Search

Indigenous breeds have a high level of genetic diversity that might contribute to develop animal breeds with desired traits such as disease resistance and high productivity. Major histocompatibilit...

Scrapie is a transmissible spongiform encephalopathy caused by prions and leads to neurodegeneration in the Central Nervous System (CNS) of sheep and goats. Genetic resistance/susceptibility to scrapie is well studied and it is known that the variations of 136th, 154th and 171st codons at the ovine PRNP gene have a major effect on the development of the disease. Many studies demonstrated that selection for PRNP genotypes has not influenced other performance traits, nevertheless, there is a knowledge gap about the possible link between the PRNP gene and the status of the other important diseases that affect the sheep population worldwide. in the present study, we tested whether there is an association between scrapie-related PRNP genotypes and fecal egg count (FEC) of gastrointestinal nematodes in seven adult Turkish sheep breeds. For this purpose, FEC scores of studied sheep (n = 253) were determined and the same animals were genotyped for the PRNP gene. Finally, an association analysis was performed for scrapie resistant (ARR), susceptible (VRQ), and wild-type (ARQ) haplotypes. Based on our statistical analysis, it is concluded that PRNP genotypes have no positive or negative effect on the FEC scores of adult sheep., Republic of Turkey Ministry of Agriculture and Forestry, General Directorate of Agricultural Research and Policies [TAGEM/HAYSUD/15/A01/P02/02-02], This research has been funded by the Republic of Turkey Ministry of Agriculture and Forestry, General Directorate of Agricultural Research and Policies (Project number: TAGEM/HAYSUD/15/A01/P02/02-02).

Visna/maedi (VM) is a multisystemic disease of sheep characterized by persistent lentiviral infection, slow progression and eventually death. The VM virus (VMV) affects sheep throughout the world and is the focus of national eradication campaigns. A major host gene associated with infection has been identified in North American sheep (TMEM154); however, its effect is unknown in Turkish sheep. Our aim was to determine VMV seroprevalence in naturally infected Turkish sheep, characterize their TMEM154 alleles, and test for association with infection. A 2017 serological census was taken of 2266 ewes from 11 flocks, at six locations, comprising seven native and four composite Turkish breeds. VMV serum antibodies were measured with an enzyme linked immunosorbent assay. Eight of 11 flocks were infected with VMV (2 to 83% seroprevalence). TMEM154 variants were typed by sequencing exon 2 from all 287 seropositive ewes and a subset of their seronegative flockmates (1059 total). TMEM154 sequencing revealed five of 12 known haplotypes encoding missense mutations, and one previously unreported variant (G38R) in Kivircik sheep. VMV seroprevalence in ewes with highly-susceptible TMEM154 haplotypes (full length E35 variants) was higher than the overall flock seroprevalence and independent of breed type. Genetic association was tested in 76 matched case-control pairs from 751 comingled ewes from a research flock. Pairwise analyses showed the risk of infection was 3-fold greater for ewes with one or two copies of highly-susceptible TMEM154 haplotypes compared to those with combinations of K35 and deletion variants (CI95 1.3–8.7, p-value 0.009). Allelic combinations of TMEM154 K35 and deletion variants had an apparent protective effect against VMV strains in Turkish sheep. The low frequencies of K35 and deletion alleles in native Turkish breeds suggests selective breeding may help reduce the seroprevalence in affected flocks and decrease the risk of outbreaks in VMV-free flocks.

Visna/maedi (VM) is a multisystemic lentivirus infection of sheep that affecting sheep industry across the globe. TMEM154 gene has been identified to be a major VM-associated host gene, nevertheless, a recent study showed that the frequency of the VM-resistant TMEM154 haplotypes was very low or absent in indigenous sheep. Thus, the present study was designed to determine other possible co-receptors associated with VM. For this purpose, DRB1 gene, which is renowned for its role in host immune response against various diseases was targeted. A total number of 151 case-control matched pairs were constructed from 2266 serologically tested sheep. A broad range of DRB1 haplotype diversity was detected by sequence-based genotyping. Moreover, a novel 2 bp deletion (del) in the DRB1 intron 1 was identified. For the final statistic, the sheep carrying VM-resistant TMEM154 diplotypes were removed and a McNemar's test with a matched pairs experimental design was conducted. Consequently, it was identified for the first time that the 2 bp del variant is a genetic risk factor for VM (p value 0.002; chi-square 8.31; odds ratio 2.9; statistical power 0.90) in the dominant model. Thus, negative selection for 2 bp del variant could decrease VM infection risk in Turkish sheep., Republic of Turkey Ministry of Agriculture and Forestry, General Directorate of Agricultural Research and Policies (TAGEM) [TAGEM/HAYSUD/15/A01/P02/02-02], Funding for this research was provided by the Republic of Turkey Ministry of Agriculture and Forestry, General Directorate of Agricultural Research and Policies (TAGEM) (Project No. TAGEM/HAYSUD/15/A01/P02/02-02).

Simple Summary Mastitis causes economic loss due to discarded milk and reduced milk production and quality, increased medical care costs and somatic cell count (SCC) penalties. The use of genetic markers associated with the variability of this trait through marker-assisted selection (MAS) could help traditional methods. Our objectives were to identify new single nucleotide polymorphisms (SNPs) and genes associated with mastitis resistance in Assaf sheep by using the Illumina Ovine Infinium® HD SNP BeadChip (680K). Firstly, corrected phenotype estimates for somatic cell score (SCS) were calculated using 6173 records from 1894 multiparous Assaf ewes, and were used to select 192 extreme animals (low SCS group: n = 96; and high SCS group: n = 96) for the genome-wide association study (GWAS). Four SNPs (rs419096188, rs415580501, rs410336647, and rs424642424), three of them totally linked, were found to be significant at the chromosome level (FDR 10%) in two different regions of OAR19 close to genes related to the immune system response. Validation studies of two SNPs (rs419096188 and rs424642424) by Kompetitive Allele-Specific PCR (KASP) genotyping in the total population (n = 1894) confirmed previous GWAS association results for the SCS trait. Finally, the SNP rs419096188 was also associated with lactose content trait. Abstract A genome-wide association study (GWAS) was performed to identify new single nucleotide polymorphisms (SNPs) and genes associated with mastitis resistance in Assaf sheep by using the Illumina Ovine Infinium® HD SNP BeadChip (680K). In total, 6173 records from 1894 multiparous Assaf ewes with at least three test day records and aged between 2 and 7 years old were used to estimate a corrected phenotype for somatic cell score (SCS). Then, 192 ewes were selected from the top (n = 96) and bottom (n = 96) tails of the corrected SCS phenotype distribution to be used in a GWAS. Although no significant SNPs were found at the genome level, four SNPs (rs419096188, rs415580501, rs410336647, and rs424642424) were significant at the chromosome level (FDR 10%) in two different regions of OAR19. The SNP rs419096188 was located in intron 1 of the NUP210 and close to the HDAC11 genes (61 kb apart), while the other three SNPs were totally linked and located 171 kb apart from the ARPP21 gene. These three genes were related to the immune system response. These results were validated in two SNPs (rs419096188 and rs424642424) in the total population (n = 1894) by Kompetitive Allele-Specific PCR (KASP) genotyping. Furthermore, rs419096188 was also associated with lactose content.

Scrapie is a transmissible spongiform encephalopathy caused by prions and leads to neurodegeneration in the Central Nervous System (CNS) of sheep and goats. Genetic resistance/susceptibility to scrapie is well studied and it is known that the variations of 136th, 154th and 171st codons at the ovine

In this study, it was aimed to carry out the design, electromagnetic analysis and noise-vibration analysis of a 3 phase, high efficient surface-mounted permanent magnet motor with a power level of 7.5kW and 1500rpm speed. Using basic analytical formulas initial design geometry of motor was obtained. This first design geometry was investigated in detail by electromagnetic analyzes. In these electromagnetic analyzes, cogging torque, torque ripple, losses and efficiency parameters have been investigated. Then, modal and harmonic analyzes were carried out in order to interpret the effect of radial harmonic forces, obtained from electromagnetic analyzes, on the stator teeth on the noise and vibration parameters of the motor. According to analysis result of initial designed motor, it was aimed to reduce cogging torque, torque ripple, efficiency, noise and vibration parameters. It is thought that the improvement studies to be perform in the cogging torque will also have a positive effect on the torque ripple and vibration on the motor. By optimizing studies performed magnet and lamination geometry, new motor geometry has been obtained. Electromagnetic, modal, harmonic analyzes were made this new motor geometry. Analysis results of the new design and the first design were studied comparatively.

Growth Hormone (GH) and Insulin like Growth Factor-I (IGF1) are members of somototrophine axis pathway. They play a role in key on several mechanisms such as postnatal growth, cell differentiation and metabolism. Due to their vital importance, polymorphisms on the genes coding are worth to be understood. In this study five native cattle breeds (Native Southern Yellow (NSY), South Anatolian Red (SAR), Anatolian Grey (AG), Native Black (NB), East Anatolian Red (EAR) were investigated by PCR-RFLP method for GH-MspI and IGF1-SnaBI loci. 198 and 194 samples were analyzed for GH-MspI and IGF1-SnaBI loci, respectively. In both two loci two alleles and three genotypes were observed. Predominant alleles were A and B for GH-MspI locus IGF1-SnaBI loci, respectively. Frequencies of A and B alleles were calculated between 0.400-0.875 and 0.846-0.903 for GH-MspI locus IGF1-SnaBI loci, respectively. While among investigated population only EAR population was at Hardy-Weinberg equilibrium for IGF1-SnaBI locus, for GH-MspI only, in SAR population no deviation from Hardy-Weinberg equilibrium.

Turkey’s biological diversity is considerable because of its biogeographical positions, therefore it is plentiful in terms of diversity in animal genetic resources. Genetic diversity is important in sustainable breeding and conservation programs in livestock. The aim of this study was to determine the genetic structure of Yalova genotype, Kivircik, Tahirova and Esme sheep breed by using twenty microsatellite markers. A total of 223 Turkish native unrelated sheep (Yalova, Kivircik, Tahirova and Esme) which were raised in sixteen flocks located in four different provinces (Kirklareli, Canakkale, Yalova ve Usak) were investigated. A total of 543 alleles were found. The number of loci showed deviations from Hardy-Weinberg equilibrium ranged from 11 (Kivircik) to 17 (Yalova). Although a total of 183 private alleles were detected, only 21 of them had allele frequency above 0.05. The number of observed alleles differed from 42 (for OarFCB20 and ILSTS5) to 20 (for OarCP34 and DRBP1). The highest Ne and PIC values (19.23 and 0.95, respectively) were also observed for ILSTS5 locus. While expected heterozygosity (He) ranged between 0.83−0.95, observed heterozygosity differed from 0.69−0.95. These results can be used for the initiation of registration studies for Yalova after combining phenotypic data evaluations.

Cattle are an important livestock species for human life, but certain breeds are at risk of extinction. Maintaining genetic diversity plays an important role in sustainable breeding and conservation programmes in farm animals. The aim of this study was to determine genetic diversity among five Turkish native cattle breeds. A total of 199 Turkish native cattle of the Native Southern Yellow (n = 40), South Anatolian Red (n = 40), Anatolian Grey Cattle (n = 40), Native Black Cattle (n = 39) and East Anatolian Red (n = 40) breeds were investigated using 22 autosomal microsatellite markers. The analysis revealed considerable genetic variation among these breeds. All loci were polymorphic, and a total of 545 alleles were found. Among these loci, only INRA032 was at Hardy-Weinberg equilibrium. Thirty-four private alleles with frequencies greater than 5% were found. Expected heterozygosity and polymorphic information content indexes were 0.87 and 0.88, respectively. Native Southern Yellow, South Anatolian Red and Native Black Cattle breeds were closely related. Keywords: animal genetic resources, microsatellite, genetic relationship, genetic conservation

Review of Şiddetin Topolojisi by Byung - Chul Han, Şiddetin Topolojisi , yazar Dilek Zaptçıoğlu(Kitap Değerlendirmesi)

Leptin bir obese (leptin; ob/LEP) gen ürünü olup, başta adipoz dokuolmak üzere çeşitli dokulardan salgılanan bir hormondur. Leptinin enerjimetobolizmasının düzenlenmesinde önemli bir rol oynadığı ve ruminantlarda kurumadde tüketimindeki rolü nedeniyle hayvansal üretim bakımından önemlifonksiyonlara sahip olduğu bilinmektedir. Buna rağmen ruminant türlerinde leptinhakkındaki bilgiler oldukça azdır ve bu hormon hakkındaki mevcut bilgilerinçoğu insan ve kemirgenlerden elde edilmiştir. Leptin konsantrasyonu yetersizbesleme koşullarında β-agonist enjekte edilmesi durumunda azalmagöstermektedir. Plazma leptin konsantrasyonu vücut kondüsyonu, pozitif enerji dengesi veya yeterli beslemedüzeyi ile pozitif ilişkilidir. Plazma leptin konsantrasyonu aynı zamanda tür,ırk, gebelik, laktasyon, genotip ve çevresel koşullara bağlıdır. Son yıllardaleptin genindeki polimorfizmlerin de plazma leptin konsantrasyonu üzerindeetkili olduğu düşünülmektedir. Bu çalışmada yetişkin ruminatların adipozdokularında ve meme bezlerindeki leptin gen ekpresyonunda veözellikle plazma leptin konsantrasyonlarında değişikliklere etkieden faktörler değerlendirmektedir.&nbsp

In this study, ten native Turkish sheep breeds were sampled to evaluate Y chromosomal genetic variation. Two regions of the SRY gene, one region each of the DBY and AMEL genes and SRYM18 Y-specific microsatellite locus were sequenced. While no base substitutions were found in the sequenced regions of SRY, DBY and AMELY, most of the Turkish sheep breeds have some variations of SRYM18. In total, we found three different SRYM18 alleles that were 141, 143 and 145 bp in length. The distribution of these alleles was different among fat-tailed sheep breeds and the thin-tailed sheep breeds. While the most common allele was 143 bp among the breeds, the 141-bp allele was also observed in both fat-tailed and thin-tailed breeds. The 145-bp allele was only found in the fat-tailed sheep at low frequency.

Elmaci, C., Oner, Y., Turkyilmaz, O. and Cetin, M. 2006. Genetic polymorphism of some blood proteins in Saanen goats. J. Appl. Anim. Res., 30: 113–116. Genetic variations of 4 protein loci (transferrin, haemoglobin, amylase and ceruloplasmin) in 70 Saanen goats from Balikesir province of Turkey were investigated by means of horizontal starch gel electrophoresis. Two loci, transferrin (Tf) and haemoglobin (Hb) were found to be polymorphic. Other loci amylase (Amy) and ceruloplasmin (Cp) did not show polymorphism. In all polymorphic loci, the observed genotype frequencies were not significantly different from those expected from Hardy-Weinberg equilibrium.

Heat stress proteins are important factors in protecting cells against environmental stress. The HSP70.1 gene is one of the most important members of the heat stress protein family, which is essential for life, production and reproduction. In this study, partial regions of HSP70.1 (3ꞌ and 5ꞌ untranslated regions (UTRs)) were sequenced in six cattle breeds. Blood samples of five native breeds, namely Yerli Kara (YK), Boz irk (BI), Yerli Guney Sarisi (YGS), Guney Dogu Anadolu Kirmizisi (GAK) and Dogu Anadolu Kirmizisi (DAK) were collected from their native regions and blood samples of the Holstein Friesian (Siyah Alaca (SA)) breed were collected from each of these regions. Totals of 249 and 206 animals were analysed for the HSP70.1 - 3ꞌ and 5ꞌ UTR regions, respectively. In the 3ꞌ UTR region, 13 single nucleotide polymorphisms (SNPs) and one indel were found, whereas this region was found to be monomorphic among animals of the Holstein Friesian breed. In the 5ꞌ UTR region, 43 SNPs and three indels were revealed in all of the investigated breeds. On the other hand, a new C983T nucleotide substitution was identified in this region, and is thought to disrupt the Sp1-hsp70 promoter binding site. The 5ꞌ UTR region was also more variable in the Turkish native breeds than in the Holstein Friesian. This study is the first to investigate the 3ꞌ and 5ꞌ UTRs of the HSP70.1 gene in Turkish native breeds. The genetic structure of these gene regions in Turkish native cattle breeds was found to be quite different from those of other cattle breeds that had been studied in the past. Keywords: Bovine, heat shock genes, heat stress, polymorphism

In this study, animals from the Kivircik breed of sheep and two closely related breeds (Pirlak and Karacabey Merino) were analysed by using 15 microsatellite markers to evaluate the genetic diversity within the Kivircik breed and to elucidate its relationship with the other two breeds. A total of 244 alleles were detected on all of the 15 microsatellite loci studied. While the Kivircik population of sheep showed a significant deviation from the Hardy- Weinberg equilibrium (HWE) for all 15 loci, both the Pirlak and Karacabey Merino breeds showed a significant deviation from the HWE for 10 loci. The mean observed heterozygosity and FIS exhibited ranges of 0.63 to 0.72 and 0.0672 to 0.2139, respectively. The highest mean number of alleles value and the greatest number of private alleles were observed in the Kivircik population. While microsatellite analysis revealed high genetic diversity in breeds investigated, a high level of inbreeding was also observed between different Kivircik populations and other two breeds. The genetic differentiation between breeds was found to be low. The Kivircik from Istanbul and Bursa were the most closely related genetically, while the Kivircik from Manisa differed from the other populations. In addition, the Karacabey Merino and Pirlak breeds grouped together.

In this study, several polymorphisms in the gene encoding the inducible form of the cytoplasmic Hsp90 (HSP90AA1) were characterized in 10 sheep breeds reared in different climatic regions of Turkey. A new indel (AA) polymorphism located at the -704 position in the HSP90AA1 5' flanking region was found in all investigated breeds. This polymorphism create/remove a GR transcription site that could affect heat stress response and is completely linked with the C/G transversion located at -660 in the same region of the gene. Genotype frequencies differed significantly between breeds. No clearcut relationship was found between this polymorphism and climate factors, but breeds from northern Turkey had higher frequencies of the indel AA allele than breeds from southern Turkey. © 2012 Elsevier B.V.

A total of 135 unrelated sheep from nine Turkish native sheep breeds (DaglA +/- c, Kivircik, Imroz, Chios, Morkaraman, Ivesi, Hemsin, Karayaka and Akkaraman) were investigated to determinate the maternal genetic diversity using a sequence of a 531-bp segment of the mtDNA control region. Analysis of the mtDNA control region sequence revealed 63 haplotypes and 53 polymorphic sites. Haplotype diversity, nucleotide diversity and the average number of nucleotide differences were estimated to be 0.9496 +/- 0.011, 0.01407 +/- 0.00060 and 7.456, respectively. The sequence analysis also revealed high level of genetic diversity among the native Turkish breeds. These breeds were grouped into three major maternal haplogroups: A, B and C, with one animal belonging from the Akkaraman breed to the rare haplogroup E. Irregular shape of mismatch distribution of haplogroup C could be an indicator that haplogroup C may represent different haplogroups. Contrarily to previous studies carried out on Turkish native breeds, majority of animals grouped in haplogroup A in the present study. This result and the irregular shape of mismatch curve of haplogroup C indicate that genetic structure of Turkish native sheep breeds could be more complicated than it is thought.

Scrapie, a transmissible spongiform encephalopathy (TSE) or prion disease, is a fatal, neurodegenerative disease in sheep and goats. This disease has been known in Europe for more than 250 years. Susceptibility to scrapie is associated with polymorphisms in the sheep prion protein gene (PrP) gene. In sheep, polymorphism in the PrP gene has been identified at a number of codons, and polymorphisms at codons 136, 154 and 171 have reported linkage with susceptibility to scrapie. Polymorphisms at the PrP locus were studied in 413 animals representing three native sheep breeds (Imroz, Chios and Kıvırcık) in Turkey. Genomic DNA was obtained from blood, and genotypes were screened using PCR and direct DNA sequencing. We report 17 genotypes derived from seven different alleles. The most frequent genotype in the Kıvırcık sheep is ARQ/ARQ, whereas the ARR/ARQ genotype is predominant in the Chios and Imroz breeds. In general, the ARQ haplotype was the predominant haplotype. ARQ haplotype was also predominant in the Kıvırcık and Chios sheep breeds, whereas the Imroz sheep predominantly had the ARR haplotype. The susceptibility-associated VRQ haplotype was found in 2.38%, 0.35% and 0.81% of the Imroz, Kıvırcık and Chios sheep, respectively. Moreover, seven additional polymorphisms have been detected at codons G127S, G127V, H143R, G145S, Y172D, N174Y and Q189L. Among these polymorphisms, the N174Y allele is a novel polymorphism, and the G145S allele is a novel allele for a known polymorphic locus.

Summary In this study polymorphism on β-lg and bGH genes in Holstein and Brown Swiss cattle reared in Bursa region were investigated by using HaeIII and MspI restriction enzymes. While frequencies of A and B allelles of β-lg were found 0.3430 and 0.6570 in Brown Swiss population, they were found as 0.5480 and 0.4520 in Holstein population, respectively. MspI (+) allelle of bGH was predominat in both Brown Swiss and Holstein populations with frequency of 0.9623 and 0.8158, respectively. Both of two populations were found in Hardy- Weinberg equilibrium for both of the two loci investigated.

The genetic diversity and phylogenetic relationships of 108 individual sheep from three Turkish sheep breeds (Kivircik, Gokceada, and Sakiz) were studied using RAPD analysis. Polymorphisms within and between populations were assayed using 15 random primers, and 82 loci were amplified ranging from 250 to 2,500 bp. The percentage of polymorphic loci was found to be 80.49, 78.05, and 73.17%, for Kivircik, Gokceada, and Sakiz sheep breeds, respectively. Total genetic diversity was 0.2265, and the average coefficient of genetic differentiation was 0.1181. Genetically, the Gokceada breed was more closely related to the Sakiz breed than to the Kivircik breed.

The genetic polymorphism of the beta-lactoglobulin gene was investigated in three native Turkish sheep breeds. The study was carried out on 108 sheep (29 Kivircik, 38 Gökçeada, and 41 Sakiz) by means of PCR-RFLP methods. Two genetic variants (A and B) and three genotypes (AA, AB, and BB) of beta-lactoglobulin have been identified. The gene frequencies of beta-LG A and B were 0.7759 and 0.2241 in Kivircik, 0.7632 and 0.2368 in Gökçeada, and 0.9756 and 0.0244 in Sakiz breeds, respectively. The populations were in Hardy-Weinberg equilibrium in all samples from the three breeds.

Milk samples from 203 Holstein cows were phenotyped for genetic variants alpha(s1)-casein, beta-casein, kappa-casein and beta-lactoglobulin using starch-gel electrophoresis. All of the four milk protein loci exhibited polymorphism with allele frequencies of 0.862 +/- 0.017 for alpha(s1)-casein B, 0.966 +/- 0.0009 for beta-casein A, 0.712 +/- 0.0224 for kappa-casein A and 0.567 +/- 0.0245 for beta-lactoglobulin B. The mean heterozygosity estimated over all the four milk protein loci was 0.3015. Genetic equilibrium was observed among all of the loci investigated, except kappa-casein. Chi-squared tests revealed that there was no significant linkage among studied milk protein phenotypes.