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In their centuries-long history, the nomads of the south of Russia developed the local cattle breeds, which are well adapted to the harsh steppe conditions. In 20th century, the population size of such cattle breeds was dramatically decreased. At the same time, intensive cross breeding with high-producing transboundary breeds had been practiced on the small remaining part of population. The aim of our study was to trace the historical genetic components in modern populations of local cattle breeds of the turano-mongolian origin. The historical specimens of Kalmyk (n = 10), Kyrgyz (n = 11) and Kazakh (n = 3) cattle dated by the first quarter of the 20th century were derived from the craniological collection of the E.F. Liskun Museum for Animal Husbandry and subjected to the study. The modern representatives of Kalmyk (n = 28), Kyrgyz (n = 20), Kazakh White-headed (n = 30), Hereford (n = 26), and Mongolian (n = 41) cattle were used for comparison. All works with historical samples were performed in dedicated facility of the L.K. Ernst research Center for Animal Husbandry. The samples were genotyped for 11 microsatellite loci (BM1818, BM2113, BM1824, ETH10, ETH225, INRA023, SPS115, TGLA53, TGLA122, TGLA126, and TGLA227). For historical samples, the PCR reactions were carried out in five replicates to determine the consensus genotypes. In total, 132 alleles were identified, including 97 alleles in historical samples and 124 alleles in modern samples. The values of unbiased expected heterozygosity were 0.767–0.776 and 0.653–0.778 for the historical and modern samples, respectively. The STRUCTURE clustering showed the visible differences in genetic structure between the historical and modern populations of Kalmyk, Kyrgyz and Kazakh cattle breeds; however, the historical genetic components were still maintained in modern representatives of all of studied breeds. The research results will be useful for the sustainable breeding and conservation of valuable local genetic resources. The study was funded by the RSF No. 19-76-20012.

Maintaining high levels of genetic diversity is a key factor of successful breeding of resilient, resistant to diseases and productive sheep. Prevention of inbreeding is of special importance in the mountainous hard-to-get habitats where gene flow is limited or absent. An assessment of inbreeding coefficients based only on pedigree information is not always correct. In addition, pedigree information is often missing for flocks of native sheep. In this regard, we performed a genomic assessment of inbreeding in 15 local sheep breeds inhabiting severe environments of Russia and neighboring Asian countries based on estimations of standardized multilocus heterozygosity (sMLH) and runs of homozygosity [F(ROH)]. For this study, we used SNP genotypes of twelve Russian local breeds (n = 316) and three Kyrgyz local breeds (n = 68), which were generated using Ovine Infinium® HD SNP BeadChip (Illumina, CA, USA). The sMLH values were calculated using R package inbreedR and visualized in R package ggplot2. The F(ROH) values were calculated using the R package detectRUNS by applying the consecutive runs method. Mean sMLH values were varied from 0.962 ± 0.006 in the Andean breed to 1.031 ± 0.002 in the Buryat breed and averaged to 1.001± 0.004. The least mean F(ROH) value was detected in the Mongolian breed (0.0043 ± 0.0009) while the greatest ones were observed in the Alai and Andean breeds (0.0364 ± 0.0049 and 0.0357 ± 0.0061, respectively). The strong negative correlations between sMLH and F(ROH) were detected for all of studied breeds (r2 = –0.8496, CI = –0.8752… –0.8192). The obtained data is relevant for control of inbreeding level in the populations and for future sustainable management of native fat-tailed sheep breeds. The study was funded by RSF No. 19-16-00070.

Native coarse wool fat-tailed sheep breeds are the main producers of mutton in mountainous, steppe and semi-desert regions of Southern Russia. An assessment of homozygosity is required to prevent loss of genetic diversity and inbreeding depression onset. The aim of our work is estimation of genomic inbreeding and distribution of the runs of homozygosity (ROH) segments in Russian sheep breeds. Sample collection included Andean (n = 20), Buryat (n = 18), Buubei (n = 11), Edilbai (n = 20), Karachaev (n = 20), Kalmyk (n = 22), Karakul (n = 20), and Lezgin (n = 15) breeds. All sheep were genotyped using Ovine Infinium® HD SNP BeadChip (Illumina, USA). Quality control and raw data processing were performed in PLINK 1.9. A consecutive runs method implemented in the R package “detectRUNS” was used for estimation of ROH segments. We detected the ROH in all breeds with mean length ranging from 0.35 in Lezgin to 11.18 Mb in Karachaev. Andean had the greatest number of the ROH segments (total of 8496), while 3094 ROH segments were found in Buubei. Short ROH segments (< 2 Mb) were predominant in all breeds and varied from 96.83% in Andean to 99.87% in Buubei. The frequencies of the ROH segments of 8–16 Mb ranged from 0.03% in Karakul to 0.18% in Andean. ROH segments of 8–16 Mb did not occur in the Buubei and Lezgin breeds. The ROH segments were found on all autosomes. The largest genome coverage in the ROH was identified on OAR1, OAR 12 and OAR 20 and the lowest was accounted for OAR 17, OAR 18 and OAR 19. The values FROH ranged from 0.042 in Buubei to 0.084 in Andean. Except of Andean, no traces of long-term inbreeding were detected in local breeds. The obtained data are relevant for future sustainable management of native fat-tailed sheep breeds in Russia. The study was funded by RSF No. 19-16-00070.

National livestock genetic resources are the valuable source of genetic variability, which are necessary to ensure the sustainability of the local animal production systems. The aim of our work was to characterize the genomic architecture and to detect signatures of selection in two oldest Russian native cattle breeds, using high-density DNA arrays. Fifty-six animals of Yaroslavl (n = 31) and Kholmogor (n = 25) were selected for the study. The Illumina Bovine HD BeadChip (777,962 SNPs) was used for genotyping. High-density SNP genotypes for Holsteins (n = 25) were used as the reference. Three methods (Fst, hapFLK, and ROH) were implemented to detect the genomic regions to be under putative selection. The results of the PCA-plot, Neighbor-Net analysis and Admixture clustering showed clear genetic differences between Yaroslavl and Kholmogor breeds as well as between them and Holsteins. Comparison of the results produced by different methods showed presence of twelve regions in genome of Yaroslavl breed and nine regions in genome of Kholmogor breeds, which were identified at least by two methods. We have confirmed nine regions under putative selection in genome of Yaroslavl cattle and six regions in genome of Kholmogor cattle, which were described previously based on medium-density SNP genotypes, herewith the flanking positions of the most of these regions were expanded. Additionally, we detected three new putative genomic regions affected by selection in each studied breed, which were localized on chromosomes 4, 15 and 17 in Yaroslavl breed and on chromosomes 12, 15 and 18 in Kholmogor breed. The functional annotation of genes localized within identified regions was carried out. Our research results can be useful for genetic improvement of the studied cattle breeds and for developing the programs for their conservation. The study was supported by RSF within project No. 19-76-20012.

Tuva breed is the oldest native sheep breed in Russia with more than 2000 year-history and comes in third place by population size among coarse wool sheep. Tuva sheep produce high-quality meat as well as coarse wool to make traditional clothing in the Republic of Tyva. In present study, we aimed to evaluate genetic diversity and to establish genetic links of the Tuva breed with the other Russian coarse wool sheep to understand the origin and current status of this valuable livestock species. Twenty samples of Tuva were genotyped using Ovine Infinium® HD SNP BeadChip (Illumina, CA, USA). SNP-data were processed in PLINKv1.9, R package ‘diveRsity’ and SneP software. High-density SNP-genotypes of 10 coarse wool sheep breeds were used as comparison groups. Observed heterozygosity (Ho) and allelic richness (Ar) in Tuva breed were 0.336 and 1.884, respectively, and were practically equal to mean values estimated across all analyzed sheep breeds (Ho=0.335, Ar=1.884). All coarse wool breeds showed moderate heterozygote excess which was the highest in Tuva breed (1.6%). Effective population sizes estimated for three and five generations ago for Tuva breed (Ne3 =118 and Ne5 =179) were less than those in other breeds (Ne3 = 314 and Ne5 = 441 for Edilbai or Ne3 = 300 and Ne5 = 450 for Kalmyk) but not the lowest (Ne3 = 49 and Ne5 = 72 for Buubei). Values of historical effective population size estimated for 60 generations ago for Tuva breed was 1457 that was compatible with those obtained for other breeds (Ne60 from 586 for Buubei to 2634 for Kalmyk). Despite the obvious decrease in effective population size, levels of genetic diversity are not critical that would allow to develop programs to ensure preservation and sustainable development of Tuva breed. The study was funded by RSF No. 19-16-00070.