Abstract
Specific local environmental and sociocultural conditions have led to the creation of various goat populations in Russia. National goat diversity includes breeds that have been selected for down and mohair production traits as well as versatile local breeds for which pastoralism is the main management system. Effective preservation and breeding programs for local goat breeds are missing due to the lack of DNA-based data. In this work, we analyzed the genetic diversity and population structure of Russian local goats, including Altai Mountain, Altai White Downy, Dagestan Downy, Dagestan Local, Karachaev, Orenburg, and Soviet Mohair goats, which were genotyped with the Illumina Goat SNP50 BeadChip. In addition, we addressed genetic relationships between local and global goat populations obtained from the AdaptMap project. Russian goats showed a high level of genetic diversity. Although a decrease in historical effective population sizes was revealed, the recent effective population sizes estimated for three generations ago were larger than 100 in all studied populations. The mean runs of homozygosity (ROH) lengths ranged from 79.42 to 183.94 Mb, and the average ROH number varied from 18 to 41. Short ROH segments (<2 Mb) were predominant in all breeds, while the longest ROH class (>16 Mb) was the least frequent. Principal component analysis, Neighbor-Net graph, and Admixture clustering revealed several patterns in Russian local goats. First, a separation of the Karachaev breed from other populations was observed. Moreover, genetic connections between the Orenburg and Altai Mountain breeds were suggested and the Dagestan breeds were found to be admixed with the Soviet Mohair breed. Neighbor-Net analysis and clustering of local and global breeds demonstrated the close genetic relations between Russian local and Turkish breeds that probably resulted from past admixture events through postdomestication routes. Our findings contribute to the understanding of the genetic relationships of goats originating in West Asia and Eurasia and may be used to design breeding programs for local goats to ensure their effective conservation and proper management.
Highlights
Domestic goats are highly valued for a combination of unique biological, ecological, and economically important characteristics
A tendency toward a smooth decrease in effective population sizes was apparent in all Russian goat groups within 60 generations (Supplementary Figure 1)
Obvious decreases in effective population sizes were displayed in all local breeds that corresponded to the global tendency in livestock species
Summary
Domestic goats are highly valued for a combination of unique biological, ecological, and economically important characteristics. These acclimatizing small ruminants are spread around the world, and Russia is no exception. Archeological data provide indirect evidence that domestic goats were already in the territory of modern Russia 2500 years ago. The history of goat breeding in Russia was not well documented until the beginning of the twentieth century. The benefits and nutritional value of goat milk were actively promoted by local departments of the Russian Society of Goat Breeding, only 19 smallholder farms with 35 goats were organized in 1913 (Beloborodova, 2014)
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