Journal of Animal Breeding and Genomics (J Anim Breed Genom)
Seungwon Oh1, Yang Mo Koo2, Seung Hwan Lee3, Duhak Yoon1,4*
1Department of Animal Science & Biotechnology, Graduate School, Kyungpook National University, Sangju 37224, Korea
2Genetic & Breeding Department, Korea Animal Improvement Association, Livestock Hall, Seoul 06668, Korea
3Division of Animal and Dairy Science, Chungnam National University, Daejeon 34148, Korea
4Research Institute for Innovative Animal Science, Kyungpook National University, Sangju 37224, Korea
Correspondence to Duhak Yoon, E-mail: dhyoon@knu.ac.kr
Volume 8, Number 4, Pages 143-152, December 2024.
Journal of Animal Breeding and Genomics 2024, 8(4), 143-152. https://doi.org/10.12972/jabng.20240407
Received on 26 September, 2024, Revised on 19 December, 2024, Accepted on 20 December, 2024, Published on 31 December, 2024.
Copyright © 2024 Korean Society of Animal Breeding and Genetics.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0).
In this study, we conducted a Genome Wide Association Study (GWAS) analysis of the reproductive traits in Hanwoo cows, Age at First Calving (AFC) and Calving Interval (CI), aiming to pinpoint candidate genes and their functional relevance. A total of 24,977 Hanwoo cows from commercial farms were genotyped using Axiom Bovine 60k version 3 (Affymetrix Inc, 2006). Subsequently, individuals with genotype and phenotype data were selected from this population, resulting in 9,508 cows and 37,999 SNPs for AFC, and 6,442 cows and 38,379 SNPs for CI after Quality Control. Bonferroni correction and False Discovery Rate (FDR) correction were applied to GWAS thresholds, leading to the identification of significant SNP markers for each trait by chromosome. AFC revealed seven SNP markers on five chromosomes, and CI identified three SNP markers on three chromosomes. Sixteen candidate genes were identified from these ten significant SNP markers. Notably, TRNAC-GCA was highlighted as a gene influencing semen quality in bovines and playing a crucial role in cow reproductive traits. Additionally, Gene Ontology (GO) was identified two GO IDs, respectively, in Biological Process (BP), Cellular Component (CC), and Molecular Function (MF) (BP: GO:0030259, GO:0005975; CC: GO:0031982, GO:0005794; MF: GO:0016758, GO:0016757), with no KEGG pathway being identified. These results contribute to advanced understanding of the genetic architecture of reproductive traits and offer valuable SNP markers for breeding programs in Hanwoo cow.
GWAS, GO, Hanwoo cow (Korean Brown Cattle), Reproductive traits
본 연구는 한국종축개량협회 ʻ한우암소 번식형질 유전체 육종가 활용에 대한 검증 연구’의 지원에 의해 이루어진 것이며 연구비 지원에 감사드립니다.
Cecchinato, A., Macciotta, N. P. P., Mele, M., Tagliapietra, F., Schiavon, S., Bittante, G., & Pegolo, S. (2019). Genetic and genomic analyses of latent variables related to the milk fatty acid profile, milk composition, and udder health in dairy cattle. Journal of dairy science, 102(6), 5254-5265.
[DOI][PubMed]
Collins, F. S., Morgan, M., & Patrinos, A. (2003). The Human Genome Project: lessons from large-scale biology. science, 300(5617), 286-290.
[DOI][PubMed]
Consortium, I. C. G. S. (2004). Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature, 432(7018), 695-716.
[DOI][PubMed]
Fang, L., Zhou, Y., Liu, S., Jiang, J., Bickhart, D. M., Null, D. J., Li, B., Schroeder, S. G., Rosen, B. D., & Cole, J. B. (2019). Comparative analyses of sperm DNA methylomes among human, mouse and cattle provide insights into epigenomic evolution and complex traits. Epigenetics, 14(3), 260-276.
[DOI][PubMed][PMC]
Georges, M., Nielsen, D., Mackinnon, M., Mishra, A., Okimoto, R., Pasquino, A. T., Sargeant, L. S., Sorensen, A., Steele, M. R., & Zhao, X. (1995). Mapping quantitative trait loci controlling milk production in dairy cattle by exploiting progeny testing. Genetics, 139(2), 907-920.
[DOI][PubMed][PMC]
Hardie, L., VandeHaar, M., Tempelman, R., Weigel, K., Armentano, L., Wiggans, G., Veerkamp, R., De Haas, Y., Coffey, M., & Connor, E. (2017). The genetic and biological basis of feed efficiency in mid-lactation Holstein dairy cows. Journal of dairy science, 100(11), 9061-9075.
[DOI][PubMed]
Hyeong, K.-E., Iqbal, A., & Kim, J.-J. (2014). A genome wide association study on age at first calving using high density single nucleotide polymorphism chips in Hanwoo (Bos taurus coreanae). Asian-Australasian journal of animal sciences, 27(10), 1406.
[DOI][PubMed][PMC]
Jia, X., Yang, Y., Chen, Y., Xia, Z., Zhang, W., Feng, Y., Li, Y., Tan, J., Xu, C., & Zhang, Q. (2019). Multivariate analysis of genome-wide data to identify potential pleiotropic genes for type 2 diabetes, obesity and coronary artery disease using MetaCCA. International journal of cardiology, 283, 144-150.
[DOI][PubMed]
Jiang, J., Cole, J. B., Da, Y., VanRaden, P. M., & Ma, L. (2018). Fast Bayesian fine-mapping of 35 production, reproduction and body conformation traits with imputed sequences of 27K Holstein bulls. BioRxiv, 428227.
[DOI]
Jiang, K., Hua, S., Mohan, R., Grigoriev, I., Yau, K. W., Liu, Q., Katrukha, E. A., Altelaar, A. M., Heck, A. J., & Hoogenraad, C. C. (2014). Microtubule minus-end stabilization by polymerization-driven CAMSAP deposition. Developmental cell, 28(3), 295-309.
[DOI][PubMed]
Júnior, G. F., Costa, R., De Camargo, G., Carvalheiro, R., Rosa, G., Baldi, F., Garcia, D., Gordo, D., Espigolan, R., & Takada, L. (2016). Genome scan for postmortem carcass traits in Nellore cattle. Journal of Animal Science, 94(10), 4087-4095.
[DOI][PubMed]
Kamiński, S., Hering, D. M., Oleński, K., Lecewicz, M., & Kordan, W. (2016). Genome-wide association study for sperm membrane integrity in frozen-thawed semen of Holstein-Friesian bulls. Animal reproduction science, 170, 135-140.
[DOI][PubMed]
King, F. J. M., Visser, C., & Banga, C. (2022). Genetic characterization of Mozambican Nguni cattle and their relationship with indigenous populations of South Africa. Livestock Science, 264, 105044.
[DOI]
Kruglyak, L. (1999). Prospects for whole-genome linkage disequilibrium mapping of common disease genes. nature genetics, 22(2), 139-144.
[DOI][PubMed]
Lai, L., & Prather, R. S. (2002). Progress in producing knockout models for xenotransplantation by nuclear transfer. Annals of medicine, 34(7), 501-506.
[DOI][PubMed]
Lázaro, S. F., Tonhati, H., Oliveira, H. R., Silva, A. A., Scalez, D. C., Nascimento, A. V., Santos, D. J., Stefani, G., Carvalho, I. S., & Sandoval, A. F. (2023). Genetic parameters and genome-wide association studies for mozzarella and milk production traits, lactation length, and lactation persistency in Murrah buffaloes. Journal of dairy science.
[DOI][PubMed]
Lee, C., Choi, J., Shin, H., & Kim, J. (2020). Genetic prediction of Hanwoo carcass traits in Kangwon regional Hanwoo cow test farms. Ann Anim Resour Sci, 31, 1-12.
[DOI]
Lee, T., Cho, S., Seo, K. S., Chang, J., Kim, H., & Yoon, D. (2013). Genetic variants and signatures of selective sweep of Hanwoo population (Korean native cattle). BMB reports, 46(7), 346.
[DOI][PubMed][PMC]
Lim, K.-S., Park, B.-H., Choi, T.-J., Lim, D., & Cho, Y.-M. (2016). Carrier testing for autosomal recessive hereditary disorder in Korean proven bulls. Journal of Biomedical and Translational Research, 17(4), 85-90.
[DOI]
Liu, Y., Qin, X., Song, X.-Z. H., Jiang, H., Shen, Y., Durbin, K. J., Lien, S., Kent, M. P., Sodeland, M., & Ren, Y. (2009). Bos taurus genome assembly. BMC genomics, 10(1), 1-11.
[DOI][PubMed][PMC]
Lopez, B. I., Son, J.-H., Seo, K., & Lim, D. (2019). Estimation of genetic parameters for reproductive traits in Hanwoo (Korean Cattle). Animals, 9(10), 715.
[DOI][PubMed][PMC]
Melo, T. P. d., De Camargo, G. M. F., De Albuquerque, L. G., & Carvalheiro, R. (2017). Genome-wide association study provides strong evidence of genes affecting the reproductive performance of Nellore beef cows. Plos one, 12(5), e0178551.
[DOI][PubMed][PMC]
Naserkheil, M., Bahrami, A., Lee, D., & Mehrban, H. (2020). Integrating single-step GWAS and bipartite networks reconstruction provides novel insights into yearling weight and carcass traits in hanwoo beef cattle. Animals, 10(10), 1836.
[DOI][PubMed][PMC]
Oh, S., & Yoon, D. (2022). Analysis of Linkage Disequilibrium and Estimation of Effective Population Size in Hanwoo Cow Population. Journal of Animal Breeding and Genomics, 6(4), 253-264.
[DOI]
Park, S., Kim, H., Lee, Y.-S., Kim, J.-W., Kim, J. B., Song, Y.-H., Lee, H.-K., & Lee, S.-J. (2013). Studies on the failure Rate of Artificial Insemination in Korean Native Cows. Reproductive and Developmental Biology, 37(1), 23-27.
[DOI]
Park, S., Lee, S., Lee, K., Shin, Y., Song, Y., & Lee, S. (2011). Analysis of reproduction and breeding status in Gangwon east area. Annals of Animal Resources Sciences, 22, 1-5.
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A., Bender, D., Maller, J., Sklar, P., De Bakker, P. I., & Daly, M. J. (2007). PLINK: a tool set for whole-genome association and population-based linkage analyses. The American journal of human genetics, 81(3), 559-575.
[DOI][PubMed][PMC]
R Core Team, R. (2023). R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing. http://www.R-project.org/
Roper, L. K., Briguglio, J. S., Evans, C. S., Jackson, M. B., & Chapman, E. R. (2015). Sex-specific regulation of follicle-stimulating hormone secretion by synaptotagmin 9. Nature communications, 6(1), 8645.
[DOI][PubMed][PMC]
Schook, L. B., Beever, J. E., Rogers, J., Humphray, S., Archibald, A., Chardon, P., Milan, D., Rohrer, G., & Eversole, K. (2005). Swine Genome Sequencing Consortium (SGSC): a strategic roadmap for sequencing the pig genome. Comparative and functional genomics, 6(4), 251-255.
[DOI][PubMed][PMC]
Shin, E., Lee, S., & Yoon, D. (2018). Accuracy of genomic estimated breeding value with Hanwoo cows in the commercial farms. J Agric Life Sci, 52, 91-98.
[DOI]
Shin, S., Lee, J., & Do, C. (2021). Genetic relationship of age at first calving with conformation traits and calving interval in Hanwoo cows. Journal of animal science and technology, 63(4), 740.
[DOI][PubMed][PMC]
Srivastava, S., Srikanth, K., Won, S., Son, J.-H., Park, J.-E., Park, W., Chai, H.-H., & Lim, D. (2020). Haplotype-based genome-wide association study and identification of candidate genes associated with carcass traits in Hanwoo cattle. Genes, 11(5), 551.
[DOI][PubMed][PMC]
Stanley, P. (2011). Golgi glycosylation. Cold Spring Harbor perspectives in biology, 3(4), a005199.
[DOI][PubMed][PMC]
Tizioto, P. C., Taylor, J. F., Decker, J. E., Gromboni, C. F., Mudadu, M. A., Schnabel, R. D., Coutinho, L. L., Mourão, G. B., Oliveira, P. S., & Souza, M. M. (2015). Detection of quantitative trait loci for mineral content of Nelore longissimus dorsi muscle. Genetics Selection Evolution, 47, 1-9.
[DOI][PubMed][PMC]
Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., & Holt, R. A. (2001). The sequence of the human genome. science, 291(5507), 1304-1351.
Venturini, G., Cardoso, D., Baldi, F., Freitas, A., Aspilcueta-Borquis, R., Santos, D., Camargo, G., Stafuzza, N., Albuquerque, L., & Tonhati, H. (2014). Association between single-nucleotide polymorphisms and milk production traits in buffalo. Genet. Mol. Res, 13(4), 10256-10268.
[DOI][PubMed]
Wang, F., Song, S., Guo, B., Li, Y., Wang, H., Fu, S., Wang, L., Zhe, X., Li, H., & Li, D. (2023). Increased TCP11 gene expression can inhibit the proliferation, migration and promote apoptosis of cervical cancer cells. BMC cancer, 23(1), 853.
[DOI][PubMed][PMC]
Yang, J., Lee, S. H., Goddard, M. E., & Visscher, P. M. (2011). GCTA: a tool for genome-wide complex trait analysis. The American journal of human genetics, 88(1), 76-82.
[DOI][PubMed][PMC]