Identification of Selection Signatures in Cattle Breeds Selected for Dairy Production

Abstract

The genomics revolution has spurred the undertaking of HapMap studies of numerous species, allowing for population genomics to increase the understanding of how selection has created genetic differences between subspecies populations. The objectives of this study were to (1) develop an approach to detect signatures of selection in subsets of phenotypically similar breeds of livestock by comparing single nucleotide polymorphism (SNP) diversity between the subset and a larger population, (2) verify this method in breeds selected for simply inherited traits, and (3) apply this method to the dairy breeds in the International Bovine HapMap (IBHM) study. The data consisted of genotypes for 32,689 SNPs of 497 animals from 19 breeds. For a given subset of breeds, the test statistic was the parametric composite log likelihood (CLL) of the differences in allelic frequencies between the subset and the IBHM for a sliding window of SNPs. The null distribution was obtained by calculating CLL for 50,000 random subsets (per chromosome) of individuals. The validity of this approach was confirmed by obtaining extremely large CLLs at the sites of causative variation for polled (BTA1) and black-coat-color (BTA18) phenotypes. Across the 30 bovine chromosomes, 699 putative selection signatures were detected. The largest CLL was on BTA6 and corresponded to KIT, which is responsible for the piebald phenotype present in four of the five dairy breeds. Potassium channel-related genes were at the site of the largest CLL on three chromosomes (BTA14, -16, and -25) whereas integrins (BTA18 and -19) and serine/arginine rich splicing factors (BTA20 and -23) each had the largest CLL on two chromosomes. On the basis of the results of this study, the application of population genomics to farm animals seems quite promising. Comparisons between breed groups have the potential to identify genomic regions influencing complex traits with no need for complex equipment and the collection of extensive phenotypic records and can contribute to the identification of candidate genes and to the understanding of the biological mechanisms controlling complex traits.

Genomic response to natural selection within alpine cattle breeds

“…The number of identified selective sweeps varied across different studies, depending on methodological approach and analysed populations. A large number of selective sweeps was presented by Stella et al (2010) for five specialized dairy cattle breeds (215 regions), and also by Druet et Mancini et al (2014) for Italian breeds. Despite the relatively lower proportion of selective sweeps identified for the breeds analysed in our study compared to others, the results indicated that the approach proposed by Duforet-Frebourg et al (2016) could be a perspective alternative for the identification of selection signatures not only in human but also in cattle.…”

The characterization of goat genetic diversity: Towards a genomic approach

“…In farm animals, they have been investigated in the framework of the HapMap project and re-sequencing projects (e.g. The Bovine HapMap Stella et al, 2010). In chicken, whole genome re-sequencing of wild and domestic animals identified 58 genomic regions under selection containing genes likely involved in the domestication process.…”

Assessing footprints of natural selection through PCA analysis in cattle

“…The number of identified selective sweeps varied across different studies, depending on methodological approach and analysed populations. A high number of selective sweeps was presented by Stella et al (2010) for five specialized dairy cattle breeds (215 regions) and also by Druet et al (2013) for 12 breeds of different production type (147 regions). The much lower proportion of selective footprints (16 regions) was found by Flori et al (2009) for French dairy cattle breeds and Mancini et al (2014) for Italian breeds.…”