Abstract
BackgroundRecent technological advances in genomics have allowed the genotyping of cattle through single nucleotide polymorphism (SNP) panels. High-density SNP panels possess greater genome coverage and are useful for the identification of conserved regions of the genome due to selection, known as selection signatures (SS). The SS are detectable by different methods, such as the extended haplotype homozygosity (EHH); and the integrated haplotype score (iHS), which is derived from the EHH. The aim of this study was to identify SS regions in Canchim cattle (composite breed), genotyped with high-density SNP panel.ResultsA total of 687,655 SNP markers and 396 samples remained for SS analysis after the genotype quality control. The iHS statistic for each marker was transformed into piHS for better interpretation of the results. Chromosomes BTA5 and BTA14 showed piHS > 5, with 39 and nine statistically significant SNPs (P < 0.00001), respectively. For the candidate selection regions, iHS values were computed across the genome and averaged within non-overlapping windows of 500 Kb. We have identified genes that play an important role in metabolism, melanin biosynthesis (pigmentation), and embryonic and bone development.ConclusionsThe observation of SS indicates that the selection processes performed in Canchim, as well as in the founder breeds (i.e. Charolais), are maintaining specific genomic regions, particularly on BTA5 and BTA14. These selection signatures regions could be associated with Canchim characterization.Electronic supplementary materialThe online version of this article (doi:10.1186/s40104-016-0089-5) contains supplementary material, which is available to authorized users.
Highlights
Recent technological advances in genomics have allowed the genotyping of cattle through single nucleotide polymorphism (SNP) panels
Single nucleotide polymorphisms (SNPs) panels are applied in several studies, including selection signatures, in which regions of the genome maintained from generation to generation due to selection are identified
The recent positive selection is characterized by increased linkage disequilibrium and decreased genetic variability in the population [12], which is caused by the rapid fixation of mutations favorable to the selected traits [13]
Summary
Recent technological advances in genomics have allowed the genotyping of cattle through single nucleotide polymorphism (SNP) panels. The aim of this study was to identify SS regions in Canchim cattle (composite breed), genotyped with high-density SNP panel. Single nucleotide polymorphisms (SNPs) panels are applied in several studies, including selection signatures, in which regions of the genome maintained from generation to generation due to selection are identified. The recent positive selection is characterized by increased linkage disequilibrium and decreased genetic variability in the population [12], which is caused by the rapid fixation of mutations favorable to the selected traits [13]. When positively selected alleles achieve high frequency, other alleles in linkage disequilibrium increase their frequencies (hitchhike), retaining the favorable allele, but a region of the genome next to it (selective sweep effect) [14]
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