The indigenous Russian Spangled Orloff chicken breed (Large Fowl) was for the first time studied by analyzing polymorphism in loci associated with viral diseases caused by Marek’s disease viruses (MDV), avian leukosis viruses (ALV), and avian influenza viruses. Samples for the analysis were collected at the farms of the All-Russian Poultry Research and Technological Institute (VNITIP), the All-Russian Institute of Farm Animal Genetics and Breeding (VNIIGRZh), and the Moscow Zoo. Assessed populations have a distinction in the frequency and range of allelic variants and as a consequence the frequencies of genotypes LEI0258. The highest level of polymorphism was found in microsatellite loci LEI0258 and Mx1 gene (VNIIGRZh population). The evaluation of polymorphism in genes Mxl (interferon-induced guanosine triphosphatase) and TVB (Tumor Virus В locus, cell receptors) showed, that the Mxl and TVB genotypes associated with resistance to avian influenza viruses and ALV, respectively, were not found in studied populations of Spangled Orloff chicken breed. The most homogeneous group for all studied loci is from the VNITIP population. These data are in good agreement with the results from the study of mtDNA polymorphism in the same samples. The observed polymorphism in nuclear and mitochondrial markers demonstrates that most representative population (about 700 individuals) of Spangled Orloff chicken breed from VNITIP during its long conservation breeding program has remained almost unchanged in the investigated molecular markers and is a source of valuable alleles 357 from microsatellite loci LEI0258 associated with Marek’s disease resistance. The observed frequency of the genotype 357/357 was 48%. The obtained data on the genetic homogeneity of Spangled Orloff chicken breed in all analyzed loci show the need for measures to maintain and increase the number of local groups of Orloffs with the aim of its further preservation.

The gene pools of beef cattle breeds bred in Russia were characterized on the basis of inter simple sequence repeat DNA analysis (ISSR analysis). Samples of Aberdeen Angus, Kalmyk, and Kazakh Whitehead breeds from Russia, as well as of Hereford breed, hybrids of Kazakh Whitehead and Hereford breeds, and Kazakh Whitehead breed from the Republic of Kazakhstan, were examined. In the examined breeds, 27 AG-ISSR fragments were identified, 25 of which were polymorphic. The examined breeds were different both in the fragment profiles (the presence/absence of individual ISSR fragments) and in their frequencies. It was demonstrated that the hybrid animals lacked some ISSR fragments that were present with high frequencies in parental forms, suggesting considerable genome rearrangement in the hybrid animals (at the regions of microsatellite localization) in crossings of the individuals from different breeds. The level of genetic diversity in Russian beef breeds was consistent with the values typical of farmed populations (breeds). The genetic diversity parameters assessed by applying Nei’s gene diversity index and the Shannon index varied from 0.0218 to 0.0605 and from 0.0225 to 0.0819, respectively. The highest Shannon index value was detected in the Kalmyk breed (0.0837) and Kazakh Whitehead breed from Russia (0.0819), and the highest level of Nei’s gene diversity index was found in the Kalmyk breed (0.0562) and in both populations of the Kazakh Whitehead breed (0.0509 and 0.0605). The high level of genetic similarity (according to Nei) was revealed between Russian beef cattle breeds and Hereford cattle: 0.839 (for the Kazakh Whitehead breed from Russia) and 0.769 (for the Kalmyk breed).

Creating farms for sable breeding was associated with the commercial destruction of natural populations and, consequently, the overall decline in the species number. The gene pool of the first farm-bred sable population in Russia, established in the vicinity of Moscow (“Pushkinskiy” fur farm), was formed by crossing of animals removed from nine natural populations. In the first eight years of farm operation, approximately one thousand animals were used for sable breeding; some of these animals were able to adapt to the farm management and, subsequently, to the selection for a number of quantitative traits in the period of industrial domestication. It took about ten years for breeders to work out the breeding and selection technologies, which became successfully employed in the established affiliated sable breeding farms. The main achievement in sable breeding over the 85-year historical period of breeding in Russia is the creation of two unique breeds, black sable (1969) and Saltykovskaya 1 (2007). In general, industrial domestication in fur farming and the subsequent breeding works made the fur of many species (mink, fox, Arctic fox) obtained from natural populations uncompetitive, which undoubtedly reduced the hunting interest in the animals living in the wild. Consequently, hunting for fur-bearing animals of most species decreased and has only local importance. Owing to the specific features of sable biology, the fur of farm-bred animals cannot yet completely replace the furs obtained by hunting; however, the farm-bred sable population is constantly growing. This review presents the results of the analysis of the level of genetic variability in natural and farm populations at nuclear and mitochondrial loci. The comparative analysis makes it possible to estimate the loss of genetic diversity upon the species adaptation to the new conditions of existence.

Впервые изучено генетическое разнообразие орловских ситцевых кур на основе анализа полиморфизма гипервариабельной области D-петли мтДНК. Образцы для анализа были собраны в хозяйствах Всероссийского научно-исследовательского и технологического института птицеводства (ВНИТИП), Всероссийского научно-исследовательского института генетики и разведения сельскохозяйственных животных (ВНИИГРЖ) и Московского зоопарка. Определены нуклеотидные последовательности фрагмента D-петли (с 57 по 523 пн согласно референсной последовательности NC_007235 мтДНК Gallus gallus spadiceus) у 39 особей из исследованных популяций (регистрационные номера КМ391754–КМ391792 в базе данных GenBank). В анализируемом фрагменте D-петли мтДНК у орловских ситцевых кур в целом описано 20 полиморфных сайтов, локализованных между позициями 167 и 368, а также в позиции 446. Один из полиморфных сайтов, в позиции 221 (гаплогруппа E, гаплотип ORL-2), является уникальным. Все обнаруженные нуклеотидные замены относятся к типу транзиций. Всего на основе анализа полиморфных сайтов в гипервариабельном фрагменте D-петли мтДНК у изученных орловских ситцевых кур нами выявлено семь гаплотипов, относящихся к четырем гаплогруппам: A, B, С и Е. Гаплогруппа Е (гаплотипы ORL-1, ORL-2 и ORL-3) представлена у абсолютного большинства исследованных особей орловских ситцевых кур (частота в суммарной выборке составила 0.77 и 0.47 в популяции из ВНИИГРЖ). Гаплогруппы А (гаплотипы ORL-4, ORL-7), B (ORL-6) и С (ORL-5) обнаружены только в генофондном хозяйстве ВНИИГРЖ. Отмечен низкий уровень полиморфизма исследуемой области мтДНК в популяциях ВНИТИП и Московского зоопарка: в них были представлены только гаплотипы ORL-1 и ORL-3 (соответственно), относящиеся к гаплогруппе Е. Таким образом, полученные данные свидетельствуют о том, что исследованные нами выборки популяций орловских ситцевых кур различаются по набору и частотам гаплогрупп и гаплотипов.

For the first time, the genetic diversity of the Spangled Orloff chickens was studied by analyzing the polymorphism of the hypervariable region in the D-loop of mitochondrial DNA (mtDNA). Samples for the analysis were collected at the farms ofthe All-Russia Poultry Research and Technological Institute (VNITIP), the All-Russia Institute of Farm Animal Genetics and Breeding (VNIIGRZh), and the Moscow Zoo. The D-loop partial sequences (between nucleotide positions 57 and 523) were determined according to the reference sequence of Gallus gallus spadiceus mtDNA, NC_007235 in 39 individuals obtained from these populations (GenBank Accession Nos. KM391754-KM391792). In the analyzed mtDNA fragment, a total of 20 polymorphic sites localized between positions 167 and 368, as well as at position 446, were described in Spangled Orloff chickens. One polymorphic site at position 221 (haplogroup E, haplotype ORL-2) was unique. All of the identified nucleotide changes were transition-type substitutions. Overall, based on the analysis of poly- morphic sites in the hypervariable fragment of the D-loop of Spangled Orloff chicken mtDNA, we found seven haplotypes belonging to four haplogroups (A, B, C, and E). Haplogroup E (haplotypes ORL-1, ORL-2, and ORL-3) was present in the majority of the studied individual, with the frequencies of 0.77 in the total sample and 0.47 in the VNIIGRZh farm population. Haplogroups A (haplotypes ORL-4 and ORL-7), B (ORL-6), and C (ORL-5) were found only in samples from the VNIIGRZh farm. The studied mtDNA region revealed a lower level of polymorphism in the VNITIP and Moscow Zoo populations, which only had the ORL-1 and ORL-3 haplotypes belonging to Haplogroup E, respectively. Our data suggested that the studied Spangled Orloff chicken populations differed in the composition and frequencies of mtDNA haplogroups and haplotypes.

The genetic variability in seven yak populations from the Sayan-Altai region and in F1 hybrids between yak and cattle (khainags) was investigated with the help of a technique that involves the use of inter simple sequence repeat (ISSR) markers generated with PCR primers (AG)9C and (GA)9C. Samples for the analysis were collected in Mongolia, Tuva, and Altai from 2008 through 2012. The examined yak populations differed in in the presence/absence of ISSR fragments, as well as in their frequency. In total, 46 ISSR fragments were identified using two marker systems; the proportion of polymorphic loci constituted 76% and 90% for the AG-ISSR and GA-ISSR markers, respectively. For the total sample of yaks, total genetic diversity (Ht), within-population diversity (Hs), and interpopulation diversity (Gst) constituted 0.081, 0.044, and 0.459 for the AG-ISSR and 0.137, 0.057, and 0.582 for the GA-ISSR markers, respectively. Based on ISSR finger printing, species- and breed-specific DNA patterns were described for the three groups of animals (yaks, cattle, khainags). For the domestic yak, the species-specific profile was represented by eight ISSR fragments. Genetic relationships between the yak populations, cattle breeds, and khainags were examined with the help of four different approaches used in the analysis of population structure: estimation of phylogenetic similarity, multidimensional scaling, principal component analysis, and cluster analysis. Clear evidence on the differentiation of the populations examined at the interspecific, as well as at intraspecific, level were obtained. Similar (relative); as well as remote (isolated), yak populations were identified. Khainags occupy an intermediate position between yak and cattle. However, the data on the ISSR-PCR marker polymorphism (genome polymorphism, population structure).indicate that part of the analyzed khainag genome was more similar to the yak genome than to the cattle genome.

Изучен аллельный и генотипический полиморфизм генов С-рецептора ретиноевой кислоты (RORC), диацилглицерол-ацилтрансферазы-1 (DGAT1) и гормона роста (bGH) у мясных российских пород крупного рогатого скота: двух популяций казахской белоголовой (казахстанской и российской селекции) и калмыцкой пород, а также монгольской породы хогорого, родственной калмыцкой породе. Исследуемые гены ассоциированы с параметрами мясной продуктивности: мраморностью (гены bGH и RORC) и мягкостью мяса (ген DGAT1), а также с увеличением выхода мяса (ген bGH). Российская и казахстанская популяции казахской белоголовой породы характеризовались высоким содержанием АА-генотипа гена RORC (0.713 и 0.608 соответственно) и АА-генотипа DGAT1 (0.913 и 0.975), предпочтительных для получения высококачественного мяса. Суммарные частоты сопряженных генотипов по генам bGH и RORC, более предпочтительных для качества и выхода мяса, в популяциях казахской белоголовой составили: GG/AA и GC/AA – 68.8 и 57% для российской и казахстанской популяций, что в 2 раза превышает соответствующие показатели у двух других изученных пород. Полученные совокупные данные указывают на высокий генетический потенциал казахской белоголовой породы крупного рогатого скота как породы мясного направления продуктивности и могут быть использованы для повышения эффективности селекции по этому признаку.

We examined the allelic and genotypic polymorphisms of genes of the retinoic acid receptor-related orphan receptor C (RORC), diacylglycerol acyltransferase-1 (DGAT1), and growth hormone (bGH) in Russian beef cattle breeds in two populations of Kazakh white-headed cattle (of Kazakh and Russian selection) and the Kalmyk cattle breed, as well as in the Mongolian hogorogo breed, which is related to Kalmyk breed. The studied genes are associated with parameters of meat quality: marbleness (bGH and RORC) and tenderness (DGAT1). They are also associated with an increase in carcass weight (bGH). We found that Russian and Kazakh populations of the Kazakh white-headed breed were characterized by a high content of the AA genotype of RORC (0.713 and 0.608, respectively) and of the AA genotype of DGAT1 (0.913 and 0.975), both of which are preferable for meat quality. The total frequencies for the combined genotypes for the bGH and RORC genes, which provide for superior meat quality and carcass weight, in the populations of Kazakh white-headed cattle (GG/AA and GC/AA—68.8 and 57% in the Russian and Kazakh populations, respectively) exceeded the frequencies in the two other studied breeds by two times. Overall, the obtained results point to the high genetic potential of both populations of Kazakh white-headed cattle breeds in beef production. Results of this study can be used to improve the selection of meat traits in industrial livestock.

Охарактеризована генетическая изменчивость семи популяций яка Cаяно-Алтайского региона и гибридов F1 между яком и крупным рогатым скотом (хайнаков) методом межмикросателлитного анализа полиморфизма ДНК (ISSR-PCR) с использованием праймеров (AG)9C и (GA)9C. Образцы для анализа были собраны в Монголии, Туве и Алтае в 2008–2012 гг. Исследованные популяции яков различались как по наличию/отсутствию ISSR-фрагментов, так и по их частотам. Всего по двум маркерным системам выявлено 46 ISSR-фрагментов, доля полиморфных локусов составила 76 и 90% для AG-ISSR и GA-ISSR маркеров соответственно. Общее генетическое разнообразие (Ht), внутрипопуляционное (Нs) и межпопуляционное (Gst) разнообразие для суммарной выборки яков составили соответственно 0.081, 0.044 и 0.459 для AG-ISSR и 0.137, 0.057 и 0.582 для GA-ISSR маркеров. На основе ISSR-анализа описаны видо- и породоспецифичные паттерны ДНК для трех групп животных (яки, крупный рогатый скот, хайнаки); для домашнего яка видоспецифичный спектр представлен восемью ISSR-фрагментами. Изучены генетические взаимоотношения между популяциями яков, породами крупного рогатого скота и хайнаками с использованием четырех различных методов анализа популяционных структур: оценки филогенетического сходства, многомерного шкалирования, метода главных компонент и кластерного анализа. Получены четкие данные по дифференциации исследованных популяций как на межвидовом, так и на внутривидовом уровне. Выявлены как близкие (родственные), так и отдаленные (изолированные) популяции яков. Хайнаки занимают промежуточное положение между яком и крупным рогатым скотом, но в соответствии с данными по анализу полиморфизма ISSR-маркеров ДНК (геномному полиморфизму, популяционной структуре) исследованная часть генома хайнаков имеет большее сходство с геномом яков, чем с геномом крупного рогатого скота.

Genetic peculiarities of bovine leukemia virus isolates (BLV) spread throughout Russia and Ukraine (BLV-1, BLV-2, and BLV-4) have been characterized based on pol gene polymorphism. Seven viral forms have been detected. The variability of BLV isolates did not exceed 1% within one form. Despite the recent inhabitation of BLV in Russia in the middle of 20th century, Russian BLV variants are characterized by several specific nucleotide substitutions. Point mutations that result in the changes in the aminoacid sequence of reverse transcriptase of BLV specific to distinct viral forms were observed. C --> G transition at the 2752 position (relatively to the reference genome AF033818), which results in the substitution of glutamic to asparaginic acid (GAG --> GAC), is specific to form BLV-2. This mutation was demonstrated in BLV isolates from Ukraine. The T --> G substitution at the 2758 position, which results in the substitution of isoleucine for methionine (ATT --> ATG), is specific to BLV-4 and BLV-7 forms. The BLV-4 form was only detected in Russia and Ukraine. The present study also includes a review of the published data concerning BLV variability. The existing classifications of BLV forms have been critically conceived and the new optimal classification of BLV forms with the maximal resolution has been suggested.

Using (AG)9C and (GA)9C primers and analysis of multilocus profile of intermicrosatellite polymorphism (ISSR-PCR), in 19 cattle breeds, a total of 66 PCR products were revealed. The statistical processing of the data obtained using standard software programs enabled the identification of the ISSR markers, the polymorphism of which made the greatest contribution to the total genomic diversity of both individual breeds and the species Bos taurus in general. These DNA fragments deserve special interest for the further analysis of their localization and functions.

Bovine leukemia virus (BLV) is a widespread specific pathogen of cattle. Analysis of the pol viral gene polymorphism has been used to characterize the polymorphism of BLV isolates at stock-breeding farms in Russia and Ukraine. The fragments of the pol gene corresponding to the reverse transcriptase and integrase 494 and 233 bp in size, respectively, have been used for analysis. Phylogenetic analysis has revealed several variants of BLV clustered with a high bootstrap support in Russia and Ukraine. A new classification of BLV variants is suggested. Comparison of phylograms based on the polymorphism of the nucleotide sequences of the integrase and reverse transcriptase domains did not show topological conflicts. Therefore, recombination between BLV variants has not been found.

The authors investigated the dependence between milk productivity of cattle of the Yaro- slavskaya breed and bGH and bPRL genes of growth hormone and prolactin, respectively, in AluI and RsaI restriction sites. The complex genotypes of these genes were established, which determined more high and low percentage of milk fat and protein. The obtained principles can be used for reve-lation of animals, having prospects in relation to milk productivity at the early detection of the appli- cant to pedigree or commercial stock.

The role of the major histocompatibility complex (MHC) in the immune response makes it an attractive candidate gene for associations with disease resistance and susceptibility. This study describes genetic variability in the BoLA-DRB3 in Iranian buffaloes. Heminested PCR-RFLP method was used to identify the frequency of BoLA-DRB3 alleles. The BoLA-DRB3 locus is highly polymorphic in the study herd (12 alleles). Almost 63.50% of the alleles were accounted for by four alleles (BoLA-DRB3.2 *48, *20, *21, and obe) in Iranian buffalo. The DRB3.2 *48 allele frequency (24.20%) was higher than the others. The frequencies of the DRB3.2 *20 and DRB3.2 *21 are 14.52 and 14.00, respectively, and obe and gbb have a new pattern. Significant distinctions have been found between Iranian buffalo and other cattle breed studied. In the Iranian buffaloes studied alleles associated with resistance to various diseases are found.

The present study investigated a genealogical structure of Kostromskaya cattle breed on blood groups in bulls-sires from the main farm bloodlines and related animal groups with different portion of Schwiss cattle blood used during the last years in breeding farms to improve milk productivity of Kostromskaya cattle. The spectrum of EAB-locus alleles of blood groups was analyzed and the genetic diversity, the degree of homozygosis and genetic consolidity of these genealogical groups were estimated. It was revealed, that Schwiss bulls-sires of American, Canadian and Austrian selection continue to influence, however, the studied farm lines and related groups have significant genetic distinguishes, confirmed by an index of genetic distance (D N = 0.647).

The present study investigated a genealogical structure of Kostromskaya cattle breed on blood groups in bulls-sires from the main farm bloodlines and related animal groups with different portion of Schwiss cattle blood used during the last years in breeding farms to improve milk produc- tivity of Kostromskaya cattle. The spectrum of EAB-locus alleles of blood groups was analyzed and the genetic diversity, the degree of homozygosis and genetic consolidity of these genealogical groups were estimated. It was revealed, that Schwiss bulls-sires of American, Canadian and Austrian selec-tion continue to influence, however, the studied farm lines and related groups have significant ge- netic distinguishes, confirmed by an index of genetic distance (D N = 0.647).