-wide association scan in pig identifies novel regions associated with feed efficiency trait1

  1. Goutam Sahana 2,
  2. Veronika Kadlecová*†,
  3. Henrik Hornshøj*,
  4. Bjarne Nielsen and
  5. Ole F. Christensen*
  1. Department of Molecular Biology and Genetics, Aarhus University, Blichers Alle 20, Postboks 50, DK-8830 Tjele, Denmark
    Department of Animal Husbandry, Czech University of Life Sciences Prague, 165 21 Prague 6-Suchdol, Czech Republic
    Pig Research Centre, Danish Agriculture and Food Council, Axeltorv 3, DK-1609 Copenhagen V, Denmark

Abstract

Feed conversion ratio (FCR) is an economically important trait in pigs, and feed accounts for a significant proportion of the costs involved in pig production. In this study we used a high-density SNP chip panel, Porcine SNP60 BeadChip, to identify the association between FCR and SNP markers and to study the genetic architecture of the trait. After quality control, a total of 30,847 SNP that could be mapped to the 18 porcine autosomes (SSC) using the pig genome assembly 10.2 were used in the analyses. Deregressed estimated breeding value was used as the response variable. A total of 3,071 Duroc pigs had both FCR data and genotype data. The linkage disequilibrium (r2) between adjacent markers was 0.56. Two association mapping approaches were used: a linear mixed model (LMM) based on single-locus regression analysis and a Bayesian variable selection approach (BVS). A total of 79 significant (P < 0.0001) SNP associations on 6 chromosomes were identified by LMM analyses. Out of these, 10 SNP crossed the genome-wide significance threshold. These 10 SNP were all located on SSC 4 and 14. In the BVS analysis, a total of 44 SNP located on 12 chromosomes had posterior probability more than or equal to 0.05 (i.e., Bayes factor ≥ 10). Thirteen SNP were identified by both LMM and BVS. These 13 SNP were located on 4 chromosomes: SSC 4, 7, 8, and 14. Hypoxia inducible factor 1, alpha subunit inhibitor (HIF1AN) and ladybird homeobox 1 (LBX1) are 2 possible candidate genes affecting FCR on SSC 4 and 14, respectively. The study provides a list of SNP associated with FCR and also offers valuable information on the genetic architecture and candidate genes for this trait.

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