Abstract
This study aimed to assess the level of biodiversity in selected local cattle populations as important food resources in Slovakia. The biodiversity level was derived from the genome-wide data collected for dairy (Jersey), dual-purpose (Slovak Pinzgau, Slovak Spotted), and beef breeds (Charolais, Limousine). The commonly used indices, genomic inbreeding (FROH, FGRM, FHOM, FUNI) and effective population size (NeLD), were used to quantify the impact of relatives mating on the genome of analysed populations. Even if the low NeLD estimates signalise significant loss of genetic variability within populations, the genomic inbreeding under 1% (except Jersey) showed that the intensity of diversity loss is not so rapid and can be managed by the re-arrangement of long-term breeding strategies. The analysis of genetic differentiation degree across populations assumed that the specialisation of breeds during their grading-up led to the specific nucleotide changes, especially in genes responsible for preferred phenotypic traits. The breed-specific differences observed mainly in the genome of Charolais (carcass traits) and Jersey (milk production traits) populations resulted from the polymorphisms in CAPN1 (μ-calpain) and CSN1S2 (casein alpha s2) genes, respectively. Obtained results confirmed that the specific haplotypes are strongly associated with the genetic nature of breed depending on production type.
Highlights
Animal biodiversity has a significant impact on the functioning of the surrounding food systems and livelihoods
The results showed that the recent genomic inbreeding could be expected at the level of 0.58% in the Charolais population and 0.43% in the Limousin population
As expected according to previous studies (e.g., [70,71]), the high genotyping call rate observed across animals and single nucleotide polymorphisms (SNPs) markers in the database reflected the fact that the applied SNP microarrays were primarily developed for commercial genotyping of highly informative markers uniformly distributed in the genome of the most commonly used dairy, dual-purpose and beef breeds worldwide
Summary
Animal biodiversity has a significant impact on the functioning of the surrounding food systems and livelihoods. It ensures numerous ecological functions and directly contributes to well-being, nutrition and food safety by providing a variety of species from domesticated and wild resources. The term animal biodiversity expresses the differences between species, breeds, sire lines or maternal families. This term can be used to denote differences between animals at the phenotype level, e.g., performance and reproduction traits, health status, or generally animals fitness that are visible and measurable. The level of livestock genetic diversity has to be quantified in other ways, e.g., by analysis of inbreeding intensity, effective population size or intraand inter-population genetic differentiation [4,5,6]
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