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Whole Genome Association Studies of Residual Feed Intake and Related Traits in the Pig

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  • Suneel K Onteru
  • Danielle M Gorbach
  • Jennifer M Young
  • Dorian J Garrick
  • Jack C M Dekkers
  • Max F Rothschild

Abstract

Background: Residual feed intake (RFI), a measure of feed efficiency, is the difference between observed feed intake and the expected feed requirement predicted from growth and maintenance. Pigs with low RFI have reduced feed costs without compromising their growth. Identification of genes or genetic markers associated with RFI will be useful for marker-assisted selection at an early age of animals with improved feed efficiency. Methodology/Principal findings: Whole genome association studies (WGAS) for RFI, average daily feed intake (ADFI), average daily gain (ADG), back fat (BF) and loin muscle area (LMA) were performed on 1,400 pigs from the divergently selected ISU-RFI lines, using the Illumina PorcineSNP60 BeadChip. Various statistical methods were applied to find SNPs and genomic regions associated with the traits, including a Bayesian approach using GenSel software, and frequentist approaches such as allele frequency differences between lines, single SNP and haplotype analyses using PLINK software. Single SNP and haplotype analyses showed no significant associations (except for LMA) after genomic control and FDR. Bayesian analyses found at least 2 associations for each trait at a false positive probability of 0.5. At generation 8, the RFI selection lines mainly differed in allele frequencies for SNPs near (

Suggested Citation

  • Suneel K Onteru & Danielle M Gorbach & Jennifer M Young & Dorian J Garrick & Jack C M Dekkers & Max F Rothschild, 2013. "Whole Genome Association Studies of Residual Feed Intake and Related Traits in the Pig," PLOS ONE, Public Library of Science, vol. 8(6), pages 1-13, June.
  • Handle: RePEc:plo:pone00:0061756
    DOI: 10.1371/journal.pone.0061756
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    1. Randy J. Seeley & Keith A. Yagaloff & Stewart L. Fisher & Paul Burn & Todd E. Thiele & Gertjan van Dijk & Denis G. Baskin & Michael W. Schwartz, 1997. "Melanocortin receptors in leptin effects," Nature, Nature, vol. 390(6658), pages 349-349, November.
    2. Jeffrey M. Friedman & Jeffrey L. Halaas, 1998. "Leptin and the regulation of body weight in mammals," Nature, Nature, vol. 395(6704), pages 763-770, October.
    3. Michael W. Schwartz & Stephen C. Woods & Daniel Porte & Randy J. Seeley & Denis G. Baskin, 2000. "Central nervous system control of food intake," Nature, Nature, vol. 404(6778), pages 661-671, April.
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