Turkish Cattle Research Articles

Molecular Characterisation and Antibody Response to Bovine Respiratory Syncytial Virus in Vaccinated and Infected Cattle in Turkey.

Bovine respiratory syncytial virus (BRSV) is one of the most important respiratory pathogens of cattle. In this study, frequency of infection, analysis of variants, and the immune status of vaccinated and non-vaccinated cattle were studied. Blood (n = 162) and nasal/oropharyngeal (n = 277) swabs were collected from 62 cattle herds in Turkey. Lung samples (n = 37) were also taken from dead animals and abattoirs. Antibodies to BRSV were detected in 76 (46%) out of 162 sera. The antibody levels in the vaccinated and non-vaccinated groups were statistically significant. Among 277 nasal/oropharyngeal swabs and 37 lungs, ten nasal/oropharyngeal and four lung samples were positive for BRSV-RNA. BRSV-G gene sequences of 5 out of 14 RT-PCR positive samples showed that all viruses clustered as Group-III in phylogenetic analysis with 88-100% homology. Similarity with previous Turkish BRSVs was 89-98%, and that with BRSVs detected in the USA and Czechia was 89.47-93.12%. BRSV continues to circulate in Turkish cattle, and vaccination seems beneficial in preventing BRSV. The diversity of the BRSVs found in this study needs be considered in vaccination strategies.

Analysing the genetic diversity and population structure of five native Turkish cattle breeds using SNP data.

The conservation and sustainable utilization of cattle genetic resources necessitate a comprehensive understanding of their genetic diversity and population structure. This study provides an analysis of five native Turkish cattle breeds: Anatolian Black (ANB), Turkish Grey (TUR), Anatolian Southern Yellow (ASY), East Anatolian Red (EAR), and South Anatolian Red (SAN) using 50 K SNP data. These breeds were compared with three European breeds, Simmental (SIM), Holstein (HOL), and Jersey (JER), and three Asian Zebu breeds: Arabic Zebu (ZAR), Nelore (NEL), and Red Sindhi (RSI). Genetic diversity indices demonstrated moderate heterogeneity among the breeds, with TUR exhibiting the highest observed heterozygosity (Ho = 0.35). Wright's Fst values indicated significant genetic differentiation, particularly between Turkish breeds and both European (Fst = 0.035-0.071) and Asian breeds (Fst = 0.025-0.150). Principal component analysis distinguished the unique genetic profiles of each breed cluster. Admixture analysis revealed degrees of shared genetic ancestry, suggesting historical gene flow between Turkish, European, and Asian breeds. Analysis of molecular variance (AMOVA) attributed approximately 58% of the variation to population differences. Nei's genetic distances highlighted the closer genetic relatedness within Turkish breeds (distance ranges between 0.032 and 0.046) and suggested a more relative affinity of TUR with European breeds. The study's phylogenetic assessments elucidate the nuanced genetic relationships among these breeds, with runs of homozygosity (ROH) analysis indicating patterns of ancestral relatedness and moderate levels of inbreeding, particularly evident in Turkish breeds. Our findings provide valuable insights into the genetic landscape of Turkish cattle, offering a crucial foundation for informed conservation and breeding strategies aimed at preserving these breeds' genetic integrity and heritage.

Genome-wide genetic variation and population structure of native and cosmopolitan cattle breeds reared in Türkiye

This is the first comprehensive study to reveal genetic variation and population structure at genome level in six Anatolian (Anatolian Black, East Anatolian Red, South Anatolian Red, South Anatolian Yellow, Turkish Grey Steppe, and Zavot) and two cosmopolitan (Brown Swiss and Holstein Friesian) cattle breeds reared in Türkiye. Being 20 samples from each population, a total of 160 blood samples retrieved from representative herds were utilized to generate genomic libraries by ddRADseq method. Genomic libraries sequenced by Illumina HiSeq X Ten instrument revealed a total of 211,119 bi-allelic SNPs with high call rate. Compared to cosmopolitan cattle breeds, a higher genetic variation was observed in native Turkish cattle with an average of 0.380 observed heterozygosity. Genetic distances were comparatively low between native cattle breeds, whereas the highest genetic distance (0.064) was detected between South Anatolian Yellow and Brown Swiss. Population structure analyses showed that the native Turkish and cosmopolitan cattle breeds were clearly different from each other according to their phylogenetic origin. Besides, a high level of genetic admixture was detected among Anatolian Black, Turkish Grey Steppe, South Anatolian Red, and South Anatolian Yellow, whereas East Anatolian Red and Zavot were distinct from the other native and cosmopolitan cattle breeds. TreeMix algorithm under the assumption of one and two migration events revealed a migration route from Anatolian clade to Anatolian Black, while a second migration edge was drawn from Brown Swiss to East Anatolian Red. This study demonstrates the importance of national conservation studies in the native breeds whose population size has dramatically decreased. In addition, SNP arrays and next-generation sequencing platforms are recommended for future studies to reveal the genetic variation of other local Turkish livestock species to arrange effective conservation programs.

Mitochondrial DNA diversity of D-loop region in three native Turkish cattle breeds.

This study aimed to reveal the genetic variability of mitochondrial DNA (mtDNA) displacement-loop (D-loop) region in 62 animals belonging to three native Turkish cattle breeds, namely Anatolian Black (AB), East Anatolian Red (EAR) and Zavot (ZAV), and to conduct phylogenetic relationship analyses to obtain deeper information on their genetic origin and breeding history by comparison of 6 taurine and 11 indicine breeds, together with 66 polymorphic sites, a total of 31 haplotypes, of which 15, 10 and 6 were detected in AB, EAR and ZAV, respectively. Mean nucleotide and haplotype diversity were 0.01 and 0.891, respectively, whereas the genetic differentiation derived from Wright's index was 0.174 across the breeds. A significant level of total variation (17.42 %) was observed among breeds in molecular variance analysis. Six main haplogroups (T, T1, T2, T3, Q and I2) were detected in Anatolian cattle populations, where T3 was the most frequent among breeds (43.55 %), whereas I2, an indicine specific haplogroup, was observed only in ZAV. At the breed level, phylogenetic analyses supported by 198 sequences of 17 cattle breeds and 3 outgroup species retrieved from the GenBank clustered native Turkish cattle breeds with the taurine group rather than the indicine one, as expected. However, indicine admixture at low frequency (8.89 %) was detected in the ZAV breed for the first time due to more likely gene flow from indicine cattle breeds raised in neighbour countries, particularly Iran. This finding should be further investigated in all native Turkish and indicine cattle breeds from nearby countries to clarify gene flow and indicine admixture in Anatolian cattle.

Current scenario of viral diseases and vaccination strategies of cattle in Turkey.

The dairy and meat industry has rapidly developed in the last decade in Turkey and is playing a key role in supplying animal proteins for human consumption. Viral pathogens continue to threaten the dairy and meat industry leading to serious economic losses worldwide, including Turkey. The Turkish cattle industry has been vulnerable to the spread of viral diseases within the country in the continent. Combating animal diseases is crucial for the economy of Turkey. A good cattle health management policy may reduce the direct losses associated with viral diseases and thereby lead to increase in export of animals and animal products. Countries that are unable to combat animal diseases remain excluded from international trade. Control and eradication of cattle diseases require the availability of effective and practical interventions including vaccination and biosecurity measures. This review summarises the currently available information about viral diseases in cattle in Turkey and emphasizes the need for disease monitoring and research, along with implementation of disease control measures to mitigate economic losses to farmers and the country. The information presented here can be of great value in the research, prevention, and control of cattle diseases.

Future Perspective of NGS Data for Evaluation of Population Genetic Structure in Turkish Cattle

Developments in sequencing and SNP chip technologies have enabled scientists to obtain high-density genomic data from different livestock species, including cattle. Moreover, many bioinformatics tools are available to analyse high-density genomic data. Via these tools, several statistical approaches such as Principal Component Analysis and clusterin-based analyses could be conducted to reveal the genetic structure of cattle populations. However, revealing the genetic structure and selection signatures of Turkish cattle breeds is a new area of research, since the previous studies are limited with a few microsatellite data. On the other hand, rearing in different geographical and environmental conditions for a long period could possibly lead to more genetic variation in native Turkish cattle breeds compared to high-yielding culture breeds. These variations obviously cannot be detected by limited number of microsatellite markers, while Next Generation Sequencing is promising for further population structure studies. Hence this review aims to summarise previous studies and give a perspective of Next Generation Sequencing possibilities to reveal the population structure of Turkish cattle for further studies.

Genotypic structure of four cattle breeds raised in Turkey by loci related to several diseases

This study aims to reveal the genotypic structure of four cattle breeds; Holstein (HS), Turkish Grey Steppe (TGS), Anatolian Black (AB) and East Anatolian Red (EAR), raised in Turkey in terms of CD14, MBL, ITGB6, SLC11A1 and TLR2 genes and to evaluate their usefulness in Marker Assisted Selection (MAS). It also assesses whether the loci associated with resistance to diseases are suitable for phylogenetic analysis. Desired alleles and/or genotypes were detected in native Turkish cattle breeds at different frequencies in terms of polymorphisms of CD14, MBL, ITGB6, SLC11A1 and TLR2 genes which were previously reported to be associated with mastitis, foot-and-mouth disease and tuberculosis. These variations offer opportunities to improve selection strategies against diseases in the future. These results preliminary indicate that associated studies between these variations and disease resistance in native Turkish cattle breeds should be conducted. On the other hand, phylogenetic tree constructed based on genetic distance clearly separated native Turkish cattle breeds from HS breed. The gene regions related to diseases can be used to distinguish native cattle breeds from exotic ones.

Determination of production losses related to lumpy skin disease among cattle in Turkey and analysis using SEIR epidemic model

BackgroundLumpy Skin Disease (LSD) is an infectious disease induced by the Capripoxvirus, causing epidemics in Turkey and several countries worldwide and inducing significant economic losses. Although this disease occurs in Turkish cattle every year, it is a notifiable disease. In this study, LSD in Turkey was modelled using the Susceptible, Exposed, Infectious, and Recovered (SEIR) epidemiological model, and production losses were estimated with predictions of the course of the disease. The animal population was categorized into four groups: Susceptible, Exposed, Infectious, and Recovered, and model parameters were obtained. The SEIR model was formulated with an outbreak calculator simulator applied for demonstration purposes.ResultsProduction losses caused by the LSD epidemic and the SEIR model’s predictions on the disease’s course were evaluated. Although 1282 cases were identified in Turkey during the study period, the prevalence of LSD was calculated as 4.51%, and the mortality rate was 1.09%. The relationship between the disease duration and incubation period was emphasized in the simulated SEIR model to understand the dynamics of LSD. Early detection of the disease during the incubation period significantly affected the peak time of the disease. According to the model, if the disease was detected during the incubation period, the sick animal's time could transmit the disease (Tinf) was calculated as 2.66 days. Production loss from LSD infection was estimated at US $ 886.34 for dairy cattle and the US $ 1,066.61 for beef cattle per animal.ConclusionDetection of LSD infection during the incubation period changes the course of the disease and may reduce the resulting economic loss.

Genetic variability of bovine herpesvirus type 4 (BoHV-4) field strains from Turkish cattle herds.

Bovine herpesvirus type 4 (BoHV‑4) is a common virus in the world that is detected in clinically ill or in apparently healthy cattle. This study provides a molecular characterization of BoHV‑4 strains from 24 cattle some showing respiratory and/or reproductive problems and some without any apparent clinical sign. This study also reported the growth properties of five BoHV‑4 field isolates. The 24 sampled cattle came from 13 different herds in 10 provinces collected between 2007 and 2018. Phylogenetic analysis using partially amplified nucleotide sequences of ORF8 genes coding glycoprotein B (n = 24) and ORF3 genes coding thymidine kinase (n = 9), demonstrated genetic variability among the BoHV‑4 strains analysed. The partial gB gene sequences clustered in three different genotypes (genotype I, II and III) were located within the genotype I cluster, such as Movar strain. The analysis of the five BoHV‑4 strains isolated from vaginal swabs (n = 2), nasal swab (n = 1), and brain samples (n = 2) revealed no significant differences in their growth properties in MDBK cell culture.

A comprehensive review on genetic diversity and phylogenetic relationships among native Turkish cattle breeds based on microsatellite markers

A comprehensive review on genetic diversity and phylogenetic relationships among native Turkish cattle breeds based on microsatellite markers

Molecular detection and phylogeny of Anaplasma spp. in cattle reveals the presence of novel strains closely related to A. phagocytophilum in Turkey

Anaplasma species are obligate intracellular rickettsial pathogens that affect the health of humans and animals. In this study, we investigated the presence and frequency of Anaplasma species by 16S rRNA PCR-RLB, RFLP, and DNA sequencing in 200 apparently healthy cattle. Anaplasma spp. overall infection rate was 38.5 % (77/200) by RLB. The frequency of single and mixed infections was 31.5 % (63/200) and 7% (14/200), respectively. The most common species was A. marginale (32.5 %), followed by A. centrale (5.5 %), Anaplasma/Ehrlichia catc-all (5.5 %) and Anaplasma sp. Omatjenne (2.5 %). No A. phagocytophilum and A. bovis were detected in the tested animals. Eleven of 77 PCR-positive amplicons gave positive reactions to the catch-all probes but did not show any signals to the species-specific probes, but PCR-RFLP results showed that these amplicons were A. phagocytophilum-like 1 and A. phagocytophilum-like 2 strains. Sequencing and phylogenetic analyses based on 16S rRNA gene validated RFLP findings and provided evidence for the circulation of A. phagocytophilum-like-1 and 2 strains in Turkish cattle. This is the first report of the presence of A. phagocytophilum-like strains in the country. These findings indicate that A. phagocytophilum-like 1 and 2 strains should be taken into account in the differential diagnosis with bovine anaplasmosis.

Circulation of Indigenous Bovine Respiratory Syncytial Virus Strains in Turkish Cattle: The First Isolation and Molecular Characterization.

Simple SummaryBovine respiratory syncytial virus (BRSV) is an important pathogen of both dairy and beef cattle, and causes huge economic losses annually across the world. This study reports the identification, isolation, and molecular characterization of a new BRSV (subgroup III) strain collected from respiratory distressed cattle in Turkey. The three field isolates obtained showed 100% similarity to each other at the nucleotide (nt) level and were found to be 99.49% and 99.22% identical to another Turkish strain—KY499619—at both (nt) and amino acid (aa) levels, respectively. They were also 97.43% (nt) and 98.44% (aa) similar to the American reference strain KU159366. This important information will inform Turkish BRSV diagnostic and control strategies, as well as highlight the urgent need to better understand the burden that BRSV is placing on the Turkish agricultural sector.Bovine respiratory disease (BRD) is a huge economic burden on the livestock industries of countries worldwide. Bovine respiratory syncytial virus (BRSV) is one of the most important pathogens that contributes to BRD. In this study, we report the identification and first isolation, with molecular characterization, of a new BRSV strain from lung specimens of three beef cows in Turkey that died from respiratory distress. After the screening of lung tissues for BRD-associated viruses using a multiscreen antigen-ELISA, a BRSV antigen was detected. This was then confirmed by real-time RT-PCR specific for BRSV. Following confirmation, virus isolation was conducted in MDBK cell cultures and clear CPE, including syncytia compatible with BRSV, were detected. RT-nested PCR, using F gene-specific primers, was performed on the cultured isolates, and the products were sequenced and deposited to Genbank with accession numbers MT179304, MT024766, and MT0244767. Phylogenetic analysis of these sequences indicated that the cattle were infected with BRSV from subgroup III and were closely related to previously identified American and Turkish strains, but contained some amino acid and nucleotide differences. This research paves the way for further studies on the molecular characteristics of natural BRSV isolates, including full genome analysis and disease pathogenesis, and also contributes to the development of robust national strategies against this virus.

First report of influenza D virus infection in Turkish cattle with respiratory disease

Bovine respiratory infections are the most economically important diseases affecting the cattle industry worldwide including Turkey. Influenza D virus (IDV) could play an important role to trigger bovine respiratory disease (BRD) complex. Since, there is no data about the presence and genotypes of IDV in Turkish cattle herds; this study was performed to investigate IDV in cattle in Turkey. Animals analyzed in this study were from commercial cattle farms having respiratory disease in calves with significant mortality. Nasal swabs and tissue samples from cattle in Marmara, Inner Anatolia and Aegean region of Turkey were analyzed by real-time RT-PCR assay to detect IDV. Among 76 samples form 12 cattle herds, IDV was detected in 3 cattle in a herd. Sequencing and phylogenetic analysis of partial hemagglutinin esterase fusion (HEF) gene showed that the Turkish strain is 95% identical to its European and US counterparts, which suggest intercontinental spread of the virus. These findings highlight the need for future continuous surveillance on larger scale to determine the distribution pattern and evolution of this novel emerging pathogen in Turkish cattle industry.

Phylogenetic relationships of native Turkish cattle breeds using microsatellite markers

A total of 20 microsatellite DNA markers were used for genetic characterization and determination of phylogenetic relationships of native cattle breeds of Turkey, including the Anatolian Grey (AG), Anatolian Black (AB), South Anatolian Red (SAR), East Anatolian Red (EAR), Southern Anatolian Yellow (SAY), and Zavot (ZAV). DNA samples were isolated from 271 blood samples using an organic method. Amplified polymerase chain reaction products were separated by capillary electrophoresis and genotypes were determined for 20 microsatellites. A total of 269 different alleles were determined. The lowest (7.80) and highest (10.80) mean allele numbers were observed for the ZAV and SAY populations, respectively. TGLA122 was the most polymorphic locus; however, only 7 different alleles were observed for INRA005. A total of 40 different private alleles were determined. The general FIS values were between 0.034 and 0.123. Due to the close location to the domestication center, higher genetic diversities were observed. The observed genetic diversities and the results of the phylogenetic analyses were in agreement with evolutionary history and the geographical origins of Turkish native cattle breeds.

Presence of bovine hepacivirus in Turkish cattle

Hepatitis C virus (HCV), a worldwide distributed human pathogen, causes one of the most important viral infections in human being. HCV is the type species of the genus Hepacivirus (Flaviviridae) in which recently discovered animal viruses i.e. from horses, bats, rodents and cattle are allocated. After preliminary reports in 2015 from German and African cattle, a wide distribution of bovine hepacivirus (BovHepV, Hepacivirus N) was proposed. We investigated the possible presence of BovHepV in serum samples from cattle in different locations of Turkey. Analyzing a total of 120 samples from 98 female (dairy) and 22 male (beef) cattle by real-time RT-PCR resulted in 15 (12.5%) positives. BovHepV infection was detected in 6 out of 10 locations included in the study. There were positive samples both from eastern and western parts of the country indicating possible wide distribution in the Turkish cattle population. Phylogenetic analysis of 9 selected positive samples clearly assigned 8 sequences to a separate cluster on the basis of NS3 gene region, while one of the sequences obtained from an imported animal from north of Italy grouped with sequences obtained from cattle in Germany. The latter finding may indicate possible occurrence of this genetic group of BovHepV not only in Germany but in other European countries. Results of the present study demonstrate the presence of BovHepV infections in Turkey and in The Middle East region.

Population structure and ancestry of Qinchuan cattle.

The aim of this study was to estimate population structure and ancestry of Qinchuan cattle by genotyping 27 individuals using the GeneSeek HD 77k BeadChip, and another 1355 cattle representing breeds distributed worldwide, which had been genotyped using the Illumina Bovine 50k BeadChip. Qinchuan cattle were characterized by a dominant Bos taurus ancestry, accompanied by a considerable proportion of Bos indicus ancestry based on principal components analysis and supervised admixture analysis. A small proportion of Bos javanicus ancestry was detected as well. A similar admixture pattern in both Qinchuan and Turkish cattle breeds reflects their similar degrees of zebu introgression. Our study presents a relatively clear view of the population structure and ancestry of Qinchuan cattle, serving to benefit our understanding of this breed and leading to better targeted conservation approaches moving forward.

Determination of Toll-Like Receptor 1 Gene Polymorphisms in Zavot, Turkish Grey, East Anatolian Red, Anatolian Black and South Anatolian Red Cattle Breeds

Toll-like receptors (TLRs) play an important role in non-specific immunity against different infectious agents such as bacterium or parasite. The aim of this work was to investigate the allele and genotype frequencies of three single-nucleotide polymorphisms (SNPs) in bovine TLR1 gene in native Turkish cattle breeds. DNA samples were extracted using the phenol chloroform protocol from 77 Zavot, 60 Turkish Grey, 51 East Anatolian Red, 69 Anatolian Black and 46 South Anatolian Red cattle. Target regions of the TLR1 gene were digested BsII and HpyI88III restriction enzymes. Results showed that the (A) allele frequency had higher in all native Turkish cattle breeds of the TLR1-G1409A locus. The (F) allele frequency was found to be higher compared to (E) allele in the TLR1-G1550A site. The frequencies of both (C) and (T) alleles were close to each other in the TLR1-C632T site. In conclusion genetic polymorphisms exist in Turkish native cattle populations in terms of known TLR1 variants.

Risk analysis of lumpy skin disease in Turkey

Lumpy Skin Disease (LSD) in Turkish cattle appeared suddenly two years ago. This study evaluates potential risks of LSD and recommends appropriate control measures. The World Animal Health Organization’s protocol was used for the risk analysis. Likelihoods for disease release and exposure were estimated with a qualitative scale ranging from negligible to high. Outbreaks were recorded in nine provinces in Turkey. Total economic loss due to the disease was estimated to be $241.903.500 US dollars. The risk analysis suggests a greater than negligible risk. Therefore, disease prevention and control strategies should be considered by the Turkish Veterinary Authority.

Mass vaccination, immunity and coverage: modelling population protection against foot-and-mouth disease in Turkish cattle.

Foot-and-mouth disease (FMD) in Turkey is controlled using biannual mass vaccination of cattle. However, vaccine protection is undermined by population turnover and declining immunity. A dynamic model of the Turkish cattle population was created. Assuming biannual mass vaccination with a single-dose primary course, vaccine history was calculated for the simulated population (number of doses and time since last vaccination). This was used to estimate population immunity. Six months after the last round of vaccination almost half the cattle aged <24 months remain unvaccinated. Only 50% of all cattle would have received >1 vaccine dose in their life with the last dose given ≤6 months ago. Five months after the last round of vaccination two-thirds of cattle would have low antibody titres (<70% protection threshold). Giving a two-dose primary vaccination course reduces the proportion of 6–12 month old cattle with low titres by 20–30%. Biannual mass vaccination of cattle leaves significant immunity gaps and over-reliance on vaccine protection should be avoided. Using more effective vaccines and vaccination strategies will increase population immunity, however, the extent to which FMD can be controlled by vaccination alone without effective biosecurity remains uncertain.

Growth hormone (GH), prolactin (PRL), and diacylglycerol acyltransferase (DGAT1) gene polymorphisms in Turkish native cattle breeds

Abstract: The aim of this study was to determine the genetic diversity of 4 native Turkish cattle breeds, based on the growth hormone (GH), prolactin (PRL), and diacylglycerol acyltransferase (DGAT1) genes. In order to study the polymorphisms in these genes, the polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) method was performed. A 329-bp fragment and a 223-bp fragment of GH, a 156-bp fragment of PRL, and a 411-bp fragment of DGAT1, thus 4 loci of 3 genes, were amplified via PCR. These fragments were then restricted with the enzymes MspI, Alu1, RsaI, and CfrI, respectively. In this study, 2 types of alleles, ( + ) and ( - ) for the GH-MspI, L and V for the GH-Alu1, A and B for the PRL, and K and A for the DGAT1 loci, were observed. The results of the present study will contribute to the polymorphism data on the world's cattle breeds. Furthermore, the above-mentioned allele frequencies of Turkish native breeds are evaluated in relation to their genetic relatedness, and to infer their milk production properties on the basis of the available literature. In turn, these results can be utilized for future breeding programs of dairy cattle in Turkey.