Person: ARDIÇLI, SENA
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ARDIÇLI
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SENA
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Publication Gender determination by PCR assay for the sex-determining region Y(SRY) gene amplification in linnaeus’s two-toed sloth (Choloepus Didactylus)(Bursa Uludağ Üniversitesi, 2023-06-15) Bozkurt, Berkay; Vatansever, Ezgi; ARDIÇLI, SENA; Veteriner Fakültesi; Genetik Ana Bilim Dalı; 0000-0003-2758-5945In Linnaeus’s two-toed sloths (Choloepus didactylus), there is no distinct sexual dimorphism. It is an obstacle for gender determination fromthe external genitalia, especially in newborns or young sloths. Hence, easy, rapid, and reliable genetics-based methods for gender identificationof the sloths are needed to continue captive breeding more successfully. In this study, a PCR-based technique that allows gender determinationof two-toed sloths by using a sex-determining region Y (SRY) gene marker was described. The hair samples from young (suspectgender) and adult sloths (known gender) were used in genetic analysis. Initially, genomic DNA was isolated from hair root samples using Roche high pure PCR template preparation kit. The SRY primers were specifically designed based on the NCBI and Ensembl databases, andthey were verified with the BLAST program concerning the two-toed sloth genome. PCR amplification with the SRY-specific primers wascarried out by a programmable thermal cycler device using FastStart High Fidelity PCR System, Roche dNTPack. The samples were then electrophoresedon 2% agarose gels and were visualized by a gel documentation and analysis system. A specific band in the electrophoresis patternis diagnostic for a male individual with a partial SRY region. Hence, the analysis demonstrated that the samples belonged to a male two-toedsloth. Two-toed sloth species are commonly preferred animals in zoos. Gender determination is inevitable for these animals in captivity tobe raised successfully and healthily. Molecular genetic techniques allow high efficiency in taxonomic evaluations and gender identification inspecies that do not display sexual dimorphism. The PCR assay described here may be helpful for a rapid genetic analysis that can be widelyused in gender determination for two-toed sloths.Publication Genetic variation in the bovine myogenic determination factor 1 (g.782g> A polymorphism) and its influence on carcass traits in Turkish grey steppe cattle(TUBİTAK, 2021-01-01) Ardıçlı, Sena; Çobanoglu, Özden; ARDIÇLI, SENA; ÇOBANOĞLU, ÖZDEN; Veteriner Fakültesi; Genetik Ana Bilim Dalı; 0000-0003-2758-5945; O-3394-2019MyoD1 gene is a member of the myogenic differentiation gene family, which plays a crucial role in growth and development. There is a lack of information about the MyoD1 variants and their phenotypic influences in Turkish Grey Steppe cattle. Therefore the present study aimed to determine the genetic variability of MyoD1 g.782G>A polymorphism and to evaluate its effects on carcass characteristics in Turkish Grey Steppe cattle. Analyses were conducted on a total of 142 Turkish Grey Steppe bulls. The PCR-RFLP technique was used for genotyping of the g.782G>A polymorphism in exon 1 of the MyoD1 gene. The population genetic parameters including compatibility with Hardy-Weinberg equilibrium, heterozygosity, number of effective alleles, the polymorphism information content, and the fixation index were calculated. Statistical analysis was carried out using the least square methods of the general linear model procedure. Results revealed that BB was the preponderant genotype (41.55%) but the AA genotype exhibited a remarkable close frequency (39.44%). Accordingly, allelic frequencies were very close to each other (A:0.49; B:0.51). The chi 2 test revealed that the corresponding MyoD1 locus did not conform to Hardy-Weinberg equilibrium (p < 0.001). Heterozygosity, number of effective alleles, and the polymorphism information content values were 0.4998, 1.9992, and 0.3749, respectively. Moreover, the fixation index value was found to be 0.6195. These results indicated that MyoD1 g.782G>A polymorphism is a mildly informative genetic marker for Turkish Grey Steppe cattle. Statistical analysis indicated that the studied MyoD1 locus was significantly associated with chilling loss, carcass bone content, and carcass length (p < 0.05). The AA genotype was characterized by a higher chilling loss percentage but lower carcass length and bone content compared to BB and heterozygous genotypes. This study may provide valuable information regarding cattle carcass assessment and improvement through marker-assisted selection.Publication The association between the STAT1 g.3141C>T polymorphism and reproductive performance in high-yielding holstein-friesian dairy cows(Sivar-soc Italiana Veterinari Animali Reddito, 2023-04-01) Güçlü, Şevket; Dursun, Serdar; Kocaer, İsmail İlker; GÜMEN, AHMET; Aldevir, Özgür; Gümen, Ahmet; ARDIÇLI, SENA; Ardıçlı, Sena; Veteriner Fakültesi; Kadın Hastalıkları ve Doğum Ana Bilim Dalı; 0000-0002-3607-4365; 0000-0003-2758-5945; O-3394-2019In dairy cattle, selection programs have mainly focused on high milk production which led to significant improvements in yield. However, it has also caused serious problems in bovine fertility. Reproductive performance is increasing in popularity worldwide. Therefore, this study aimed to evaluate the effects of g.3141C>T polymorphism of bovine STAT1 gene on reproductive traits in high-yielding Holstein-Friesian cows. The data of 4800 cows were used and the initial experimental population consisted of 500 purebred cows housed in three free-stall barns. All animals were fed the same diets and had the same management procedures. The phenotypic traits analyzed in this study were total milk yield, 305-day milk yield, days open, the number of inseminations, and culling rates based on repeat-breeding. Body condition scores, lactation season, and lactation rank were also evaluated in statistical models. Initially, all of the cows were ranked by a selection index based on individual milk yield records and health traits. Next, a total of 75 cows were selected and genotyped for the STAT1 marker located in 3'UTR by the PCR-RFLP method. Genotype-phenotype association analysis was carried out by the least-squares method as applied in a general linear model (GLM) procedure with Tukey's test as a post-hoc comparison. The association between the cull rates and the genotypes was evaluated by Pearson's chi-square test. Population genetics parameters including heterozygosity (He), homozygosity (Ho), number of effective alleles (Ne), and the polymorphic information content (PIC) were evaluated and the deviation from Hardy-Weinberg Equilibrium (HWE) was tested. Results revealed that g.3141C>T polymorphism exhibited admissible levels of population parameters (He=0.4801; Ne=1.9231) indicating that this marker is moderately informative for the selected population (PIC=0.3648). There was a deviation from HWE (P<0.001). In GLM, the association between the STAT1 marker and the number of inseminations was found to be statistically significant (P<0.05). The TT animals were characterized by the highest number of inseminations (3.71 +/- 0.73). On the other hand, heterozygous animals were shown to be associated with desirable reproduction performance. This is a critical result because the STAT1 g.3141C>T marker is included in many SNP-panels or SNP-chips for its previously reported effects on milk yield. To the best of our knowledge, this study has shown a novel effect of this STAT1 marker on the number of inseminations per conception. Considering the TT genotype has a frequency of 26.67%, ignoring this association can lead to a significant reproduction performance decrease on a herd basis. Moreover, there was a significant association between the STAT1 and cull rates (P<0.01). There was no association between the STAT1 and any other traits analyzed. This study demonstrates novel effects of the STAT1 gene, and hence, may contribute to the adequate genotypic evaluation of dairy cattle reproduction performance.Publication Beef colour defined based on ph in holstein bull carcasses(Agricultural Research Communication Centre, 2019-11-01) ARDIÇLI, SENA; DİNÇEL, DENİZ; Balci, Faruk; BALCI, ÖMER FARUK; Veteriner Fakültesi; Genetik Ana Bilim Dalı; 0000-0003-2758-5945; 0000-0002-8015-9032; 0000-0003-2382-1330; AAH-6192-2021; O-3394-2019The present study was carried out on 510 Holstein-Fresian bulls and it aimed to evaluate the effects of season, age at slaughter and pH on meat colour characteristics. An additional aim of this analysis was to determine the impact of environmental factors including season and slaughter age on meat pH. A cluster analysis applied to all the colour coordinates divided the samples into six groups according to their ultimate pH. L*, a*, b* and C* values were significantly higher in cattle slaughtered in the winter season. Moreover, a significant effect of age at slaughter on colour coordinates was found with the exception of a* value. Meat from bulls slaughtered at 16/17 months of age was characterized by brighter colour. Among the pH groups, the highest value of L* was found in meat with pH<5.40, whereas, the highest a* and C* in pH 5.415.50. The present results may be useful and indicative for both beef industry and future studies on meat colour.Publication Analysis of FecB, BMP15 and CAMP gene mutations in sakiz sheep(Kafkas Üniversitesi Veteriner Fakültesi Dergisi, 2015-07-01) Dincel, Deniz; Ardıçlı, Sena; Soyudal, Bahadir; Er, Mehlika; Alpay, Fazlı; Şamlı, Hale; Balcı, Faruk; DİNÇEL, DENİZ; ARDIÇLI, SENA; Soyudal, Bahadir; Er, Mehlika; ALPAY, FAZLI; ŞAMLI, HALE; BALCI, ÖMER FARUK; Veteriner Fakültesi; 0000-0002-8015-9032; 0000-0003-2758-5945; 0000-0003-2382-1330; O-3394-2019; AAE-4562-2019; AAH-6488-2021; AAH-6192-2021; FXS-6181-2022; CNK-1840-2022; I-5009-2019Fertility traits, such as the ovulation rate and the number of offspring at birth, are genetically regulated by fecundity genes. This study was performed to identify DNA polymorphisms in Booroola (FecB), Galway (FecX(G)), Inverdale (FecX(I)) and Calpastatin (CAST) genes in Sakiz sheep. A total of 71 ewes were genotyped for gene or allelic polymorphisms in the genes listed above using the PCR-RFLP method. The results obtained from this study indicated that all of the Sakiz ewes sampled were non-carriers for FecB, FecX(G) or FecX(I) mutations. However, genotypic frequencies in the CAST gene were 0.59, 0.36 and 0.05 for AA, AB and BB, respectively. A significant deviation from Hardy-Weinberg equilibrium for the CAST gene was not observed in the investigated breed (P>0.05). As a result, more extensive screening is required as tests for newly discovered mutations are developed. Additionally, this study is the first to report a genetic polymorphism in the CAST gene in Sakiz sheep.Publication Evaluation of candidate gene effects and environmental factors on reproductive performance of holstein cows(South African Journal Of Animal Sciences, 2019-01-01) Ardıçlı, Sena; ARDIÇLI, SENA; Şamlı, Hale; ŞAMLI, HALE; Dinçel, Deniz; DİNÇEL, DENİZ; Soyudal, B.; Balcı, F.; BALCI, ÖMER FARUK; Veteriner Fakültesi; 0000-0003-2758-5945; 0000-0002-8015-9032; 0000-0003-2382-1330; O-3394-2019; AAH-6488-2021; AAH-6192-2021This study investigated the impact of nine polymorphisms located in the CSN2, CSN3, CSN1S1, CSN1S2, and parity on reproductive traits. The analysis was conducted on 165 Holstein-Friesian cows. Genotypes were identified using PCR-RFLP. The data of reproductive traits for four lactations were evaluated. Statistical analysis was carried out using least squares of the GLM procedures. Results indicated that CSN2 had significant effects on days before first insemination and first insemination to pregnancy interval. The SNP at the CSN3 was significantly associated with gestation length. A novel effect of OLR1-C223A on age at first calving was observed in the present study. Moreover, DGAT1 and LGB markers were significantly associated with calving interval and days before first insemination, respectively. In addition, significant environmental effects were as follows: calving year with days before first oestrus, days open, and first insemination to pregnancy interval; season with days open, first insemination to pregnancy interval, and calving interval; parity with days before first oestrus and days open. The present results and novel associations may therefore be useful and indicative for future studies on a genetic basis of cattle reproduction traits.Publication Dietary intake of Spirulina platensis alters HSP70 gene expression profiles in the brain of rats in an experimental model of mixed stress(Indian Acad Sciences, 2022-10-26) Seyidoğlu, Nilay; ARDIÇLI, SENA; Ardıçlı, Sena; Gurbanli, Rovshan; Köseli, Eda; Aydin, Cenk; AYDIN, CENK; Veteriner Fakültesi; ; 0000-0003-2758-5945; 0000-0002-4812-4024; 0000-0002-3090-0099; KIC-9651-2024; O-3394-2019; JTT-0803-2023; AAS-2344-2020; GRJ-2026-2022Spirulina platensis has gradually gained more attention for its therapeutic, antioxidant, and anti-inflammatory potential worldwide. However, the current molecular knowledge about the effects of spirulina on stress-related genes is rather limited. The effects of dietary intake of spirulina on the HSP70 gene expression were assessed in a controlled in vivo experimental design. Moreover, alterations in serum corticosterone levels, IL-2, IL-4, IFN-gamma, triglyceride, ALT, AST, relative gene expression values, and the correlations between them were evaluated. A total of 36 rats were divided into four groups: control group, stress-only group, spirulina group, and spirulina+stress group. To control the dose administration, S. platensis was applied by a gastric gavage in stress groups. Crowded environment stress and hosting alone stress were applied to the stress-only group and spirulina + stress group. RNA was extracted from brain samples using TRlpure and the relative gene expression assessment was performed using Roche-LightCycler-480-II real-time PCR-System. Gene expression values were remarkably different among the four experimental groups. The differences between stress-only and the spirulina groups were statistically significant (P<0.05). The correlation between the HSP70 gene expression and the IFN-gamma was found to be statistically significant (P<0.05; r=0.50). Results indicate a novel effect of spirulina on the HSP70 expression related to the stress-response. Data presented in this study may be useful for further studies to define not only the molecular genetic aspects through dietary S. platensis but also the effects of spirulina on stress-response and animal welfare.Publication Association of the caprine calpastatin Msp polymorphism with growth and reproduction traits in Saanen goats(Hellenic Veterinary Medical Soc, 2021-07-01) Ardıçlı, Sena; Üstüner, Hakan; Arslan, Oğuzhan; ARDIÇLI, SENA; ÜSTÜNER, HAKAN; ARSLAN, OĞUZHAN; Veteriner Fakültesi; Genetik Ana Bilim Dalı; 0000-0003-2758-5945; 0000-0002-1439-8502; O-3394-2019; GRY-9670-2022; JHO-8192-2023This study was designed to evaluate the effects of calpastatin (CAST) Mspl polymorphism on some growth and reproduction traits, including birth weight, first breeding weight, litter size, and average daily weight gain in Saanen goats. In this sense, blood samples obtained from 73 purebred female Saanen goats were used for genotyping. Genomic DNA was isolated by the phenol-chloroform method and used to determine CAST genotypes, including MM, MN, and NN, by means of the PCR-RFLP method. The population genetic parameters were estimated based on allelic distribution and the data were statistically analysed using analysis of variance (ANOVA) using a general linear model (GLM). Results revealed that N allele frequency was remarkably high (0.64) and the MM genotype was not present. The frequency of the heterozygous genotype was 59.62%. Concerning ANOVA results, significant differences were found between genotypes of the CAST locus concerning birth weight (P<0.05). In this respect, animals with the NN genotype were associated with higher birth weight means (2.85 +/- 0.29 kg) compared to heterozygous animals (2.53 +/- 0.24 kg). There was no significant association between the CAST marker and any of the remaining phenotypic traits evaluated. The present results suggest that focusing on this genomic region may be particularly useful in improving birth weight in goats which can be considered as an early indicator of post-weaning animal growth and survival.Publication Analysis of bovine beta-casein a1 and a2 allele frequency in holstein-friesian cows by real-time pcr with fluorescent hybridization probes(Univ Zagreb Vet Faculty, 2023-01-01) Ardıçlı, Sena; ARDIÇLI, SENA; Balcı, Faruk; BALCI, ÖMER FARUK; Şamlı, Hale; ŞAMLI, HALE; Veteriner Fakültesi; Genetik Ana Bilim Dalı; 0000-0003-2758-5945; 0000-0003-2382-1330; O-3394-2019A2 milk popularity is increasing across the world and novel molecular techniques have been evaluated to develop reliable methods. This study aimed to genotype Holstein-Friesian cows concerning their A1/A2 status using Real-time PCR assay with the specifically designed FRET hybridization probes. In this context, DNA samples were obtained from 310 Holstein-Friesian milk samples. Concerning the Real-time PCR assay, the melting temperature of each amplicon was analyzed and the melting data was converted to a derivative plot using the LightCycler 480 System. The sensor probe was designed to match the wild-type sequence in the target DNA. In the Real-time PCR assay, the melting peaks obtained in the Real-time PCR assay were highly decisive and consistent for each genotype regarding CCT?CAT alteration. The results indicated a remarkably high frequency of the A2 allele (68%) and a considerable frequency of heterozygous animals (0.41). Population genetic analysis showed intermediate levels of genetic variability and biodiversity. The A2-herd conversion process is a complex process consisting of genetic testing of both cows and calves, evaluating replacement rates, and the conversion of heterozygotes by using A2-genotyped bull semen. In this sense, the key point is a reliable and rapid genotyping method to produce A1-free milk. This study suggests that Real-time PCR assay with the specifically designed FRET hybridization probes is a preferable method for A2 genotyping, and may be useful for further studies and instructive for companies or breeders who aim to produce A2 milk.Publication Genetic variation at the olr1, anxa9, myf5, ltf, igf1, lgb, csn3, pit1, mbl1, cacna2d1, and abcg2 loci in Turkish Grey Steppe, Anatolian Black, and East Anatolian Red Cattle(Tubitak Scientific & Technological Research Council Turkey, 2022-01-01) ÇOBANOĞLU, ÖZDEN; ARDIÇLI, SENA; Veteriner Fakültesi; Genetik Ana Bilim Dalı; 0000-0003-2758-5945; O-3394-2019Native breeds are excellent sources of genetic variation. Anatolian native breeds are relatives of the first cattle domesticated and are ancestors of many European breeds. Therefore, this study aimed to evaluate the genetic variation of OLR1, ANXA9, MYF5, LTF, IGF1, LGB, CSN3, PIT1, MBL1, CACNA2D1, and ABCG2 markers in Turkish Grey Steppe, Anatolian Black, and East Anatolian Red cattle. The analysis included 367 cattle and the genotyping was performed by the PCR-RFLP. Population genetics indices including heterozygosity, the number of effective alleles, the polymorphism information content, fixation index, and the level of possible variability realization, and moreover, the genetic diversity parameters including Shannon???Weaver diversity index and Simpson dominance index were estimated. Hardy???Weinberg equilibrium was evaluated based on the number of individuals per genotype. Native breeds exhibited admissible population genetics and diversity levels. There was no animal with the MYF5-AA, IGF1-CC, LGB-BB, CSN3-BB, CACNA2D1- GG, and ABCG2-AC genotypes in the Anatolian Black breed. The frequencies of the genotypes/alleles favorable for milk production traits were remarkably low in all breeds. These findings could provide useful information on the genetic variation of Anatolian native cattle and the genetic investigations of resistance and health traits in bovine breeding and genetics.