title: Copy number variations in high and low fertility breeding boars.
abstract: BACKGROUND
  In this study we applied the extreme groups/selective genotyping approach for identifying copy number variations in high and low fertility breeding boars. The fertility indicator was the calculated Direct Boar Effect on litter size (DBE) that was obtained as a by-product of the national genetic evaluation for litter size (BLUP). The two groups of animals had DBE values at the upper (high fertility) and lower (low fertility) end of the distribution from a population of more than 38,000 boars. Animals from these two diverse phenotypes were genotyped with the Porcine SNP60K chip and compared by several approaches in order to prove the feasibility of our CNV analysis and to identify putative markers of fertility.
  
  
  RESULTS
  We have identified 35 CNVRs covering 36.5 Mb or ~1.3% of the porcine genome. Among these 35 CNVRs, 14 were specific to the high fertility group, while 19 CNVRs were specific to the low fertility group which overlap with 137 QTLs of various reproductive traits. The identified 35 CNVRs encompassed 50 genes, among them 40 were specific to the low fertility group, seven to the high fertility group, while three were found in regions that were present in both groups but with opposite gain/loss status. A functional analysis of several databases revealed that the genes found in CNVRs from the low fertility group have been significantly enriched in members of the innate immune system, Toll-like receptor and RIG-I-like receptor signaling and fatty acid oxidation pathways.
  
  
  CONCLUSIONS
  We have demonstrated that our analysis pipeline could identify putative CNV markers of fertility, especially in case of low fertility boars.
authors.affiliation: University of Guelph, Ontario Veterinary College, Department of Biomedical Sciences, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada. trevay@uoguelph.ca.
authors.forename: Tamas
authors.initials: T
authors.lastname: Revay
authors.affiliation: University of Guelph, Ontario Veterinary College, Department of Biomedical Sciences, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada. tquach@uoguelph.ca.
authors.forename: Anh T
authors.initials: AT
authors.lastname: Quach
authors.affiliation: Canadian Centre for Swine Improvement Inc. (CCSI), Central Experimental Farm, Building #75, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada. laurence@ccsi.ca.
authors.forename: Laurence
authors.initials: L
authors.lastname: Maignel
authors.affiliation: Canadian Centre for Swine Improvement Inc. (CCSI), Central Experimental Farm, Building #75, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada. brian@ccsi.ca.
authors.forename: Brian
authors.initials: B
authors.lastname: Sullivan
authors.affiliation: University of Guelph, Ontario Veterinary College, Department of Biomedical Sciences, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada. waking@uoguelph.ca.
authors.forename: W Allan
authors.initials: WA
authors.lastname: King
mesh_terms: D000818:Animals; D001947:Breeding; D056915:DNA Copy Number Variations / Q000235:genetics*; D005298:Fertility / Q000235:genetics* / Q000502:physiology; D005838:Genotype; D008297:Male; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D040641:Quantitative Trait Loci / Q000235:genetics*; D013552:Swine