Abstract
BackgroundDomestication, breed formation and intensive selection have resulted in divergent cattle breeds that likely exhibit their own genomic signatures. In this study, we used genotypes from 27,612 autosomal single nucleotide polymorphisms to characterize population structure based on 9214 sires representing nine Swiss dairy cattle populations: Brown Swiss (BS), Braunvieh (BV), Original Braunvieh (OB), Holstein (HO), Red Holstein (RH), Swiss Fleckvieh (SF), Simmental (SI), Eringer (ER) and Evolèner (EV). Genomic inbreeding (FROH) and signatures of selection were determined by calculating runs of homozygosity (ROH). The results build the basis for a better understanding of the genetic development of Swiss dairy cattle populations and highlight differences between the original populations (i.e. OB, SI, ER and EV) and those that have become more popular in Switzerland as currently reflected by their larger populations (i.e. BS, BV, HO, RH and SF).ResultsThe levels of genetic diversity were highest and lowest in the SF and BS breeds, respectively. Based on FST values, we conclude that, among all pairwise comparisons, BS and HO (0.156) differ more than the other pairs of populations. The original Swiss cattle populations OB, SI, ER, and EV are clearly genetically separated from the Swiss cattle populations that are now more common and represented by larger numbers of cows. Mean levels of FROH ranged from 0.027 (ER) to 0.091 (BS). Three of the original Swiss cattle populations, ER (FROH: 0.027), OB (FROH: 0.029), and SI (FROH: 0.039), showed low levels of genomic inbreeding, whereas it was much higher in EV (FROH: 0.074). Private signatures of selection for the original Swiss cattle populations are reported for BTA4, 5, 11 and 26.ConclusionsThe low levels of genomic inbreeding observed in the original Swiss cattle populations ER, OB and SI compared to the other breeds are explained by a lesser use of artificial insemination and greater use of natural service. Natural service results in more sires having progeny at each generation and thus this breeding practice is likely the major reason for the remarkable levels of genetic diversity retained within these populations. The fact that the EV population is regionally restricted and its small census size of herd-book cows explain its high level of genomic inbreeding.
Highlights
Domestication, breed formation and intensive selection have resulted in divergent cattle breeds that likely exhibit their own genomic signatures
On BTA19, we found that up to 35% of the Brown Swiss (BS) bulls had a runs of homozygosity (ROH) between 45 and 50 Mb, which is concordant with the high level of genetic differentiation at ~ 46 Mb reported by the Bovine HapMap Consortium [22]
We report several private signatures of selection in regions that harbor genes such as INHBA, STAT6, PROKR1, CAPN14, CAPN13, FGF8 and SCD for these original populations
Summary
Domestication, breed formation and intensive selection have resulted in divergent cattle breeds that likely exhibit their own genomic signatures. The results build the basis for a better understanding of the genetic development of Swiss dairy cattle populations and highlight differences between the original populations (i.e. OB, SI, ER and EV) and those that have become more popular in Switzerland as currently reflected by their larger populations (i.e. BS, BV, HO, RH and SF). Domestication, breed formation and intensive selection have led to divergent cattle breeds that likely exhibit distinctive genomic signatures of selection. Another study that investigated population structure, selection signatures and demographic history in cattle was published by Oroczo-ter Wengel et al [7]
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