Genomic characterization of Holstein–Jersey crossbred cattle in Korea using genome-wide SNP data

Seul Gy Lee; Gyeonglim Ryu; Mi-Na Park; Chang Gwan Dang; Jae Hyuk Jang; Dajeong Lim; Tae-Jeong Choi

doi:10.7744/kjoas.520426

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2025 Vol.52, Issue 4 Preview Page

Animal

Genomic characterization of Holstein–Jersey crossbred cattle in Korea using genome-wide SNP data

1 December 2025. pp. 725-733

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Abstract

The number of Jersey cattle raised in the Korean dairy industry has been steadily increasing; however, their population size remains small compared with Holsteins, and studies on their genetic characteristics are still limited. This study aimed to establish a genetic reference for the Jersey population in Korea by characterizing the genetic structure of domestic Jersey and Holstein populations and quantitatively evaluating changes in breed composition across successive backcross generations (F1 to F6) produced by mating Jerseys to Holsteins. Using the Illumina BovineSNP50 V3 SNP chip, a total of 53,218 SNPs were genotyped, and after quality control, 26,931 SNPs shared among 494 Jersey, 742 Holstein, and 98 crossbred animals were retained for downstream analyses. Principal component analysis (PCA) clearly separated Holstein and Jersey cattle into two distinct genetic clusters, demonstrating substantial genetic differentiation between the breeds. Supervised ADMIXTURE analysis revealed a progressive increase in Jersey ancestry across backcross generations, with mean Jersey proportions of 0.55 in F1, 0.74 in F2, 0.87 in F3, and 0.99 in F4. Notably, animals from the F4 and later generations clustered almost entirely within the Jersey group in the PCA plot, indicating convergence toward a genetic composition effectively indistinguishable from purebred Jerseys. These patterns were consistent with theoretical expectations of backcrossing (F1: 50%, F2: 75%, F3: 87.5%, F4: 93.75%) as well as international criteria for breed purity recognition (e.g., the 7/8 standard of the Canadian Animal Pedigree Act and the U.S. Council on Dairy Cattle Breeding (CDCB) purity threshold of Breed Base Representation (BBR) ≥ 94%). Overall, this study provides a foundational reference population for Jerseys in Korea and establishes an analytical framework for accurately determining breed composition in crossbred cattle. The findings offer essential resources for setting registration criteria for backcross progeny, improving pedigree management, supporting breeding program decisions, and guiding national strategies for genetic resource conservation in the Korean dairy industry.

Keywords

admixture

Holstein

Jersey

population

principal component analysis

References

Aikman PC, Reynolds CK, Beever DE. 2008. Diet digestibility, rate of passage, and eating and rumination behavior of Jersey and Holstein cows. Journal of Dairy Science 91:1103-1114.

10.3168/jds.2007-0724

Alexander DH, Lange K. 2011. Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC Bioinformatics 12:246.

10.1186/1471-2105-12-24621682921PMC3146885

Alexander DH, Novembre J, Lange K. 2009. Fast model-based estimation of ancestry in unrelated individuals. Genome Research 19:1655-1664.

10.1101/gr.094052.10919648217PMC2752134

Anderson CA, Pettersson FH, Clarke GM, Cardon LR, Morris AP, Zondervan KT. 2010. Data quality control in genetic case-control association studies. Nature Protocols 5:1564-1573.

10.1038/nprot.2010.11621085122PMC3025522

CDCB (Council on Dairy Cattle Breeding). 2023. Breed Base Representation.

Goli RC, Chishi KG, Mahar K, Ganguly I, Singh S, Dixit SP, Sruthi OS, Choudhary S, Diwakar V, Rathi P, et al. 2025. Genome wide locus-specific ancestry analysis revealed adaptive admixtures in crossbred cattle of India. Scientific Reports 15:17069.

10.1038/s41598-025-01971-740379730PMC12084602

Heins BJ, Hansen LB, Seykora AJ, Hazel AR, Johnson DG, Linn JG. 2008. Crossbreds of Jersey × Holstein compared with pure Holsteins for body weight, body condition score, dry matter intake, and feed efficiency during the first one hundred fifty days of first lactation. Journal of Dairy Science 91:3716-3722.

10.3168/jds.2008-1094

Lee D, Cho M, Hong WY, Lim D, Kim HC, Cho YM, Jeong JY, Choi BH, Ko Y, Kim J. 2016. Evolutionary analyses of Hanwoo (Korean cattle) - Specific single-nucleotide polymorphisms and genes using whole-genome resequencing data of a Hanwoo population. Molecules and Cells 39:692-698.

10.14348/molcells.2016.014827640093PMC5050534

Lim DH, Kim TI, Park SM, Ki KS, Kim Y. 2021. Evaluation of heat stress responses in Holstein and Jersey cows by analyzing physiological characteristics and milk production in Korea. Journal of Animal Science and Technology 63:872-883.

10.5187/jast.2021.e6234447963PMC8367404

Lim DH, Mayakrishnan V, Ki KS, Kim Y, Kim TI. 2020. The effect of seasonal thermal stress on milk production and milk compositions of Korean Holstein and Jersey cows. Animal Bioscience 34:567-574.

10.5713/ajas.19.092632777906PMC7961267

Marees AT, de Kluiver H, Stringer S, Vorspan F, Curis E, Marie-Claire C, Derks EM. 2018. A tutorial on conducting genome-wide association studies: Quality control and statistical analysis. International Journal of Methods in Psychiatric Research 27:e1608.

10.1002/mpr.160829484742PMC6001694

McAllister AJ. 2002. Is crossbreeding the answer to questions of dairy breed utilization. Journal of Dairy Science 85:2352-2357.

10.3168/jds.S0022-0302(02)74315-4

Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, et al. 2007. PLINK: A tool set for whole-genome association and population-based linkage analyses. The American Journal of Human Genetics 81:559-575.

10.1086/51979517701901PMC1950838

Richardson C, Van Doormaal B. 2022. Defining breed purity. Lactanet Article. Accessed in https://lactanet.ca/en/defining-breed-purity on 15 November 2025.

Royal MD, Darwash AO, Flint APF, Webb R, Woolliams JA, Lamming GE. 2000. Declining fertility in dairy cattle: Changes in traditional and endocrine parameters of fertility. Animal Science 70:487-501.

10.1017/S1357729800051845

Strucken EM, Swaminathan M, Gibson JP. 2021. Small SNP panels for breed proportion estimation in Indian crossbred dairy cattle. Journal of Animal Breeding and Genetics 138:698-707.

10.1111/jbg.1254433687116PMC8519156

Information

Publisher :Institute of Agricultural Science, Chungnam National University
Publisher(Ko) :충남대학교 농업과학연구소
Journal Title :Korean Journal of Agricultural Science
Journal Title(Ko) :농업과학연구
Volume : 52
No :4
Pages :725-733
Received Date : 2025-11-20
Revised Date : 2025-11-25
Accepted Date : 2025-11-25
DOI :https://doi.org/10.7744/kjoas.520426

Korean Journal of Agricultural Science ISSN:2466-2402(Print) 2466-2410(Online) 농업과학연구

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