Abstract
BackgroundCattle include a large number of breeds that are characterized by marked phenotypic differences and thus constitute a valuable model to study genome evolution in response to processes such as selection and domestication. Detection of “signatures of selection” is a useful approach to study the evolutionary pressures experienced throughout history. In the present study, signatures of selection were investigated in five cattle breeds farmed in Italy using a multivariate approach.MethodsA total of 4094 bulls from five breeds with different production aptitudes (two dairy breeds: Italian Holstein and Italian Brown Swiss; two beef breeds: Piemontese and Marchigiana; and one dual purpose breed: Italian Simmental) were genotyped using the Illumina BovineSNP50 v.1 beadchip. Canonical discriminant analysis was carried out on the matrix of single nucleotide polymorphisms (SNP) genotyping data, separately for each chromosome. Scores for each canonical variable were calculated and then plotted in the canonical space to quantify the distance between breeds. SNPs for which the correlation with the canonical variable was in the 99th percentile for a specific chromosome were considered to be significantly associated with that variable. Results were compared with those obtained using an FST-based approach.ResultsBased on the results of the canonical discriminant analysis, a large number of signatures of selection were detected, among which several had strong signals in genomic regions that harbour genes known to have an impact on production and morphological bovine traits, including MSTN, LCT, GHR, SCD, NCAPG, KIT, and ASIP. Moreover, new putative candidate genes were identified, such as GCK, B3GALNT1, MGAT1, GALNTL1, PRNP, and PRND. Similar results were obtained with the FST-based approach.ConclusionsThe use of canonical discriminant analysis on 50 K SNP genotypes allowed the extraction of new variables that maximize the separation between breeds. This approach is quite straightforward, it can compare more than two groups simultaneously, and relative distances between breeds can be visualized. The genes that were highlighted in the canonical discriminant analysis were in concordance with those obtained using the FST index.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-016-0236-7) contains supplementary material, which is available to authorized users.
Highlights
Cattle include a large number of breeds that are characterized by marked phenotypic differences and constitute a valuable model to study genome evolution in response to processes such as selection and domestication
Detection of significant single nucleotide polymorphisms (SNP) The average amount of variance explained by the four canonical variables (Table 1) ranged from 0.56 for CVA1 on BTA23 to 0.08 for CVA4 on BTA28
An increase in the amount of variance extracted by the first CVA was observed from longer to shorter chromosomes (i.e. 0.44 for BTA1 and 0.54 for BTA29, respectively)
Summary
Cattle include a large number of breeds that are characterized by marked phenotypic differences and constitute a valuable model to study genome evolution in response to processes such as selection and domestication. Sorbolini et al Genet Sel Evol (2016) 48:58 techniques, together with developments in comparative genomics, have opened great opportunities for the study of genomic modifications due to natural and artificial selection These selective pressures increase the frequency of the most favorable allele at a target locus. This process affects allele frequencies at loci at nearby locations and results in a loss of heterozygosity across that chromosomal region [9,10,11] This phenomenon, known as “hitchhiking”, leads to the formation of selective sweeps or “signatures of selection”, that are characterized by distributions of allele frequencies around favorable mutations that statistically differ from those expected by chance [12]
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