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Open Access Highly Accessed Research article

Genome wide analysis reveals single nucleotide polymorphisms associated with fatness and putative novel copy number variants in three pig breeds

Katie E Fowler1, Ricardo Pong-Wong2, Julien Bauer3, Emily J Clemente3, Christopher P Reitter3, Nabeel A Affara3, Stephen Waite4, Grant A Walling4 and Darren K Griffin1*

Author Affiliations

1 School of Biosciences, University of Kent, Canterbury, Kent CT2 7NH, UK

2 Roslin Institute, The University of Edinburgh, Roslin Biocentre, Midlothian, Scotland EH25 9PS, UK

3 Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK

4 JSR Genetics, Southburn, Driffield, East Yorkshirea YO25 9ED, UK

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BMC Genomics 2013, 14:784  doi:10.1186/1471-2164-14-784

Published: 13 November 2013

Abstract

Background

Obesity, excess fat tissue in the body, can underlie a variety of medical complaints including heart disease, stroke and cancer. The pig is an excellent model organism for the study of various human disorders, including obesity, as well as being the foremost agricultural species. In order to identify genetic variants associated with fatness, we used a selective genomic approach sampling DNA from animals at the extreme ends of the fat and lean spectrum using estimated breeding values derived from a total population size of over 70,000 animals. DNA from 3 breeds (Sire Line Large White, Duroc and a white Pietrain composite line (Titan)) was used to interrogate the Illumina Porcine SNP60 Genotyping Beadchip in order to identify significant associations in terms of single nucleotide polymorphisms (SNPs) and copy number variants (CNVs).

Results

By sampling animals at each end of the fat/lean EBV (estimate breeding value) spectrum the whole population could be assessed using less than 300 animals, without losing statistical power. Indeed, several significant SNPs (at the 5% genome wide significance level) were discovered, 4 of these linked to genes with ontologies that had previously been correlated with fatness (NTS, FABP6, SST and NR3C2). Quantitative analysis of the data identified putative CNV regions containing genes whose ontology suggested fatness related functions (MCHR1, PPARĪ±, SLC5A1 and SLC5A4).

Conclusions

Selective genotyping of EBVs at either end of the phenotypic spectrum proved to be a cost effective means of identifying SNPs and CNVs associated with fatness and with estimated major effects in a large population of animals.

Keywords:
SNP; CNV; Pig; QuantiSNP; cnvPartition; Fatness; Obesity; Genotyping; GWAS