High density LD-based structural variations analysis in cattle genome

Genomic structural variations represent an important source of genetic variation in mammal genomes, thus, they are commonly related to phenotypic expressions. In this work, ∼770,000 single nucleotide polymorphism genotypes from 506 animals from 19 cattle breeds were analyzed. A simple LD-based structural variation was defined, and a genome-wide analysis was performed. After applying some quality control filters, for each breed and each chromosome we calculated the linkage disequilibrium (r 2) of short range (≤100 Kb). We sorted SNP pairs by distance and obtained a set of LD means (called the expected means) using bins of 5 Kb. We identified 15,246 segments of at least 1 Kb, among the 19 breeds, consisting of sets of at least 3 adjacent SNPs so that, for each SNP, r 2 within its neighbors in a 100 Kb range, to the right side of that SNP, were all bigger than, or all smaller than, the corresponding expected mean, and their P-value were significant after a Benjamini-Hochberg multiple testing correction. In addition, to account just for homogeneously distributed regions we considered only SNPs having at least 15 SNP neighbors within 100 Kb. We defined such segments as structural variations. By grouping all variations across all animals in the sample we defined 9,146 regions, involving a total of 53,137 SNPs; representing the 6.40% (160.98 Mb) from the bovine genome. The identified structural variations covered 3,109 genes. Clustering analysis showed the relatedness of breeds given the geographic region in which they are evolving. In summary, we present an analysis of structural variations based on the deviation of the expected short range LD between SNPs in the bovine genome. With an intuitive and simple definition based only on SNPs data it was possible to discern closeness of breeds due to grouping by geographic region in which they are evolving.