ORIGINAL RESEARCH article
Front. Genet.
Sec. Livestock Genomics
Volume 16 - 2025 | doi: 10.3389/fgene.2025.1650836
Genome-Wide Association Study on Dairy Goat Milk Production Traits Using Three Models
Provisionally accepted
Zhengang Huang1
Hegang Li1*Yuanping Tang1Jianyu Zhou1Dongliang Xu1Xiaokun Lin1Ming Cheng2Jianguang Wang3
Qinan Zhao4
Jianning He1Xiaoxiao Gao1Jinshan Zhao1- 1Qingdao Agricultural University, Qingdao, China
- 2Qingdao Institute of Animal Husbandry and Veterinary Medicine, Qindao, China
- 3Inner Mongolia Shengjian Biotechnology Co., Ltd, Hohhot, China
- 4Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
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Identifying genetic markers associated with economically important traits in dairy goats helps enhance breeding efficiency, thereby increasing industry value. However, the potential genetic structure of key economic traits in dairy goats is still largely unknown. This study used three genome-wide association study (GWAS) models (GLM, MLM, FarmCPU) to analyze dairy goat milk production traits (milk yield, fat percentage, protein percentage, lactose percentage, ash percentage, total dry matter, and somatic cell count). The goal was to identify SNPs and positional and functional candidate genes significantly associated with these traits. The GWAS analysis results identified a total of 242 significant SNPs. Among these, 45 SNPs exhibited genome-wide significance, while 197 SNPs demonstrated suggestive associations, corresponding to 99 positional candidate genes within a 50kb upstream and downstream range. 15 significant SNP loci were consistently identified across all three models, corresponding to 18 candidate genes.The integrated analysis of three models detected 2, 19,17,4, 115,23, and 62 significant SNPs associated with milk yield, ash percentage, protein percentage, lactose percentage, somatic cell count, fat percentage, and total dry matter percentage, respectively. Correspondingly, 6, 24, 9, 12, 37, 14, and 30 candidate genes were identified for these traits.Additionally, several new candidate genes related to milk production traits were proposed (LCORL, TNFRSF1A, VWF, SPATA6, MAN1C1, MASP1, BRCA2).In summary, the results of this study provide an important reference for further exploration of the genetic mechanisms underlying dairy goat milk production traits and the development of molecular breeding markers.
Keywords: Genome-Wide Association Study, candidate genes, Milk production, Dairy goat, significant SNPs 1 Introduction
Received: 20 Jun 2025; Accepted: 05 Aug 2025.
Copyright: © 2025 Huang, Li, Tang, Zhou, Xu, Lin, Cheng, Wang, Zhao, He, Gao and Zhao. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Hegang Li, Qingdao Agricultural University, Qingdao, China
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