Genomics of a revived breed: Case study of the Belgian campine cattle

Abstract

Through centuries of both natural and artificial selection, a variety of local cattle populations arose with highly specific phenotypes. However, the intensification and expansion of scale in animal production systems led to the predominance of a few highly productive cattle breeds. The loss of local populations is often considered irreversible and with them specific qualities and rare variants could be lost as well. Over these last years, the interest in these local breeds has increased again leading to increasing efforts to conserve these breeds or even revive lost populations, e.g. through the use of crosses with similar breeds. However, the remaining populations are expected to contain crossbred individuals resulting from introgressions. They are likely to carry exogenous genes that affect the breed’s authenticity on a genomic level. Using the revived Campine breed as a case study, 289 individuals registered as purebreds were genotyped on the Illumina BovineSNP50. In addition, genomic information on the Illumina BovineHD and Illumina BovineSNP50 of ten breeds was available to assess the current population structure, genetic diversity, and introgression with phenotypically similar and/or historically related breeds. Introgression with Holstein and beef cattle genotypes was limited to only a few farms. While the current population shows a substantial amount of within-breed variation, the majority of genotypes can be separated from other breeds in the study, supporting the re-establishment of the Campine breed. The majority of the population is genetically close to the Deep Red (NL), Improved Red (NL) and Eastern Belgium Red and White (BE) cattle, breeds known for their historical ties to the Campine breed. This would support an open herdbook policy, thereby increasing the population size and consequently providing a more secure future for the breed.

Unraveling the genetic diversity of Belgian Milk Sheep using medium‐density SNP genotypes

“…Effective population size ( N e ) in BMS was estimated based on LD, using the method implemented by François et al (), following Weir & Hill () and Waples (, ).…”

Evolution and domestication of the Bovini species

“…2018), Belgium and the Netherlands (François et al . 2017), France (Gautier et al . 2010), Ireland (Browett et al .…”

Genomic Characterisation of the Indigenous Irish Kerry Cattle Breed

“…The availability of powerful and cheap tools for genotyping large numbers of single nucleotide polymorphisms (SNPs) has provided conservation biologists and animal geneticists with the opportunity to characterise genomic variation and estimate population genetic parameters at very high resolution in threatened or endangered livestock breeds (Pertoldi et al, 2014 ; Ben Jemaa et al, 2015 ; Beynon et al, 2015 ; Mészáros et al, 2015 ; Burren et al, 2016 ; Decker et al, 2016 ; Iso-Touru et al, 2016 ; Manunza et al, 2016 ; Mastrangelo et al, 2016 ; Visser et al, 2016 ; Williams et al, 2016 ; François et al, 2017 ). These studies are already providing important baseline data for genetic conservation and will underpin programmes for managed breeding and biobanking of these populations (Groeneveld et al, 2016 ).…”