Abstract
Russian sheep breeds traditionally raised in specific environments are valuable parts of sociocultural heritage and economic component of the regions. However, the import of commercial breeds negatively influences the population sizes of local sheep populations and might lead to biodiversity loss. Estimation of the runs of homozygosity (ROH) in local sheep genomes is an informative tool to address their current genetic state. In this work, we aimed to address the ROH distribution and to estimate genome inbreeding based on SNP data to evaluate genetic diversity in Russian local sheep breeds. Materials for this study included SNP-genotypes from twenty-seven Russian local sheep breeds which were generated using the Illumina OvineSNP50 BeadChip (n = 391) or the Illumina Ovine Infinium HD BeadChip (n = 315). A consecutive runs method was used to calculate ROH which were estimated for each animal and then categorized in the ROH length classes. The ROH were found in all breeds. The mean ROH length varied from 86 to 280 Mb, while the ROH number ranged from 37 to 123. The genomic inbreeding coefficient varied from 0.033 to 0.106. Our findings provide evidence of low to moderate genomic inbreeding in major local sheep populations.
Highlights
The introduction of high throughput arrays for single nucleotide polymorphisms genotyping has led to the development of new bioinformatic approaches, which allow evaluation of genetic diversity more fully and address demographic history of the mammalian species
The aim of our present study is to address the distribution of the runs of homozygosity and to estimate genome inbreeding in Russian local sheep breeds based on SNP-genotyping data for better understanding of current levels of genetic diversity in these valuable livestock resources
Principal Component Analysis performed for 15 coarse wool sheep populations (Figure 1A) showed that the first Principal Component (PC1) accounting for 13.34% of genetic variability clearly separated the Romanov and the Kuchugur breeds from the other populations which were clustered together
Summary
Estimation of genomic inbreeding and the analysis of patterns of distribution of runs of homozygosity regions in the genome are gaining popularity among the geneticists and are used in addition to classical methods to assess genetic processes in the populations. The number and length of ROH reflect individual demographic history and evaluate the homozygosity burden [3,4]. The length of ROH indicates whether inbreeding was recent or ancient in a population [1,2]. To trace the inbreeding events, the genome scanning for ROH segments was performed in various livestock species including cattle [5] (for example, Angus, Charolais, Hereford, Holstein, Simmental [6], Russian Kholmogory and Yaroslavl breeds [7]) and small ruminant species (for example, German White-headed Mutton sheep [8] and African native goats [9])
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