Runs of homozygosity (ROH) are contiguous stretches of homozygous genotypes that are passed from parents to their offspring. ROHs are suitable for determining population history, inbreeding rates, and the genetic relationships between individuals in the populations, as well as to detect candidate genes responsible for economic traits in farm animals. In this study, we observed that the Kazakh white-headed (KWh) cattle breed (ROH n = 55,976) had a higher number of ROH compared to the Auliekol (AK) breed (ROH n = 13,137). When calculating the mean length of ROH, there were considerable differences between Kazakh white-headed (211.59 ± 92.98 Mb) and Auliekol (99.62 ± 46.48 Mb) populations. The maximum length of ROH was higher in Auliekol cattle (510.25 Mb) than in Kazakh white-headed cattle (498.91 Mb). The average inbreeding coefficient rate was equal to 0.084 ± 0.037 in Kazakh white-headed cattle and 0.039 ± 0.018 in Auliekol cattle. The high frequency of genomic regions showed that the strongest patterns were observed on chromosomes 2, 6, and 26 for KWh and 1, 5, and 14 for AK. The estimation of ROH numbers per animal showed that the number of ROH decreased with increasing ROH length in both populations. The genomic inbreeding coefficient of both cattle breeds was calculated based on the ROH, and ancient inbreeding was observed. The harbored genes within ROH islands were associated with meat growth and milk production.

Background and Aim: Bacterial and viral infections affect the welfare of animals and lead to large economic losses in dairy cattle breeding due to decreased productive indicators and increased culling rates. In modern dairy farming, farmers are looking for effective solutions to prevent and minimize infectious disease risks. To this end, the most relevant study field is the search for gene sites that impact production and health. This study aimed to determine the nature of the distribution of the relative frequencies of alleles and genotypes of polymorphic prolactin (PRL) and nitric oxide synthase (NOS2) in Holstein cows and identify the relationship of these genes with resistance to mastitis and bovine leukemia. Materials and Methods: For this study, we chose cows because infectious diseases affect the amount of lactation and milk quality. Holstein cattle with mastitis and bovine leukemia were selected. Animal genotypes were determined by restriction fragment length polymorphism (RFLP) of polymerase chain reaction (PCR) products. The results were analyzed using a nonparametric statistical method using Microsoft Excel 2010 and Statistica 6.0. Results: In healthy animals, 94 genotypes were identified for both genes under study. For bPRL, bPRL-RsaIAA (72) was the most common genotype and bPRL-RsaIBB (4) the least; for NOS2, bNOS2-HinfIAB (47) was the most common genotype and bNOS2-HinfIAA the least (21). In animals with leukemia, 34 genotypes were identified. For PRL, bPRL-RsaIAA (25) was the most common genotype and bPRL-RsaIBB (2) the least; for NOS2, bNOS2-HinfIBB (17) was the most common genotype and bNOS2-HinfIAA (3) the least. In animals with mastitis, 67 genotypes were identified. For PRL, bPRL-RsaIAA (43) was the most common genotype and bPRL-RsaIBB (6) the least; for NOS2, bNOS2-HinfIBB (31) was the most common genotype and bNOS2-HinfIAA (7) the least. The distribution of genotypes of polymorphic bPRL and bNOS2 generally coincides, and bPRL-RsaIBB is the most common genotype. In groups of sick animals, the number of bNOS2-HinfIAA homozygotes was lower than that of the control group. In particular, the proportion of animals with the bNOS2-HinfIAA genotype with bovine leukemia was 8.7% and with mastitis was 10.3% compared with 22.4% in healthy animals. These data support the possible association of the bNOS2-HinfIAA genotype with resistance to infection. The frequency of the bPRL-RsaIB allele was higher in groups of sick animals. This allele is associated with increased milk productivity, suggesting that highly productive animals are less resistant to the incidence of viral bovine leukemia and mastitis of bacterial etiology. Conclusion: DNA amplification of Holstein cattle for the polymorphic regions of PRL and NOS2 using the PCR-RFLP method revealed a possible connection between the distribution of relative allele frequencies of bPRL and bNOS2 and resistance to viral and bacterial infections. Thus, in groups of sick animals, the frequency of bPRL-RsaIBB, associated with increased milk production compared with the theoretically calculated equilibrium value was higher and the number of homozygotes bNOS2-HinfIAA was lower than in the control group. In conclusion, animals with increased milk production were more prone to diseases, such as mastitis and bovine leukemia.

Kazakh white-headed and Auliekol breeds are mostly spread through Kazakhstan and are animals with dual purpose productivity directions including meat and milk. Kazakh native cattle breeds are still largely unexplored based on the genetic markers and are of great interest in the country. In this study, we for the first time applied high-density SNP genotyping for two indigenous cattle breeds to study genetic diversity, population structure and relationships with the different foreign breeds. Using of GGP Bovine 150K SNP array the principal component analysis (PCA), populations estimates of the genetic structure (ADMIXTURE), genetic diversity and distances (Fst), and phylogenetic tree showed that the Kazakh white-headed and Auliekol breeds have certain separate genetic structure that differ from European and Russian cattle breeds The two of these Kazakh cattle breeds have their genetic background according to observed results as distinct breeds. The obtained results will be aided in the development breeding system and conservation programs of the Kazakh white-headed and Auliekol breeds of beef cattle in the Kazakhstan.

The work aims to analyze the associations of polymorphic variants of the PRL and BLG genes with resistance and susceptibility to mastitis in Holstein cows. The experimental study consisted of the selection of biomaterial samples from 250 heads of Holstein cows aged 3 years divided into two groups (healthy and with a confirmed diagnosis of mastitis). The determination of animal genotypes was carried out using polymerase chain reaction and restriction fragment length polymorphism. The study of the nature of the association of polymorphic variants of the PRL and BLG gene with resistance/increased risk of mastitis established a significant deviation from the theoretically expected distribution of bBLG-HaeIII genotypes in the group of animals suffering from mastitis (the value of χ² was 0.24). The bBLG-HaeIII^BB genotype can act as a marker of an increased risk of developing mastitis in Holstein cows; its frequency in the group of sick animals exceeds the frequency in the control group by more than 2 times (44.0 compared to 17.0%, respectively). The bBLG-HaeIII^AB genotype is significantly associated with mastitis resistance in Holstein cows; its frequency is 2 times lower than in the control group (28.0 compared to 54.0%).

В статье представлены результаты исследования генетического разнообразия отечественных пород лошадей на основании полногеномного анализа однонуклеотидных полиморфизмов (single nucleotide polymorphism, SNP), проведенного с использованием микрочипов Equine 80k HTS («Illumina Inc.», США). В качестве материала для исследований использовали образцы волосяных луковиц лошадей казахской породы типов джабе (ZHB, n = 631), адайского (ADA, n = 303) и найманского (NMN, n = 158), мугалжарской (MUG, n = 584), кушумской (KSH, n = 226) и костанайской (KOS, n = 116) пород. Контроль качества SNP-генотипирования проводили с помощью программного обеспечения PLINK1.9. Для обработки и визуализации данных применяли программы PLINK1.9, R-пакет, BEAGLE, ADMIXTURE, CLUMPAK и FigTree. Конечный набор маркеров, отобранный по результатам контроля качества и использованный для анализа, включал 60 987 SNP. Все исследуемые породы лошадей имели очень близкие значения ожидаемой и наблюдаемой гетерозиготности - в среднем 0,3478 и 0,3443. Степень наблюдаемой гетерозиготности в исследуемых породах лошадей изменялась от 0,3402 у казахской породы адайского типа и мугалжарской породы до 0,3514 у кушумской породы. С помощью метода главных компонент (principal component analysis, PCA), программы ADMIXTURE, ожидаемой и наблюдаемой гетерозиготности (He и Ho), попарных значений индекса фиксации (Fst) было выявлено отсутствие генетической изменчивости между исследуемыми породами лошадей. Сравнение с ранее опубликованными данными о генетическом разнообразии пород лошадей выявило относительно высокий уровень индивидуального разнообразия отечественных лошадей по сравнению с зарубежными породами. При этом монгольская и тувинская породы были выделены как наиболее близкие породы лошадей. Таким образом, впервые с использованием полногеномного анализа SNP мы изучили генетическое разнообразие у отечественных пород лошадей. Эти результаты служат началом углубленного изучения генофонда пород и оценки их значения для перспектив сельскохозяйственного производства.

В настоящей работе представлены результаты полногеномного поиска ассоциаций однонуклеотидных полиморфизмов (SNP) с продуктивными качествами у отечественных пород лошадей, полученные на основании данных SNP-генотипирования животных, проведенного с помощью набора реагентов Equine 80k HTS («Illumina Inc.», США). Объектом исследований являлись лошади следующих пород и типов: казахской типов джабе (n = 631), адай (n = 303) и найман (n = 158), мугалжарской (n = 584), кушумской (n = 226) и костанайской (n = 116) пород. Сбор информации по фенотипическим данным лошадей проводили до отбора проб, при этом измеряли следующие показатели: высота в холке, косая длина туловища, обхват груди, обхват пясти и живую массу. Общее число SNP, отобранных по результатам контроля качества, составило 60 987. Полногеномный поиск ассоциаций был проведен с помощью линейной регрессии с адаптивным методом перестановок Монте-Карло с коррекцией p-значения для множественных сравнений в программе PLINK1.9. В ходе анализа были выявлены 60 полиморфизмов, сцепленных с генами, участвующими в регуляции процессов развития соединительной ткани и костной системы, нервной системы, регуляции иммунной системы и других процессах. Проведенная работа подтвердила актуальность применения подобного подхода в полногеномно-ассоциативных исследованиях для детектирования единичных SNP, связанных с отдельными признаками.