Person: ÖNER, YASEMİN
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ÖNER
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YASEMİN
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Publication Documentation of extensive genetic diversity in the Ovar-DRB1 gene in native Turkish sheep(Taylor, 2021-02-02) Bay, Veysel; Keles, Murat; Aymaz, Ramazan; Hatipoğlu, Ecem; Öner, Yasemin; Yaman, Yalçın; ÖNER, YASEMİN; Bursa Uludağ Üniversitesi/Ziraat Fakültesi/Biyometri ve Genetik Bölümü; 0000-0002-2904-8986; ABB-3181-2020Indigenous 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 histocompatibility complex (MHC) is a key component of adaptive immune system and consists of highly polymorphic genes that take part in adaptive immune response and disease resistance. Exploring and understanding the effect of polymorphisms in MHC could be beneficial to future animal breeding strategies. In this study, we sequenced the highly polymorphic Exon2 of the ovine DRB1 gene using Sanger sequencing to explore the diversity of this gene in six indigenous Turkish sheep breeds and two crossbreeds. In total, 894 haplotypes from 447 sheep were investigated, and 69 different haplotypes including 27 novel ones were identified. Among the identified haplotypes there were common and breed specific haplotypes. There was a relatively high diversity of the alleles within indigenous breeds. Allelic diversity patterns were mostly associated with geographical differences. The results of this study highlight the genetic variation within indigenous breeds which has important implications for biodiversity and the adaptability of breeds to specific environments. There is value to further studies which include other genomic regions and traits, and these could guide breeding strategies.Publication Genome-wide association studies of somatic cell count in the assaf breed(Mdpi, 2021-06-01) Serrano, Malena; Sarto, Pilar; Iguacel, Laura Pilar; Piquer-Sabanza, Maria; Estrada, Olaia; Juan, Teresa; Calvo, Jorge Hugo; Öner, Yasemin; ÖNER, YASEMİN; Bursa Uludağ Üniversitesi/Ziraat Fakültesi.; 0000-0002-2904-8986; ABB-3181-2020Simple 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 (R) 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. 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.Publication Genetic identification and characterisation of some Turkish sheep(Elsevier, 2021-06-14) Alarslan, Emre; Ata, Nezih; Yılmaz, Onur; Öner, Yasemin; Kaptan, Cüneyt; Savaş, Türker; Yılmaz, Alper; ÖNER, YASEMİN; Bursa Uludağ Üniversitesi/Ziraat Fakültesi/Zootekni Bölümü.; 0000-0002-2904-8986; ABB-3181-2020Turkey'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 Es,me sheep breed by using twenty microsatellite markers. A total of 223 Turkish native unrelated sheep (Yalova, Kivircik, Tahirova and Es,me) which were raised in sixteen flocks located in four different provinces (Kirklareli, canakkale, Yalova ve Us,ak) 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.Publication Detecting fecal egg count (FEC) for gastrointestinal nematodes of adult Turkish sheep with different scrapie related PRNP haplotypes(Taylor & Francis, 2020-12-10) Yaman, Yalçın; Şenlik, Bayram; Özuiçli, Mehmet; Keleş, Murat; Aymaz, Ramazan; Bay, Veysel; Hatipoğlu, Ecem; Koncagül, Seyrani; Öner, Yasemin; Ün, Cemal; ŞENLİK, BAYRAM; ÖZÜİÇLİ, MEHMET; ÖNER, YASEMİN; Bursa Uludağ Üniversitesi/Veteriner Fakültesi/Parazitoloji Anabilim Dalı.; Bursa Uludağ Üniversitesi/Ziraat Fakültesi/Biyometri ve Genetik Bölümü.; GBN-0139-2022 ; JIF-7199-2023 ; ABB-3181-2020Scrapie 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.Publication Genetic diversity and population structure of Turkish native cattle breeds(South African Journal Of Animal Sciences, 2019-01-01) Yilmaz, O.; Ata, N.; Koncagül, S.; Öner, Y.; ÖNER, YASEMİN; Eris, Cüneyt; Ünal, Cihan; ÜNAL, CİHAN; Bursa Uludağ Üniversitesi/Veteriner Fakültesi; Bursa Uludağ Üniversitesi/ZiraatFakültesi; EAB-3526-2022; ABB-3181-2020; CNZ-7411-2022Cattle 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.Publication A novel 2 bp deletion variant in ovine DRB1 gene is associated with increased visna/maedi susceptibility in Turkish sheep(Nature Portfolio, 2021-07-14) Yaman, Yalçın; Bay, Veysel; Aymaz, Ramazan; Keleş, Murat; Öner, Yasemin; Teferedegn, Eden Yıtna; Ün, Cemal; Öner, Yasemin; ÖNER, YASEMİN; Bursa Uludağ Üniversitesi/Ziraat Fakültesi.; JKO-1528-2023Visna/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.