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GWAS Reveals Key Candidate Genes Associated with Milk-Production in Saanen Goats
by
Fu Li
†,
Yonglong He
†,
Hanbing Yan
,
Jiaqi Bu
,
Zhanhang Wang
,
Xiaolong Xu
,
Danni Li
,
Binyun Cao
and
Xiaopeng An
* 
College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Animals 2025, 15(22), 3282; https://doi.org/10.3390/ani15223282 (registering DOI)
Submission received: 15 October 2025
/
Revised: 11 November 2025
/
Accepted: 11 November 2025
/
Published: 13 November 2025
(This article belongs to the Section Animal Genetics and Genomics)
Simple Summary
Milk-production is crucial for dairy goats’ value. We sought genes affecting this by studying 350 Saanen goats. We found four genes linked to milk-production, working through certain pathways. Breeders can use this research to boost yields. Scientists gain knowledge on mammary function, aiding dairy research and industry.
Abstract
Milk-production is one of the most important economic traits in dairy goats. Fundamentally, increasing milk-production at the genetic level can provide potential genetic markers for improving milk-production in dairy goats. Previous studies have shown that milk-production traits in dairy goats are highly polygenic and can be influenced by multiple genes. We therefore performed high-throughput sequencing on 350 Saanen dairy goats and conducted a genome-wide association study (GWAS) on the sequencing and production data. A total of 9,667,930 valid SNPs were identified, among which approximately 51% of the mutations were synonymous changes, and apart from unknown mutations, only a few changes affected gene expression. Finally, 318 SNP loci and 244 candidate genes were selected. We selected 10 loci most likely to influence these traits for large-scale population-based identification. Finally, four candidate genes, CDC14A, F11, RBPJL and ZFAND2A, were identified as the most likely to affect milk-production traits in dairy goats. To prevent spurious association analyses, we conducted subsequent experiments. Further results showed that the four candidate genes could regulate the proliferation and secretion of dairy goat mammary epithelial cells by regulating MAPK, mTOR and other pathways. These findings provide more valuable genetic markers and a theoretical basis for better understanding the intrinsic mechanisms of dairy goat mammary glands.
Keywords:
GWAS; dairy goat; milk-production; candidate genes; SNP
