Identification of Candidate Variants Associated with Milk Production, Health and Reproductive Traits for Holstein Cows in Southern China

Tingxian Deng, Lei Cheng, Chenhui Liu, Min Xiang, Qing Liu, Bo Yu and Hongbo Chen ()
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Tingxian Deng: Laboratory of Genetic Breeding, Reproduction and Precision Livestock Farming & Hubei Provincial Center of Technology Innovation for Domestic Animal Breeding, School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan 430023, China
Lei Cheng: Institute of Animal Science and Veterinary Medicine, Wuhan Academy of Agricultural Sciences, Wuhan 430208, China
Chenhui Liu: Institute of Animal Science and Veterinary Medicine, Wuhan Academy of Agricultural Sciences, Wuhan 430208, China
Min Xiang: Institute of Animal Science and Veterinary Medicine, Wuhan Academy of Agricultural Sciences, Wuhan 430208, China
Qing Liu: Laboratory of Genetic Breeding, Reproduction and Precision Livestock Farming & Hubei Provincial Center of Technology Innovation for Domestic Animal Breeding, School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan 430023, China
Bo Yu: Laboratory of Genetic Breeding, Reproduction and Precision Livestock Farming & Hubei Provincial Center of Technology Innovation for Domestic Animal Breeding, School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan 430023, China
Hongbo Chen: Laboratory of Genetic Breeding, Reproduction and Precision Livestock Farming & Hubei Provincial Center of Technology Innovation for Domestic Animal Breeding, School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan 430023, China

Agriculture, 2025, vol. 15, issue 19, 1-19

Abstract: Genome-wide association studies (GWAS) have been a successful tool for identifying quantitative trait loci (QTL) for economically important traits in dairy cows. However, the availability of QTLs linked to phenotypic traits is limited in the literature. In this study, we used GWAS, haplotype association, and fine-mapping analyses to identify candidate variants associated with milk production, health, and reproductive traits in 380 Chinese Holstein cattle from Southern China using whole-genome sequence data. GWAS identified 91 genome-wide significant signals that were annotated to 63 genes associated with milk production, health, and reproductive traits in dairy cattle. Haplotype association analysis further revealed that eight GWAS signals within three QTLs were associated with milk production and health traits of cows. Fine-mapping analysis revealed that 3 GWAS signals (6_92530313_G_A, 10_17185230_G_A, and 10_17209112_T_G) were the potential causal variants. Several candidate genes, including ANKS1B , IL17RD , CNOT6L , AOC1 , and TLE3 , have been confirmed to be associated with milk production, health, and reproductive traits in dairy cows. These findings significantly contribute to unraveling the genetic basis of economically important traits in Holstein cattle.

Keywords: cattle; economically important traits; haplotype association analysis; fine-mapping analysis; genome-wide association study (search for similar items in EconPapers)
JEL-codes: Q1 Q10 Q11 Q12 Q13 Q14 Q15 Q16 Q17 Q18 (search for similar items in EconPapers)
Date: 2025
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