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A Multi-Breed GWAS for Carcass Weight in Jeju Black Cattle and Hanwoo × Jeju Black Crossbreds
by
, , and
Miyoung Won
1, 
Jongan Lee
2,
Sang-Min Shin
1,
Seung-Eun Lee
1,
Won-Jae Kim
1,
Eun-Tae Kim
1,
Tae-Hee Kim
3,
Hee-Bok Park
3 and
Borhan Shokrollahi
1,* 1
Subtropical Livestock Research Center, National Institute of Animal Science, RDA, Jeju 63242, Republic of Korea
2
Animal Breeding and Genetics Division, National Institute of Animal Science, RDA, Cheonan 31041, Republic of Korea
3
Department of Animal Resources Science, Kongju National University, Yesan 3249, Republic of Korea
*
Author to whom correspondence should be addressed.
Biology 2025, 14(12), 1699; https://doi.org/10.3390/biology14121699 (registering DOI)
Submission received: 28 October 2025
/
Revised: 17 November 2025
/
Accepted: 27 November 2025
/
Published: 28 November 2025
(This article belongs to the Special Issue Advances in Animal Functional Genomics)
Simple Summary
Carcass weight is one of the most important traits determining beef yield and economic value in Korea. Jeju Black cattle are a native breed valued for their unique meat quality, but their smaller body size limits productivity. To better understand the genetic factors that influence carcass weight, we analyzed DNA from Jeju Black cattle and Jeju Black × Hanwoo crossbreds using a genome-wide association study (GWAS). We identified several genomic regions and genes that may affect carcass growth, including genes related to skeletal development, muscle formation, and metabolism. These findings provide new genetic information that can support breeding programs aimed at improving carcass yield while preserving the unique characteristics of Jeju Black cattle. The results also help establish a scientific foundation for the sustainable conservation and utilization of this important Korean native breed.
Abstract
Carcass weight (CW) is a major determinant of beef yield and market value in Korea, yet the genetic basis of this trait remains largely unexplored in cattle from Jeju Island. In this study, we performed a genome-wide association study (GWAS) using both a mixed linear model (MLM) and the FarmCPU approach, followed by pathway and network analyses to identify loci and biological functions underlying CW variation. A total of 256 Jeju cattle (92 Jeju Black and 164 Jeju Black × Hanwoo crossbreds) were initially sampled. One crossbred sample failed genotyping, leaving 255 animals (92 Jeju Black and 163 crossbreds) for analysis. Animals were genotyped using the Illumina BovineSNP50 v3 BeadChip, and 39,055 high-quality single nucleotide polymorphisms (SNPs) were retained after quality control. The MLM analysis detected no genome-wide significant associations, whereas the FarmCPU analysis identified six significant loci on Bos taurus chromosomes 3, 5, 6, 10, and 13, each explaining 2.55–9.58% of the phenotypic variance. Candidate genes located near these loci included EIF2B3, HECTD3, SOX5, KLF6, PHACTR3, and two uncharacterized protein-coding genes. Functional enrichment analysis identified biologically relevant pathways including lysine degradation, tryptophan metabolism, glycerolipid metabolism, fatty acid biosynthesis, extracellular matrix–receptor interaction, and signaling cascades such as PI3K–Akt and Rap1, although most pathways were not statistically significant after FDR correction. Protein–protein interaction (PPI) network analysis using STRING highlighted modules of signaling, extracellular matrix, and metabolic genes. These clusters suggest that coordinated interactions among these pathways contribute to carcass growth and development. These findings provide new insights into the molecular basis of CW in Jeju Black and Hanwoo × Jeju Black crossbred cattle and identify candidate genes and pathways that may be useful for genomic selection and the sustainable improvement of Jeju Black cattle populations.
