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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Reproduction Research » Research » Publications at this Location » Publication #312562

Research Project: Genetic and Genomic Approaches to Improve Swine Reproductive Efficiency

Location: Reproduction Research

Title: Genome-wide copy number variations using SNP genotyping in a mixed breed swine population

Author
item Wiedmann, Ralph
item Nonneman, Danny - Dan
item Rohrer, Gary

Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/27/2015
Publication Date: 7/14/2015
Publication URL: http://handle.nal.usda.gov/10113/61125
Citation: Wiedmann, R.T., Nonneman, D.J., Rohrer, G.A. 2015. Genome-wide copy number variations using SNP genotyping in a mixed breed swine population. PLoS One. 10(7):e0133529. DOI: 10.1371/journal.pone.0133529.

Interpretive Summary: Superior pigs come, in large part, from superior genetics. Most of the studies of pig genetics concentrate on individual, alternate nucleotides. While that can explain some of the differences in physical traits, this study examines larger, less frequent changes in porcine genome sequence, namely copy number variants (CNVs). CNVs are sections of the genome approximately 1000 nucleotides or larger that can appear multiple times in an individual, with the exact number of copies varying between individuals. Previous studies in a wide variety of plants and animals have linked CNVs to important traits. Most previous studies of swine CNVs took place in China and used predominantly Chinese breeds of pigs. This study has discovered 503 CNVs in the mixed breed swine population that was developed at USMARC. Similarities and differences with the Chinese results are reported. Because the USMARC pig population has been heavily phenotyped, and is composed of breeds important to US agriculture, the new results reported in this study can be used to further determine what makes for superior genetics in domestic pig production.

Technical Abstract: Copy number variations (CNVs) are increasingly understood to affect phenotypic variation. This study uses SNP genotyping of trios of mixed breed swine to add to the catalog of known genotypic variation in an important agricultural animal. Porcine SNP60 BeadChip genotypes were collected from 1802 pigs that combined to form 1621 trios. These trios were from the crosses of 50 boars with 525 sows producing 1621 piglets. The pigs were part of a population that was a mix of ¼ Duroc, ½ Landrace and ¼ Yorkshire breeds. Merging the overlapping CNVs that were observed in individuals to form CNV regions (CNVRs) yielded 949 CNVRs across the autosomes, 503 of which were observed in more than one animal. CNVRs observed exactly once covered 22.4% of the genome, while those observed at least twice covered 8.2% of the autosomal genome sequence. The CNVRs observed more than once intersected genes, as defined by RefSeq, 78% of the time – 393 out of 503. The results of this study are compared and contrasted to other swine studies using similar and different methods of detecting CNVR. While progress is being made in this field, more work needs to be done to improve consistency and confidence in CNVR results.