Do you really know where this SNP goes?

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.

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