Browsing by Author "Koyun, H."

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Genome-Wide Association Studies for Conformation Traits in the Turkish Holstein Cattle Population
(Shiraz Univ, 2025) Koncagul, S.; Kasakolu, A.; Yildirir, M.; Unay, E.; Koyun, H.; Karakoyunlu, I; Sen, A. O.
Background: Conformation traits (CNTs) are part of the selection goals that significantly affect cow economic efficiency, health, welfare, and productive life in the dairy industry. Aims: This study focused on a genome-wide association study (GWAS) and genetic parameters estimation for 21 CNTs, including udder, leg-foot, body, type, and final classification traits in the Turkish Holstein (THol) dairy cattle population. Methods: A restricted maximum likelihood with a univariate model including the fixed effects of herd-year-season and days in milk was used. The total dataset consisted of CNTs records and Affymetrix BovineSNP54K data for 3,008 THol cows that calved from 2019 to 2022. The gene ontology and Kyoto Encyclopedia of genes and genome pathway databases were used to assign genes to functional categories. The biological pathways were performed in BioMart databases. Results: The heritability of these 21 CNTs ranged from 0.01 (udder index) to 0.133 (udder depth). A total of 16 significant single nucleotide polymorphisms (SNP) associated with 13 CNTs was identified. Significant SNP overlap in the candidate genes, which include ITGB1, TNN, and SEMA3D, have potential for researchers and breeders for CNTs in cattle breeding. Conclusion: These results provide valuable knowledge and contribute to the elucidation of the genetic factors responsible for conformation traits in dairy cattle populations.
Genome-Wide Association Studies for Conformation Traits in the Turkish Holstein Cattle Population
(Shiraz University, 2025) Koncagul, S.; Kasakolu, A.; Yıldırır, M.; Ünay, E.; Koyun, H.; Karakoyunlu, İ.; Yiğit, O.
Background: Conformation traits (CNTs) are part of the selection goals that significantly affect cow economic efficiency, health, welfare, and productive life in the dairy industry. Aims: This study focused on a genome-wide association study (GWAS) and genetic parameters estimation for 21 CNTs, including udder, leg-foot, body, type, and final classification traits in the Turkish Holstein (THol) dairy cattle population. Methods: A restricted maximum likelihood with a univariate model including the fixed effects of herd-year-season and days in milk was used. The total dataset consisted of CNTs records and Affymetrix BovineSNP54K data for 3,008 THol cows that calved from 2019 to 2022. The gene ontology and Kyoto Encyclopedia of genes and genome pathway databases were used to assign genes to functional categories. The biological pathways were performed in BioMart databases. Results: The heritability of these 21 CNTs ranged from 0.01 (udder index) to 0.133 (udder depth). A total of 16 significant single nucleotide polymorphisms (SNP) associated with 13 CNTs was identified. Significant SNP overlap in the candidate genes, which include ITGB1, TNN, and SEMA3D, have potential for researchers and breeders for CNTs in cattle breeding. Conclusion: These results provide valuable knowledge and contribute to the elucidation of the genetic factors responsible for conformation traits in dairy cattle populations. © 2025 Elsevier B.V., All rights reserved.
Genome-Wide Association Study in the Holstein Cattle Population Highlights Candidate Variants for Milk Production Traits
(Elsevier, 2025) Koncagul, S.; Sen, A. o.; Yildirir, M.; Koyun, H.; Unay, E.; Karakoyunlu, I.; Kasakolu, A.
Understanding the genetic basis of production traits in dairy cattle is important for both improving productivity and its economic significance. Although genome-wide association studie has been widely used internationally to investigate the genetic factors of milk production traits, limited genomic data are available for the Holstein cattle population. In this study, the most comprehensive genomic analysis conducted in T & uuml;rkiye to date, we aimed to identify single-nucleotide polymorphisms (SNPs) associated with milk yield (MY), fat yield (FY), protein yield (PY), and milking speed (MS) in the Holstein cattle population. Data were obtained from 79 dairy herds comprising 17 166 cows born between 2012 and 2019, as provided by the Cattle Breeders' Association of T & uuml;rkiye. Genotyping was performed using the Affymetrix Axiom Bovine 54K SNP Chip; after quality control procedures, 15 288 cows and 31 944 SNPs were included in the analysis. A total of 7 SNPs were identified as significantly associated with the studied traits. Two SNPs on BTA14 (rs109146371 and rs109350371) were significantly associated with 305MY. A significant SNP associated with PY (rs41718954) was identified on BTA14, and another SNP (rs10451141) on BTA18 showed a significant association with FY. Additionally, three SNPs significantly associated with MS were detected on BTA2, BTA11, and BTA12 (rs29009916, rs109459144, and rs42647772). Notably, the association of four SNPs (rs10451141 for FY, and rs29009916, rs109459144, and rs42647772 for MS) was identified for the first time in this study. These variants were located near genes with potential roles in mammary gland function and milk component synthesis. These variants are located near genes potentially involved in mammary gland function and milk component synthesis. Although identified in the Holstein cattle population, these findings have international relevance and applicability due to the importation of semen from various countries. Ultimately, this study contributes to the development of effective selection strategies for specific populations and provides valuable insights into the genetics of milk production traits on a global scale. (c) 2025 The Author(s). Published by Elsevier B.V. on behalf of The animal Consortium. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).