High density LD-based structural variations analysis in cattle genome.

ABSTRACT: 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 (r2) 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, r2 within its neighbors i

SUBMITTER: Salomon-Torres R 

PROVIDER: S-EPMC4106904 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature