This study explored the genomic diversity and selection signatures in two Slovakian national breeds, the Original Valachian and the Improved Valachian sheep. As they are an important animal genetic resource within the country, but with decreasing population size, our aim is to identify potentially valuable genomic regions. A total of 97 sheep (18 male and 79 female) from the Original Valachian, and 69 sheep (25 male and 44 female) from the Improved Valachian populations were genotyped using the GeneSeek GGP Ovine 50 K chip. The inbreeding levels were assessed with runs of homozygosity (ROH). The selection signatures within breeds were identified based on the top 1% of most homozygous regions within the breed, the so-called ROH islands. The selection signatures between breeds were assessed based on variance in linkage disequilibrium. Overall, we have identified selection signatures with quantitative trait loci (QTL) and genes pointing towards all three production purposes of the Valachian sheep, milk, meat, and wool, including their quality characteristics. Another group with apparent large importance was the various traits related to health and resistance to parasites, which is well in line with the sturdy nature of this breed.
Licensed under a Creative Commons Attribution 4.0 International LicenseThe use of single nucleotide polymorphism (SNP) data had become commonplace in animal breeding activities and management of livestock populations. The cost-effective genotyping allowed us to assess entire populations and learn about their history on the genomic level. This paper reviews several approaches that are commonly used in the context of genomic diversity in livestock, such as the linkage disequilibrium (LD) and assessment of autozygosity via runs of homozygosity (ROH). Both methods, however, are being used to assess the impact of natural or artificial selection on the livestock genome. Apart from these selection signatures, both the LD and ROH are used to assess the effective population size (Ne), which likewise, serves as a diversity management tool and describes the historical events in populations.
Licensed under a Creative Commons Attribution 4.0 International License With the availability of dense SNP genotype data various types of estimation methods were developed to estimate relatedness of any two individuals, even in absence of traditional pedigrees. One of the most prominent method was the identity by descent (IBD), widely used in genetic diversity studies. IBD itself could be estimate using different approaches and software that might provide different results. The purpose of this study was to compare the estimates from two established software, probabilistic approach by Plink and a non-probabilistic approach based on haplotypes by refinedIBD. High density SNP genotypes from 98 Leonberger dogs were used to estimate IBD coefficients based on two data types: with one of the SNP markers in high linkage disequilibrium removed, as required by Plink, and SNP markers subjected only to standard quality control, as required by refinedIBD. The Pearson correlation coefficients from pairwise estimates were 0.97 when estimated with the same software and 0.84 between the two software and data types, as required by the respective user manuals. The numerical differences were clustered around zero (i.e. no to little difference) for half of the pairwise comparisons, and up to ±0.1 for the vast majority of cases. The most extreme differences were consistently estimated higher by Plink. Because of these differences a follow up investigation should be done, including pedigrees, as well as simulated data to provide a comprehensive analysis.
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