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ORIGINAL PAPER
Genome-wide association analysis of milk yield, composition and somatic cell count in Holstein dairy cattle
1
Aksaray University, Faculty of Veterinary Medicine, Department of Animal Science, 68100, Aksaray, Türkiye
2
Erciyes University, Faculty of Agriculture, Department of Animal Science, 38280, Kayseri, Türkiye
3
Erciyes University, Faculty of Veterinary Medicine, Department of Genetics, 38280, Kayseri, Türkiye
4
University of Wisconsin–Madison, Department of Animal and Dairy Sciences, Madison, WI 53706, USA
5
Washington State University, College of Veterinary Medicine, Department of Veterinary Microbiology and Pathology, Pullman, WA 99164, USA
Publication date: 2026-06-25
Corresponding author
J. Metin Kiyici
Erciyes University, Faculty of Agriculture, Department of Animal Science, 38280, Kayseri, Türkiye
Erciyes University, Faculty of Agriculture, Department of Animal Science, 38280, Kayseri, Türkiye
KEYWORDS
TOPICS
ABSTRACT
This study investigated the genetic basis of milk production traits in Holstein dairy cattle using a genome-wide association study approach with high-density single nucleotide polymorphism (SNP) genotyping. A total of 1 431 observations from 147 Holstein cows reared in Türkiye were analysed. The cows were phenotyped for milk somatic cell count (SCC), fat, protein, lactose, solid-not-fat, freezing point, density, electrical conductivity, pH, and milk yield. After quality control, 79 769 SNPs were retained for association analysis. Significant associations were identified, with 3 SNPs exceeding genome-wide significance thresholds and 12 exceeding chromosome-wide thresholds. Key findings included SNPs (rs109536476, rs110213695, rs135761188, rs109679567) associated with SCC were located in or near the CBY3 and CNOT6 genes on BTA7, while variants associated with both fat content and density were located in the RAB27B gene on BTA24, indicating potential pleiotropic effects. The results emphasise the importance of functional validation to clarify the biological roles of the identified SNPs and genes. The findings contribute to understanding the genetic architecture of economically significant milk traits and supports the development of genomic selection strategies to improve dairy production. Future studies with larger populations and diverse environmental conditions are recommended to refine these associations.
ACKNOWLEDGEMENTS
The authors would like to thank Saray Farm Dairy Operations Co. (Kayseri, Türkiye) for their help during the experiments. Special thanks are extended to the farm staff for their invaluable assistance in managing the animals and collecting data. We also express our gratitude to the laboratory personnel of Genome and Stem Cell Center at Erciyes University (GEN-KOK) for providing laboratory facilities. Finally, we are grateful to the reviewers and collaborators for their valuable comments, which improved the quality of this work.
FUNDING
This study was supported by the Scientific Research Projects Department of Erciyes University under Project ID: FBA-2022-11669.
CONFLICT OF INTEREST
The Authors declare that there is no conflict of interest.
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