Skip to main content
ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Reproduction Research » Research » Publications at this Location » Publication #323663

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

Location: Reproduction Research

Title: Do you really know where this SNP goes?

Author
item Rohrer, Gary
item Nonneman, Danny - Dan
item Schroeder, Steven - Steve
item Chin, Jason - Pacific Biosciences Inc
item Koren, Sergey - National Biodefense Analysis And Countermeasures Center
item Phillippy, Adam - National Biodefense Analysis And Countermeasures Center
item Green, Richard - Dovetail Genomics
item Putnam, Nicholas - Dovetail Genomics
item Smith, Timothy - Tim

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 1/9/2016
Publication Date: 1/9/2016
Citation: Rohrer, G.A., Nonneman, D., Schroeder, S.G., Chin, J., Koren, S., Phillippy, A., Green, R., Putnam, N., Smith, T.P.L. 2016. Do you really know where this SNP goes? [abstract] Plant and Animal Genome XXIV Conference Proceedings. Abstract #W909.

Interpretive Summary:

Technical Abstract: The release of build 10.2 of the swine genome was a marked improvement over previous builds and has proven extremely useful. However, as most know, there are regions of the genome that this particular build does not accurately represent. For instance, nearly 25% of the 62,162 SNP on the Illumina Porcine SNP60v1 BeadChip do not map to a unique position in build 10.2. To resolve these issues of the swine genome, we utilized advances in long-read sequencing combined with new technologies for scaffolding the resulting contigs to create a de novo build of the genome for a male pig from the USMARC swine population. A total of 85% of the SNP sequences uniquely mapped to the new genome assembly. More importantly, when comparing SNP genomic position between both builds, several inconsistencies arose. Eighty inconsistencies involving assignments to different chromosomes or large discrepancies in location (> 20 Mb) were investigated. These inconsistencies were evaluated by comparing linkage disequilibrium values between subsets of markers involved in these inconsistencies with flanking markers of both predicted regions. Linkage disequilibrium values were computed from genotypes collected on over 3,000 pigs in the USMARC swine commercial population. A total of 223 SNP markers were studied and 22% of the inconsistencies could not be resolved, 2% agreed with build 10.2 and 76% of the inconsistencies indicated that the new build was correct.