Animal Bioscience

Asian Australasian Association of Animal Production Societies (아세아태평양축산학회)
권호 표지
DOI QR코드

DOI QR Code

Evaluation of accuracies of genomic predictions for body conformation traits in Korean Holstein

  • Received : 2023.06.28
  • Accepted : 2023.11.22
  • Published : 2024.04.01
Download PDF
⟨ Previous Next ⟩

Abstract

Objective: This study aimed to assess the genetic parameters and accuracy of genomic predictions for twenty-four linear body conformation traits and overall conformation scores in Korean Holstein dairy cows. Methods: A dataset of 2,206 Korean Holsteins was collected, and genotyping was performed using the Illumina Bovine 50K single nucleotide polymorphism (SNP) chip. The traits investigated included body traits (stature, height at front end, chest width, body depth, angularity, body condition score, and locomotion), rump traits (rump angle, rump width, and loin strength), feet and leg traits (rear leg set, rear leg rear view, foot angle, heel depth, and bone quality), udder traits (udder depth, udder texture, udder support, fore udder attachment, front teat placement, front teat length, rear udder height, rear udder width, and rear teat placement), and overall conformation score. Accuracy of genomic predictions was assessed using the single-trait animal model genomic best linear unbiased prediction method implemented in the ASReml-SA v4.2 software. Results: Heritability estimates ranged from 0.10 to 0.50 for body traits, 0.21 to 0.35 for rump traits, 0.13 to 0.29 for feet and leg traits, and 0.05 to 0.46 for udder traits. Rump traits exhibited the highest average heritability (0.29), while feet and leg traits had the lowest estimates (0.21). Accuracy of genomic predictions varied among the twenty-four linear body conformation traits, ranging from 0.26 to 0.49. The heritability and prediction accuracy of genomic estimated breeding value (GEBV) for the overall conformation score were 0.45 and 0.46, respectively. The GEBVs for body conformation traits in Korean Holstein cows had low accuracy, falling below the 50% threshold. Conclusion: The limited response to selection for body conformation traits in Korean Holsteins may be attributed to both the low heritability of these traits and the lower accuracy estimates for GEBVs. Further research is needed to enhance the accuracy of GEBVs and improve the selection response for these traits.

Keywords

Acknowledgement

This work was carried out with the support of "Cooperative Research Program for Agriculture Science and Technology Development (Project title: Development of Information Linkage and Provision Technology for Genomic Omics Data, Project No. RS-2023-00232298)" from the Rural Development Administration, Republic of Korea.

References

  1. Wu X, Fang M, Liu L, et al. Genome wide association studies for body conformation traits in the Chinese Holstein cattle population. BMC Genomics 2013;14:897. https://doi.org/10.1186/1471-2164-14-897 
  2. Stefani G, El Faro L, Santana ML, Tonhati H. Association of longevity with type traits, milk yield and udder health in Holstein cows. Livest Sci 2018;218:1-7. https://doi.org/10.1016/j.livsci.2018.10.007 
  3. Abo-Ismail MK, Brito LF, Miller SP, et al. Genome-wide association studies and genomic prediction of breeding values for calving performance and body conformation traits in Holstein cattle. Genet Sel Evol 2017;49:82. https://doi.org/10.1186/s12711-017-0356-8 
  4. Pozveh ST, Shadparvar AA, Shahrbabak MM, Taromsari MD. Genetic analysis of reproduction traits and their relationship with conformation traits in Holstein cows. Livest Sci 2009;125:84-7. https://doi.org/10.1016/j.livsci.2009.02.015 
  5. Gibson KD, Dechow CD. Genetic parameters for yield, fitness, and type traits in US Brown Swiss dairy cattle. J Dairy Sci 2018;101:1251-7. https://doi.org/10.3168/jds.2017-13041 
  6. Zink V, Stipkova M, Lassen J. Genetic parameters for female fertility, locomotion, body condition score, and linear type traits in Czech Holstein cattle. J Dairy Sci 2011;94:5176-82. https://doi.org/10.3168/jds.2010-3644 
  7. Perez-Cabal MA, Alenda R. Genetic relationships between lifetime profit and type traits in Spanish Holstein cows. J Dairy Sci 2002;85:3480-91. https://doi.org/10.3168/jds.S0022-0302(02)74437-8 
  8. Vollema AR, Van Der Beek S, Harbers AG, De Jong G. Genetic evaluation for longevity of Dutch dairy bulls. J Dairy Sci 2000;83:2629-39. https://doi.org/10.3168/jds.S0022-0302(00)75156-3 
  9. Goddard ME, Hayes BJ. Genomic selection. J Anim Breed Genet 2007;124:323-30. https://doi.org/10.1111/j.1439-0388.2007.00702.x 
  10. Meuwissen T, Hayes B, Goddard M. Genomic selection: a paradigm shift in animal breeding. Anim Front 2016;6:6-14. https://doi.org/10.2527/af.2016-0002 
  11. CRV. Manual for type classification of cows [Internet]. Arnhem, Netherlands: CRV: Better cows | Better life; c2023 [cited 2023 Sept 1]. Available from: https://crv4all.com/en/service/confirmation-and-linear-traits 
  12. Cho C, Alam M, Cho K, et al. Genetic parameters for eighteen linear type traits in Holstein cattle. Ann Anim Resour Sci 2014;25:89-96. https://doi.org/10.12718/aars.2014.25.2.89 
  13. Holstein Association USA. Linear descriptive traits [Internet]. Brattleboro, VT, USA: Holstein Association USA, Inc.; c2023 [cited 2023 Sept 1]. Available from: https://www.holsteinusa.com/ 
  14. Purcell S, Neale B, Todd-Brown K, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007;81:559-75. https://doi.org/10.1086/519795 
  15. Gilmour AR, Gogel BJ, Cullis BR, Welham SJ, Thompson R. ASReml user guide release 4.1 functional specification. Hemel Hempstead, UK: VSN International Ltd; 2015. www.vsni.co.uk 
  16. Yang J, Lee SH, Goddard ME, Visscher PM. GCTA: a tool for genome-wide complex trait analysis. Am J Hum Genet 2011;88:76-82. https://doi.org/10.1016/j.ajhg.2010.11.011 
  17. VanRaden PM. Efficient methods to compute genomic predictions. J Dairy Sci 2008;91:4414-23. https://doi.org/10.3168/jds.2007-0980 
  18. Meher PK, Rustgi S, Kumar A. Performance of Bayesian and BLUP alphabets for genomic prediction: analysis, comparison and results. Heredity (Edinb) 2022;128:519-30. https://doi.org/10.1038/s41437-022-00539-9 
  19. Badke YM, Bates RO, Ernst CW, Fix J, Steibel JP. Accuracy of estimation of genomic breeding values in pigs using low-density genotypes and imputation. G3 (Bethesda) 2014;4:623-31. https://doi.org/10.1534/g3.114.010504 
  20. Olasege BS, Zhang S, Zhao Q, et al. Genetic parameter estimates for body conformation traits using composite index, principal component, and factor analysis. J Dairy Sci 2019;102:5219-29. https://doi.org/10.3168/jds.2018-15561 
  21. Campos RV, Cobuci JA, Costa CN, Neto JB. Genetic parameters for type traits in Holstein cows in Brazil. Rev Bras Zootec 2012;41:2150-61. https://doi.org/10.1590/S1516-35982012001000003 
  22. Wasana N, Cho G, Park S, et al. Genetic relationship of productive life, production and type traits of korean holsteins at early lactations. Asian-Australas J Anim Sci 2015;28:1259-65. https://doi.org/10.5713/ajas.15.0034 
  23. National genetic evaluation forms provided by countries [Internet]. Interbull; c2012 [cited 2023 Sept 11]. Available from: https://interbull.org/ib/geforms 
  24. Oliveira Junior GA, Schenkel FS, Alcantara L, et al. Estimated genetic parameters for all genetically evaluated traits in Canadian Holsteins. J Dairy Sci 2021;104:9002-15. https://doi.org/10.3168/jds.2021-20227 
  25. Battagin M, Sartori C, Biffani S, Penasa M, Cassandro M. Genetic parameters for body condition score, locomotion, angularity, and production traits in Italian Holstein cattle. J Dairy Sci 2013;96:5344-51. https://doi.org/10.3168/jds.2012-6352 
  26. Van Dorp TE, Boettcher P, Schaeffer LR. Genetics of locomotion. Livest Prod Sci 2004;90:247-53. https://doi.org/10.1016/j.livprodsci.2004.06.003 
  27. Zavadilova L, Stipkova M. Genetic correlations between longevity and conformation traits in the Czech Holstein population. Czech J Anim Sci 2012;57:125-36. https://doi.org/10.17221/5566-CJAS 
  28. Petrini J, Iung LHS, Rodriguez MAP, et al. Genetic parameters for milk fatty acids, milk yield and quality traits of a Holstein cattle population reared under tropical conditions. J Anim Breed Genet 2016;133:384-95. https://doi.org/10.1111/jbg.12205 
  29. Utrera AR, Van Vleck LD. Heritability estimates for carcass traits of cattle: a review. Genet Mol Res 2004;3:380-94. 
  30. Pantelic V, Niksic D, Trivunovic S. Variability and heritability of type traits of Holstein-Friesian bull dams. Biotechnol Anim Husb 2011;27:305-13. https://doi.org/10.2298/bah1103305p 
  31. Sewalem A, Kistemaker GJ, Miglior F, Van Doormaal BJ. Analysis of the relationship between type traits and functional survival in Canadian Holsteins using a Weibull proportional hazards model. J Dairy Sci 2004;87:3938-46. https://doi.org/10.3168/jds.S0022-0302(04)73533-X 
  32. Kramer M, Erbe M, Bapst B, Bieber A, Simianer H. Estimation of genetic parameters for novel functional traits in Brown Swiss cattle. J Dairy Sci 2013;96:5954-64. https://doi.org/10.3168/jds.2012-6236 
  33. Seykora AJ, McDaniel BT. Heritabilities of teat traits and their relationships with milk yield, somatic cell count, and percent two-minute milk. J Dairy Sci 1985;68:2670-83. https://doi.org/10.3168/jds.S0022-0302(85)81152-8 
  34. Houle D. Comparing evolvability and variability of quantitative traits. Genetics 1992;130:195-204. https://doi.org/10.1093/genetics/130.1.195 
  35. Getu A, Misganaw G. The role of conformational traits on dairy cattle production and their longevities. Open Access Libr J 2015;2:e1342. https://doi.org/10.4236/oalib.1101342 
  36. Zhou L, Mrode R, Zhang S, et al. Factors affecting GEBV accuracy with single-step Bayesian models. Heredity (Edinb) 2018;120:100-9. https://doi.org/10.1038/s41437-017-0010-9 
  37. Haque MA, Iqbal A, Bae H, et al. Assessment of genomic breeding values and their accuracies for carcass traits in Jeju Black cattle using whole-genome SNP chip panels. J Anim Breed Genet 2023;140:519-31. https://doi.org/10.1111/jbg.12776 
  38. Misztal I, Aggrey SE, Muir WM. Experiences with a single-step genome evaluation. Poult Sci 2013;92:2530-4. https://doi.org/10.3382/ps.2012-02739 
  39. Hayes BJ, Bowman PJ, Chamberlain AJ, Goddard ME. Invited review: Genomic selection in dairy cattle: progress and challenges. J Dairy Sci 2009;92:433-43. https://doi.org/10.3168/jds.2008-1646 
  40. Song H, Li L, Ma P, et al. Short communication: improving the accuracy of genomic prediction of body conformation traits in Chinese Holsteins using markers derived from high-density marker panels. J Dairy Sci 2018;101:5250-4. https://doi.org/10.3168/jds.2017-13456