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A study for genomic variation that may reflect putative selective signaling and be associated with economically important traits is instrumental for obtaining information about demographic and selection history in domestic animal species and populations. A rich variety of the Russian chicken gene pool breeds warrants a further detailed study. Specifically, their genomic features can derive implications from their genome architecture and selective footprints for their subsequent breeding and practical efficient exploitation. In the present work, whole genome genotyping of 19 chicken breeds (20 populations with up to 71 samples each) was performed using the Chicken 50 K BeadChip DNA chip. The studied breed sample included six native Russian breeds of chickens developed in the 17th–19th centuries, as well as eight Russian chicken breeds, including the Russian White (RW), created in the 20th century on the basis of improving local chickens using breeds of foreign selection. Five specialized foreign breeds of chickens, including the White Leghorn (WL), were used along with other breeds representing the Russian gene pool. The characteristics of the genetic diversity and phylogenetic relationships of the native breeds of chickens were represented in comparison with foreign breeds. It was established that the studied native breeds demonstrate their own genetic structure that distinguishes them from foreign breeds, and from each other. For example, we previously made an assumption on what could cause the differences between two RW populations, RW1 and RW2. From the data obtained here, it was verified that WL was additionally crossed to RW2, unlike RW1. Thus, inherently, RW1 is a purer population of this improved Russian breed. A significant contribution of the gene pool of native breeds to the global genetic diversity of chickens was shown. In general, based on the results of a multilateral survey of this sample of breeds, it can be concluded that phylogenetic relationships based on their genetic structure and variability robustly reflect the known, previously postulated and newly discovered patterns of evolution of native chickens. The results herein presented will aid selection and breeding work using this gene pool.

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.

Based on the analysis of genome-wide SNP genotypes, a study of the genetic diversity and genetic structure of modern and historical samples of cattle of the Kholmogor and Yaroslavl breeds was performed. The preservation of historical genomic components in modern representatives of breeds is shown.

Simple Summary: The search for genomic regions of putative selective signaling is instrumental in obtaining information about selection history in various species and populations. Domestic animals are subject to long-term artificial selection that leaves certain footprints in their genomes one can explore using genome-wide SNP screen. We examined here genomes of two contrasting chicken breeds, the native egg-type Russian White and meat-type White Cornish. Using three statistics, we identified genomic regions under putative selection, both breed-specific and shared between two breeds, that harbor key candidate genes for economically important traits. Our findings will be useful in further understanding selection history and genomic diversity in domestic chickens that would be pivotal in their productive breeding.\ud Abstract: Comparison of genomic footprints in chicken breeds with different selection history is a powerful tool in elucidating genomic regions that have been targeted by recent and more ancient selection. In the present work, we aimed at examining and comparing the trajectories of artificial selection in the genomes of the native egg-type Russian White (RW) and meat-type White Cornish (WC) breeds. Combining three different statistics (top 0.1% SNP by FST value at pairwise breed comparison, hapFLK analysis, and identification of ROH island shared by more than 50% of individuals), we detected 45 genomic regions under putative selection including 11 selective sweep regions, which were detected by at least two different methods. Four of such regions were breed-specific for each of RW breed (on GGA1, GGA5, GGA8, and GGA9) and WC breed (on GGA1, GGA5, GGA8, and GGA28), while three remaining regions on GGA2 (two sweeps) and GGA3 were common for both breeds. Most of identified genomic regions overlapped with known QTLs and/or candidate genes including those for body temperatures, egg productivity, and feed intake in RW chickens and those for growth, meat and carcass traits, and feed efficiency in WC chickens. These findings were concordant with the breed origin and history of their artificial selection. We determined a set of 188 prioritized candidate genes retrieved from the 11 overlapped regions of putative selection and reviewed their functions relative to phenotypic traits of interest in the two breeds. One of the RW-specific sweep regions harbored the known domestication gene, TSHR. Gene ontology and functional annotation analysis provided additional insight into a functional coherence of genes in the sweep regions. We also showed a greater candidate gene richness on microchromosomes relative to macrochromosomes in these genomic areas. Our results on the selection history of RW and WC chickens and their key candidate genes under selection serve as a profound information for further conservation of their genomic diversity and efficient breeding.

The comparative molecular genetic study of museum and modern representatives of cattle breeds can help to elucidate the origin and maintenance of historical genetic components in modern populations. We generated the consensus genotypes for 11 microsatellite loci for 24 museum samples of Kalmyk, Kyrgyz, and Kazakh cattle, dated from the first quarter of the 20th century, and compared them with those of modern Kalmyk, Kyrgyz, and Kazakh white-headed breeds. The level of genetic diversity of the modern Kalmyk and Kyrgyz cattle (uHe = 0.771–0.778) was similar to those observed in the museum samples (uHe = 0.772–0.776), while a visible decrease in genetic variability in the modern Kazakh white-headed breed compared to museum Kazakh cattle was detected (uHe = 0.726 and 0.767, respectively). The PCA plot, FST- and Jost’s D-based networks, and STRUCTURE clustering provided strong evidence of the maintenance of the historical genetic background in modern populations of Kalmyk and Kyrgyz cattle. In spite of the allele pool of Kazakh white-headed cattle having undergone great changes compared to the museum Kazakh cattle, several animals still carry the visible aspect of the historical genetic components. Our results can be used for the selection of individuals for the creation of gene banks and may significantly improve the efficiency of conservation programs aimed at preserving genetic diversity in the national genetic resources of cattle.

При ведении селекционной работы важно учитывать степень инбридинга в популяции, чтобы избежать перехода летальных и полулетальных рецессивных аллелей в гомозиготное состояние и проявления инбредной депрессии. Широко применяемая оценка только на основе информации из родословной животного не всегда является корректной. Расчет показателей инбридинга на основании полногеномных данных позволяет оценить степень гетерозиготности как в целом в популяции, так и у каждой особи в отдельности. Целью работы было проведение геномной оценки инбридинга в популяциях крупного рогатого скота холмогорской, ярославской и голштинской пород с использованием двух методов расчета sMLH и F(ROH). Выполнен анализ полногеномных SNP-профилей (SNP однонуклеотидный полиморфизм) животных вышеуказанных пород. Обработку данных, расчеты и визуализацию результатов проводили в программах PLINK 1.9, Admixture 1.3 и R пакетах pophelper, detectRUNS, inbreedR, ggplot2. После проведения контроля качества для исследований были отобраны 36837 SNP. Кластерный анализ показал четкую дифференциацию обеих российских пород как друг от друга, так и от голштинской. Наибольшими средними значениями коэффициента инбридинга F(ROH) (0,1260,005) и мультилокусной гетерозиготности sMLH (1,0180,006) отличались животные голштинской породы. Это объясняется эффектом смещения выборки при генотипировании из-за особенностей дизайна чипа. Оценка степени инбредности популяций с помощью полногеномного анализа SNP целесообразна при учете дизайна чипа, на котором было проведено генотипирование.The inbreeding level in a population should be taken into account in the framework of breeding programs in order to avoid the transition of lethal and semi-lethal recessive alleles into a homozygous state and resulting in inbreeding depression. The assessment of inbreeding level based only on the information from pedigree is not always correct. Calculation of inbreeding indices based on genome-wide data allows evaluation of the heterozygosity degree both individually and population-wise. The work was aimed at conducting the genomic assessment of inbreeding in cattle populations of the Kholmogor, Yaroslavl and Holstein breeds using two methods sMLH and F(ROH). We performed the genome-wide SNP analysis (SNP single nucleotide polymorphism) of individuals of the above listed breeds. Data processing, calculations and visualization of the results were carried out in the programs PLINK 1.9, Admixture 1.3 and R packages pophelper, detectRUNS, inbreedR, ggplot2. After quality control, 36837 SNPs were selected for the analyses. Cluster analysis showed a clear differentiation of the Russian breeds both from each other and from Holstein. The highest average values of the inbreeding coefficient F(ROH) (0,1260,005) and sMLH (1,0180,006) were observed in Holstein animals. It can be caused by the ascertainment bias due to the design features of the chip. Therefore the assessment of the inbreeding degree in populations using the whole-genome SNP analysis is advisable when taking into account the chip design.

Local breeds can serve as an important source of genetic variability in domestic animal species. This study aimed to assess the genetic diversity and population structure of Belarusian Red cattle and their differentiation from other European cattle populations based on genome-wide SNP genotypes. Twenty pedigree-recorded non-closely related cows of Belarusian Red cattle were genotyped using the Illumina BovineHD BeadChip. Genotypes of 22 other European cattle breeds were included in the study for comparison. A total of 28 562 SNPs passed through the quality control checks and were selected for analysis. The Belarusian Red cattle displayed a moderate level of genetic variability (U HE = 0.341, HO = 0.368), and the highest heterozygote excess (U FIS = -0.066), among the studied breeds; this reflects the contribution of multiple breeds to their formation. The principal component analysis, FST -based Neighbor-Net tree and Admixture clustering, clearly distinguished the Belarusian Red cattle from the other European cattle breeds. Moreover, the presence of ancestral genomic components of Danish Red and Brown Swiss breeds were clearly visible, which agrees with the breed's history and its recent development. Our study highlights the importance of maintaining the specific genomic components, which makes a significant contribution to the global genetic diversity in the modern population of Belarusian Red cattle, allowing us to consider them a valuable national genetic resource. Our research results will be useful for the development of conservation programs for this local cattle breed.

Kazakh White-headed is the local beef cattle breed, which is bred in Central Asia countries. It was created in the beginning of 20 century by improving native Kazakh cattle by Hereford breed. The aim of our work was to characterize the genetic structure and to trace the presence of ancestral genetic components in the modern population of Kazakh White-headed cattle. The samples of modern representatives of Kazakh White-headed (KZWH_M, n=29) and Hereford (HRFD_M, n=25) breeds as well as historical specimens of native Kazakh breed (KZKH_H, n=2), dated by the first quarter of 20th century, were subjected to the study. All works with historical specimen were performed in dedicated facility of the L.K. Ernst research Centre for Animal Husbandry. DNA from modern samples was extracted using DNA Extran 2 kit (JSC Syntol, Russia) and from historical specimen – using COrDIS Extract Decalcine kit (GORDIZ LLC, Russia). We genotyped 11 microsatellite loci (BM1818, BM2113, BM1824, ETH10, ETH225, INRA023, SPS115, TGLA53, TGLA122, TGLA126, and TGLA227). For historical samples the PCR reaction were carried out in five replicates to determine the consensus genotypes for each locus. In total, we identified 82 microsatellite alleles. Five alleles, which were found in the historical specimens, were lost in the modern population of Kazakh White-headed cattle. We observed the highest level of genetic diversity (unbiased heterozygosity, allelic richness) in historical samples. The modern population of Kazakh White-headed cattle was closer to Hereford breed as was revealed by calculation of pairwise Nei and FST genetic distances. The STRUCTURE clustering confirmed the more similarity of genetic structure of modern Kazakh White-headed cattle with Herefords, but showed the visible presence the historical genetic components. The research results will be useful for developing the programs of conservation and sustainable use of Kazakh White-headed cattle.

Increasing animal stature is one of the goals of modern breeding programs for many dairy cattle breeds, because stature related to higher milk yield. The PLAG1 gene was shown to be a strong candidate responsible for stature in different cattle breeds. The polymorphic SNP BovineHD1400007259, located within PLAG1 gene, is considered as a causal mutation responsible for stature. The aim of our work was to evaluate the effect of long selection for the increased body height on the alterations of the allele’s frequencies of the PLAG1 gene in the historical and modern populations of the Russian Yaroslavl and Kholmogor dairy cattle breeds. The historical specimens of Yaroslavl (n = 22) and Kholmogor (n = 12) 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. The modern representatives of Yaroslavl (n = 31) and Kholmogor (n = 25) breeds 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 using high-density DNA arrays (Illumina Inc., USA). The historical DNA was treated by USER enzyme before genotyping to avoid the misincoporated nucleotides occurred due to postmortem DNA damage. We observed significant differences in allele frequencies of PLAG1 genes between historical and modern populations of both breeds. The frequencies of G allele, which is associated with higher stature, were increased from 0.114 in historical Yaroslavl cattle and from 0.167 in historical Kholmogor cattle to 0.633 and 0.860 in the modern breeds’ representatives, respectively. Our data suggest that PLAG1 gene was affected by artificial selection in studied cattle breeds. The research results will be useful for elucidation of the history of these two oldest Russian dairy cattle breeds. The study was funded by the RSF No. 21-66-00007.

Among the variety of cattle breeds in Russia, the Russian red dual-purpose cattle breeds have great importance because of their ability to produce high milk yields as well as to provide excellent milk quality. The low census size of the Russian red cattle breeds requires development of programs for conservation of their biodiversity. Our study aimed to investigate selection footprints in Russian red cattle breeds, using high values of linkage disequilibrium (LD) in SNP haplotype blocks as indicators. For finding such LD blocks, we used the genotypes (≈35K SNPs) of Red Gorbatov (RGB, n = 26), Bestuzhev (BST,n = 27), and Suksun (SKS,n = 17) breeds, as well as Red Holstein (RH,n = 16) as an outgroup. Quality control and LD calculations for different distances were performed in Plink 1.90. Top 0.01% SNP pairs by LD value (0.9≤r2< 1.0) were selected for further analysis. The effective population size derived from LD patterns was estimated using SNeP tool. Comparison of LD values for 70 kb interval between breeds and chromosomes by MANOVA pairwise testing significantly distinguished RH/RGB and BST/SKS breeds (P < 0.05-0.001). LD values among chromosomes were 0.195–0.287 for RH, 0.194–0.272 for RGB, 0.172–0.237 for BST, and 0.157–0.217 for SKS. The SKS and BST breeds had higher Ne values (84 and 113, respectively) compared to RH (63) and RGB (79). Selection footprints by LD blocks in Russian red cattle genome covered several relevant genes on BTA1 (EPHA6,DGKG), BTA2 (LRP1B,THSD7B,STAT1), BTA5 (CPM,BAIAP2L2), BTA9 (TRDN,UTRN), BTA10 (KCNN2,CAPN3), BTA11 (SH3RF3,RABGAP1,RALGPS1), BTA14 (ZNF16,ARHGAP39,TOX,DGAT1), and BTA19 (MYH10), BTA22 (FHIT). Detected genes were found to be responsible for milk fat and protein contents, fatty acid composition, somatic cells score, fertility, feet and legs, and udder conformation traits. Our results can be useful for developing the breeding and conservation programs of the Russian red cattle genetic resources. The study was funded by RFBR within project No. 20-516-00020

Drastic decline of population size of Russian local cattle breeds observed during last three decades has led to the decrease of genetic diversity. Due to the limited number of bulls used for artificial insemination, inbreeding in herds can be increased, which can lead to the decrease of reproduction capacity and adaptability of animals. Our aim was to assess genomic inbreeding in two Russian local cattle breeds, including Kholmogor (n = 26) and Istoben (n = 21). Two transboundary cattle breeds used for milk production in Russia including Holstein (n = 49) and Simmental (n = 38) were chosen for comparison. SNP genotyping was performed using the Bovine GGP 150K BeadArray (Illumina, CA, USA). After the quality control, 117591 autosomal SNPs were selected for analyzes. The degree of genomic inbreeding was assessed by calculations of inbreeding coefficient based on run of homozygosity (F(ROH)) and multilocus heterozygosity (sMLH). We found the strong negative correlations between the F(ROH) and sMLH values in animals of all of studied breeds (r2 = -0.805). The average F(ROH) values were 0.065 < mo >±< /mo >< /math >“>±± 0.003 for Kholmogor, 0.048 < mo >±< /mo >< /math >“>±± 0.006 for Istoben, 0.129 < mo >±< /mo >< /math >“>±± 0.007 for Holstein, and 0.102 < mo >±< /mo >< /math >“>±± 0.007 for Simmental breed. The sMLH values in Kholmogor, Istoben, Holstein and Simmental breeds varied from 0,99 to 1,076, from 0,829 to 1,102, from 0,890 to 1,069 and from 0,866 to 1,041, and averaged to 1.030, 1.013, 1.000, and 0.974, respectively. According to our research results, two studied Russian cattle breeds are characterized by lower levels of genomic inbreeding compared to transboundary cattle breeds. Our results will be helpful for developing the conservation programs for Russian Kholmogor and Istoben cattle breeds. The study was funded by the Russian Ministry of Science and Higher Education within theme No. 0445-2019-0024 and RFBR within project 19-316-90017 (the study of Kholmogor cattle).

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.

Analysis of ancient and historical DNA has great potential to trace the genetic diversity of local cattle populations during their centuries-long development. Forty-nine specimens representing five cattle breeds (Kholmogor, Yaroslavl, Great Russian, Novgorod, and Holland), dated from the end of the 19th century to the first half of the 20th century, were genotyped for nine polymorphic microsatellite loci. Using a multiple-tube approach, we determined the consensus genotypes of all samples/loci analysed. Amplification errors, including allelic drop-out (ADO) and false alleles (FA), occurred with an average frequency of 2.35% and 0.79%, respectively. A significant effect of allelic length on ADO rate (r2 = 0.620, p = 0.05) was shown. We did not observe significant differences in genetic diversity among historical samples and modern representatives of Kholmogor and Yaroslavl breeds. The unbiased expected heterozygosity values were 0.726&ndash, 0.774 and 0.708&ndash, 0.739, the allelic richness values were 2.716&ndash, 2.893 and 2.661&ndash, 2.758 for the historical and modern samples, respectively. Analyses of FST and Jost&rsquo, s D genetic distances, and the results of STRUCTURE clustering, showed the maintenance of a part of historical components in the modern populations of Kholmogor and Yaroslavl cattle. Our study contributes to the conservation of biodiversity in the local Russian genetic resources of cattle.

Native cattle breeds can carry specific signatures of selection reflecting their adaptation to the local environmental conditions and response to the breeding strategy used. In this study, we comprehensively analysed high-density single nucleotide polymorphism (SNP) genotypes to characterise the population structure and detect the selection signatures in Russian native Yaroslavl and Kholmogor dairy cattle breeds, which have been little influenced by introgression with transboundary breeds. Fifty-six samples of pedigree-recorded purebred animals, originating from different breeding farms and representing different sire lines, of the two studied breeds were genotyped using a genome-wide bovine genotyping array (Bovine HD BeadChip). Three statistical analyses—calculation of fixation index (FST) for each SNP for the comparison of the pairs of breeds, hapFLK analysis, and estimation of the runs of homozygosity (ROH) islands shared in more than 50% of animals—were combined for detecting the selection signatures in the genome of the studied cattle breeds. We confirmed nine and six known regions under putative selection in the genomes of Yaroslavl and Kholmogor cattle, respectively; the flanking positions of most of these regions were elucidated. Only two of the selected regions (localised on BTA 14 at 24.4–25.1 Mbp and on BTA 16 at 42.5–43.5 Mb) overlapped in Yaroslavl, Kholmogor and Holstein breeds. In addition, we detected three novel selection sweeps in the genome of Yaroslavl (BTA 4 at 4.74–5.36 Mbp, BTA 15 at 17.80–18.77 Mbp, and BTA 17 at 45.59–45.61 Mbp) and Kholmogor breeds (BTA 12 at 82.40–81.69 Mbp, BTA 15 at 16.04–16.62 Mbp, and BTA 18 at 0.19–1.46 Mbp) by using at least two of the above-mentioned methods. We expanded the list of candidate genes associated with the selected genomic regions and performed their functional annotation. We discussed the possible involvement of the identified candidate genes in artificial selection in connection with the origin and development of the breeds. Our findings on the Yaroslavl and Kholmogor breeds obtained using high-density SNP genotyping and three different statistical methods allowed the detection of novel putative genomic regions and candidate genes that might be under selection. These results might be useful for the sustainable development and conservation of these two oldest Russian native cattle breeds.

Poaching is one of the major types of wildlife crime in Russia. Remnants of goats (presumably the wild endemic species, the Caucasian tur) were found in an area of the Caucasian mountains. The case study involves a suspected poacher whose vehicle was found to have two duffel bags containing pieces of a carcass, which he claimed was that of a goat from his flock. The aim of the forensic genetic analysis for this case was to (i) establish individual identity and (ii) perform species identification. DNA typing based on fourteen microsatellites revealed that STR-genotypes generated from pieces of evidence found at crime scene fully matched those obtained from the evidence seized from the suspect. The results of genome-wide SNP-genotyping, using Illumina Goat SNP50 BeadChip, provided evidence that the poached animal was a wild Caucasian tur (Capra caucasica). Thus, based on comprehensive molecular genetic analysis, evidence of poaching was obtained and sent to local authorities. To our knowledge, this case study is the first to attempt to use DNA chips in wildlife forensics of ungulates.

Russia is reach by local cattle genetic resources, which are well adapted to the different environment. However, the modern cattle husbandry tends to the replacing the local cattle breeds by highly productive commercial breeds, which can lead to the decline of genetic diversity. The aim of our work was to estimate the genetic identity of five Russian local cattle breeds, including Yaroslavl (n = 52), Kholmogor (n = 26), Istoben (n = 21), Tagil (n = 26), and Black-and-White (n = 44). The Holstein breed (n = 49), which is actively used for improvement of above breeds was included in the study for comparison. The genotyping was performed using GGP Bovine 150K Array (Illumina, San Diego, CA, USA) and more than 112000 autosomal SNPs passed through the quality control and were selected for the analysis. We observed the significant excess of heterozygotes in four studied breeds (the values of unbiased inbreeding coefficient were varied from -0.009 to -0.022), except for Black-and-White breed. The effective population size (Ne) for Istoben, Tagil and Kholmogor breeds was declined until present, while Holstein and Black-and-White breeds showed the increase of Ne values starting at 5 generations ago. The Black-and-White breed was the closest to the Holsteins (Fst=0.014), while the Yaroslavl breed was the most distant (Fst=0.115). The highest ratio of Holstein specific genomic components was shown for Tagil (18.79%) and Black-and-White (59.73%) breeds. Our results indicated replacing the part of aboriginal genomic components in several Russian local cattle breeds by Holstein specific components. The comprehensive strategies for conservation of the Russian local cattle breeds are needed to avoid the further decline of genetic diversity of these valuable national animal genetic resources. The study was funded by the Ministry of Science and Higher Education of the Russian Federation within theme 0445-2019-0024.

During the last centuries, a variety of cattle breeds adapted to the local climatic conditions have been developed in different countries. However, in the 20th century many of them were replaced by high-producing industrial breeds, which can lead to the losses of biodiversity. Our aim was to estimate the genetic diversity of Russian native cattle breeds based on the analysis of historical (museum) and modern samples. Historical samples were derived from the craniological collection of the Museum of Livestock named after E.F. Liskun (Moscow). Forty-six samples including Kholmogor (n = 18), Yaroslavl (n = 19), Saratov (n = 5), Novgorod (n = 2) and Great Russian cattle (n = 2) were subjected to the study. Holland cattle (n = 3) was additionally included in the study due to their possible contribution in forming Russian cattle breeds. The modern samples were presented by Yaroslavl (n = 62) and Kholmogor (n = 177) breeds, and Holstein breed (n = 158) was used as an outgroup. All of the works with historical samples were carried out in the facility of the L.K. Ernst Federal Science Center dedicated for the work with ancient DNA. Nine microsatellite loci (TGLA227, BM2113, ETH10, SPS115, TGLA122, INRA23, TGLA126, ETH225, and BM1824) were successfully amplificated in all samples. We observed the higher variability in historical samples comparing to modern samples: the values of unbiased expected heterozygosity were 0.65–0.85 and 0.70–0.74; the values of rarified allele richness were 2.72–3.11 and 2.63–2.76, respectively. The total number of private alleles was higher in historical populations (16) comparing to modern ones (12). The genetic relationship between historical and modern populations were evaluated. Our results indicate a decrease in genetic diversity in modern populations and a possible loss of valuable allelic combinations. The research results will be useful for development of comprehensive strategies for the conservation of the Russian native genetic resources of cattle. The study was funded by RSF №19-76-20012.

Involvement in research of historical samples can help to clarify the demographic processes in livestock populations. In most cases, bone powder derived from teeth or skull bones are used for molecular genetic studies of historical samples. The aim of our study was to evaluate genetic differences between historical and modern samples of the Russian Large White pigs. Eight historical specimens of the Large White pigs dated by 60s of the 20th century which are maintained in the Craniological collection of the Livestock Museum named after E.F. Liskun were used for the study. The modern representatives of breed were presented by the samples from eight different farms (LW_New1 - LW_New8, n = 152). All works with historical DNA were carried out in the special facilities of the L.K. Ernst Federal Science Center for Animal Husbandry dedicated for work with ancient DNA. DNA was isolated using COrDIS “Extract” Decalcin kit (COrDIS, Russia) and Prep Filer™ BTA Forensic DNA Extraction Kit (Thermo Fisher Scientific, USA). The whole-genome genotyping was performed using Porcine GGP HD BeadChip chips (Illumina/Novogene, USA). The quality control was performed in PLINK 1.9 using the following settings: geno-0.2, mind-0.2, MAF-0.01, HWE-P< 8.27×10−7. The fixation index (Fst) was calculated using the ADMIXTURE software. The concentration of DNA isolated from the historical samples was varied from 0.550 to 600 ng/μl (A260/280 = 1.46–1.96). The genotypes’ call rates were 0.187–0.986. Six historical samples passed through the quality control were used for the further study. Calculation of Fst values showed, that the historical samples were closer to the LW_new1 and LW_new4 groups (Fst = 0.151 and 0.157, respectively), and the most divergent from the LW_new3 group (Fst = 0.304). Our research result will help to elucidate the genetic architecture of the Russian Large White pigs. This research was supported by the RSF (Project No. 19-16-00109).