Genetic Variants in the ATF6 Gene and Their Relationship with Milk-Quality Traits in Yaks

Yaks (Bos grunniens) are a predominant livestock species on the Tibetan Plateau, known for their adaptability to the cold and dry climate typical of this region. This study investigates the association of two SNPs within the ATF6 gene (Chr3:9812652G>T (CM016692.1) and Chr3:9900243C>T (CM016692.1)) with key milk-quality traits in yaks. Due to the low frequency of TT homozygotes (<5%), analysis focused on major genotypes: GG vs. GT and CC vs. CT. Both one-way ANOVA and general linear models (adjusted for lactation number) showed that g.3_9812652G>T was significantly associated with higher levels of casein, protein, acidity, and solid-not-fat (SNF) in GT individuals (p < 0.01). No significant differences were observed for lactose, urea, citric acid, or fat. For g.3_9900243C>T, CT individuals showed higher casein, protein, SNF, and citric acid levels compared to CC (p < 0.05). These results suggest both SNPs are linked to key milk traits, especially protein, casein, and SNF. The g.3_9812652G>T variant had a stronger and more consistent effect, indicating it may play a larger role in milk composition regulation. Overall, ATF6 is a promising candidate gene for marker-assisted selection (MAS) to improve milk quality in yaks. Further studies in larger and more diverse populations are needed to confirm these findings and explore the gene’s functional role.