Samet Çinkaya
Assistant Professor
Afyonkarahisar,03
Summary
I am a veterinarian with a Ph.D. in Animal Science and have research experience in animal breeding, quantitative genetics, and bioinformatics. Involved in projects related to genetic and genomic evaluation, GWAS, and gene expression analysis in cattle, sheep, and buffalo. Experienced in statistical data analysis, molecular techniques, and applied programming for genetic studies. Currently working as an Assistant Professor at the Department of Animal Science, Faculty of Veterinary Medicine, Afyon Kocatepe University, contributing to teaching and research activities. My strongest professional passion is to uncover the genetic basis behind production, reproduction, disease and any other physiological traits in animals. Open to learning new methods and collaborating on studies aiming to improve animal production and welfare.
Overview
10
10
years of professional experience
Work History
Assist. Prof., Dep. of Anim. Sci., Fac. of Vet. Med.
University of Afyon Kocatepe
03.2024 - Current
- Currently leading a competitive national project as a principal investigator funded by Scientific and Technological Research Council of Türkiye (TÜBİTAK) titled "Identifying Candidate Genes for Growth-Development Related Hormone Levels in Prepubertal Anatolian Buffaloes".
- Conducted a GWAS in yearling Anatolian buffaloes to identify novel candidate genes for body measurements and ultrasound carcass traits, followed by functional enrichment analysis; manuscript is published in a peer-reviewed journal (BMC Veterinary Research).
- Performed the quantitative genetic analysis estimating for variance parameters of growth traits considering animal and maternal effects with the covariances of them in native Dağlıç sheep in Türkiye and drafted the manuscript (Publication 7).
- Presented an abstract revealing the MAPKAP1 gene is associated with days open of Holstein heifers in Türkiye with moderate genomic heritability in the Animal Reproduction Congress (TIAR 2024).
- Performed metagenomic analysis for taxonomic classification and DEGs analyses using non-rRNA-seq data.
- Involved in sheep welfare assessment research using the AWIN protocol for semi-extensive commercial farms located in Afyonkarahisar, Türkiye.
- Identified breed-specific SNPs discriminating the Bulgarian pacing horse genotype from the Turkish native pacing horse population based on per-SNP Fst values; work unpublished.
- Developed an Excel program for parentage analysis using a mismatched genotypes algorithm.
- Currently teaching undergraduate and graduate courses in cattle husbandry and animal breeding and genetics.
Veterinarian Researcher, Dep. of Anim. Sci., Fac. of Vet. Med.
University of Afyon Kocatepe
07.2017 - 03.2024
- I have played significant roles in several projects during my PhD by collecting data, performing molecular and statistical analysis, and drafting manuscripts.
- Participated to introgression of the myostatin mutation conferring a double-muscling phenotype from Texel into native Turkish breeds, resulting in more heavily muscled lambs.
- Included in enhancing survivability and resilience of imported Texel sheep by transferring MHC alleles for native breeds (unpublished).
- Investigated growth hormone receptor gene variations in Anatolian Water Buffalo and their associations with growth and milk yield.
- Acted a crucial role in a GWAS to identify candidate genomic regions for growth and milk production traits in Anatolian Water Buffalo and developed a custom mixed real-time PCR kit for selection (unpublished).
- Participating community-based sheep and buffalo improvement programs and I estimates EBVs annually for ~50,000 sheep and 1,500 buffalo in Afyonkarahisar and also performed GEBVs estimation by creating an index considering production, reproduction, health, herd life and ease of birth traits for Holstein cows on a private farm in Çanakkale province of Türkiye.
- Created Excel VBA macros and add-ins for data handling, including a worksheet program to compute the numerator relationship matrix for EBV estimation.
- Developed an Excel VBA program to impute missing SNPs from microarray data for GWAS.
Vet. Health Technician, Animal Hospital
12.2015 - 07.2017
- I was an experienced veterinary technician working in a hospital for pet and farm animals, including treatment and surgery skills.
Education
Ph.D. - Department of Animal Science
University of Afyon Kocatepe
Afyonkarahisar, Türkiye03-2023
B.S. - Department of Veterinary Medicine
University of Afyon Kocatepe
Afyonkarahisar, Türkiye07-2017
Skills
DNA and RNA extraction from blood, tissue, milk, rumen fluid, hair
cDNA synthesis
Polymerase Chain Reaction (PCR) and RFLP Techniques
Sanger Sequencing
Microarray Technology
MS Office
Minitab and SPSS
WOMBAT
ASREML
GEBV and EBV estimation
Genetic and Phenotypic correlation analysis
Genetic trend analysis
Bash
SQL
VBA
Python
R
BioEdit
Slurm, Apptainer, Snakemake
TRUBA HPC Cluster
Timeline
Assist. Prof., Dep. of Anim. Sci., Fac. of Vet. Med.
University of Afyon Kocatepe
03.2024 - Current
Veterinarian Researcher, Dep. of Anim. Sci., Fac. of Vet. Med.
University of Afyon Kocatepe
07.2017 - 03.2024
Vet. Health Technician, Animal Hospital
12.2015 - 07.2017
B.S. - Department of Veterinary Medicine
University of Afyon Kocatepe
Ph.D. - Department of Animal Science
University of Afyon Kocatepe
PUBLICATIONS
- Çinkaya, S., Tekerli, M., Erdoğan, M., Demirtaş, M., Koçak, S., Çelikeloglu, K., Hacan, Ö., Demirtaş, E., Çinkaya, Z.N., Arzık, Y., Demiray, A., Selçuk, S.E., Akçay, A., Bozkurt, Z., Eser, O., Kaplan, Y. Decoding the DNA of Anatolian Water Buffalo by Genome-Wide Discoveries for Body Size and Ultrasound Carcass Traits. BMC Veterinary Research (accepted)
- Koçak, S., Tekerli, M., Çelikeloglu, K., Bozkurt, Z., Hacan, Ö., Erdoğan, M., Çinkaya, S., Demirtaş, M. (2025). Evaluation of some reproductive traits, growth, and survival in native Dağlıç sheep. Veterinarski arhiv, 95(3), 273-281.
- Koçak, S., Bozkurt, Z., Hacan, Ö., Çelikeloglu, K., Tekerli, M., Demirtaş, M., Çinkaya, S. (2025). On-farm welfare assessment of semi-extensively managed sheep using Animal Welfare Indicators (AWIN) protocol. Archives Animal Breeding, 68(3), 459-472. https://doi.org/10.5194/aab-68-459-2025
- Hacan, Ö., Tekerli, M., Çinkaya, S., Demirtaş, M. (2024). Genetic trends in body measurements at birth for Arabian Horse in Türkiye. Archives Animal Breeding, 67(4), 561-570. https://doi.org/10.5194/aab-67-561-2024
- Erdoğan, M., Çinkaya, S., Brenig, B., Çelikeloglu, K., Demirtaş, M., Saribrahimoglu, S., & Tekerli, M. (2024). Genome-wide Association Studies for Milk Production Traits and Persistency of First Calving Holstein Cattle in Türkiye. Frontiers in Veterinary Science, 11, 1461075. https://doi.org/10.3389/fvets.2024.1461075
- Koçak, S., Tekerli, M., Erdoğan, M., Çelikeloglu, K., Yazıcı, E., Bozkurt, Z., Hacan, Ö., Demirtaş, M., and Çinkaya, S. (2024). Myostatin mutation (g+ 6723G> A) introgression: comparative analysis of growth, slaughter, and carcass traits in Texel, Pırlak, and their crosses (F 1 and BC 1). Archives Animal Breeding, 67(2), 207-216. https://doi.org/10.5194/aab-67-207-2024
- Koçak, S., Çinkaya, S., Tekerli, M., Demirtaş, M., Bozkurt, Z., Çelikeloglu, K., Hacan, Ö., Erdoğan, M. (2023). Estimation of (Co) variance components and genetic parameters for pre-and post-weaning growth traits in Dağlıç sheep. Animals, 14(1), 108. https://doi.org/10.3390/ani14010108
- Çinkaya, S. and Tekerli, M. (2023) Inheritance of body size and ultrasound carcass traits in yearling Anatolian buffalo calves. Archives Animal Breeding, 66, 325–333, https://doi.org/10.5194/aab-66-325-2023
- Çelikeloglu, K., Tekerli, M., Erdoğan, M., Koçak, S., Yazıcı, E., Güçlüyener Hacan, Ö., Bozkurt, Z., Çinkaya, S., Demirtaş, M. (2022). Marker-assisted introgression of myostatin from Texel to Ramlıç sheep: Growth and real-time ultrasound carcass traits in F1 and BC1 lambs. Ankara
- Niversitesi Veteriner Fakültesi Dergisi, 69(1), 25-31. https://doi.org/10.33988/auvfd.795247
- Tekerli, M., Erdoğan, M., Koçak, S., Çelikeloglu, K., Yazıcı, E., Hacan, Ö., Bozkurt, Z., Demirtaş, M., and Çinkaya, S. (2022). The comparative results of myostatin introgression from donor Texel to recipient Ramlıç sheep with the aspects of growth, pre-, and post-slaughter carcass traits in the second backcross generation, Archives Animal Breeding, 65, 231–238, https://doi.org/10.5194/aab-65-231-2022
- Erdoğan, M., Tekerli, M., Çelikeloglu, K., Hacan, Ö., Koçak, S., Bozkurt, Z., Çinkaya, S., Demirtaş, M. (2021). Associations of SNPs in GHR gene with growth and milk yield of Anatolian buffaloes. Turkish Journal of Veterinary & Animal Sciences, 45(6), 1080-1086. https://doi.org/10.3906/vet-2103-40
- Çinkaya, S., Tekerli, M., Demirtaş, M., Çelikeloglu, K. (2019). EasyNRM: A Visual Basic Application Approach for Computing Numerator Relationship Matrix of Pedigreed Animals. KSU Journal of Agriculture and Nature, 22, 418-423. https://doi.org/10.18016/ksutarimdoga.vi.571575
- Çinkaya, S., Tekerli, M., Demirtaş, M., Çelikeloglu, K., Erdoğan, M., Saribrahimoglu, S. MAPKAP1 Gene Identified by a GWAS is Associated with Days Open in Holstein Heifers (Oral Abstract Presentation). In Turkish & Italian Joint International Congress of Animal Reproduction, Antalya, Türkiye, 10-13 October 2024, Frontiers in Veterinary Science.
- Erdoğan, M., Tekerli, M., Çelikeloglu, K., Hacan, Ö., Koçak, S., Bozkurt, Z., Çinkaya, S., Demirtaş, M. Influence of Environment and Some Single Nucleotide Polymorphisms in Growth Hormone Receptor Gene on The Weight of Anatolian Buffalo Calves at 12 Months of Age (Oral Abstract Presentation). In Proceedings of the 12th World Buffalo Congress, İstanbul, Türkiye, 18-20 September 2019, Namık Kemal University, Faculty of Agriculture, Tekirdağ, Türkiye 2019.
- Kaplan, Y., Çinkaya, S., Demirtaş, M., Tekerli, M. Application with A Practical Selection Method of Buffalo Calves (Poster Presentation). In Proceedings of the 12th World Buffalo Congress, İstanbul, Türkiye, 18-20 September 2019, Namık Kemal University, Faculty of Agriculture, Tekirdağ, Türkiye 2019.