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Identification of the putative ancestral allele of bovine single‐nucleotide polymorphisms
Author(s) -
Rocha D.,
Billerey C.,
Samson F.,
Boichard D.,
Boussaha M.
Publication year - 2014
Publication title -
journal of animal breeding and genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.689
H-Index - 51
eISSN - 1439-0388
pISSN - 0931-2668
DOI - 10.1111/jbg.12095
Subject(s) - biology , genetics , genotyping , allele , single nucleotide polymorphism , snp genotyping , snp , selection (genetic algorithm) , allele frequency , population , tag snp , genotype , evolutionary biology , gene , demography , artificial intelligence , sociology , computer science
Summary Identifying the action of natural selection from patterns of standing genetic variation has long been of interest to the population genetic community. Thanks to the availability of large single‐nucleotide polymorphism ( SNP ) data sets for many species and of high‐throughput SNP genotyping methods, whole‐genomic surveys to detect selective sweeps are now possible. Knowing the ancestral allele increases the power to detect selection. We present here a comparative genomic approach to determine the putative ancestral allele of bovine SNP s deposited in public databases. We analysed 19 551 488 SNP s and identified the putative ancestral allele for 14 339 107 SNP s. Our predicted ancestral alleles were in agreement with ancestral alleles detected by genotyping outgroup species for 97% SNP s from the B ovineSNP50 B ead C hip. This comparison indicates that our comparative genomic‐based approach to identify putative ancestral alleles is reliable.