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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).

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).