Yak meat is nutritionally superior to beef cattle but has a low fat content and is slow-growing. The liver plays a crucial role in lipid metabolism, and in order to determine whether different feeding modes affect lipid metabolism in yaks and how it is regulated, we employed RNA sequencing (RNA-seq) technology to analyze the genome-wide differential gene expression in the liver of yaks maintained under different raising systems. A total of 1663 differentially expressed genes (DEGs) were identified (|log2FC| ≥ 0 and p-value ≤ 0.05), including 698 down-regulated and 965 up-regulated genes. According to gene ontology (GO) and KEGG enrichment analyses, these DEGs were significantly enriched in 13 GO terms and 26 pathways (p < 0.05). Some DEGs were enriched in fatty acid degradation, PPAR, PI3K-Akt, and ECM receptor pathways, which are associated with lipid metabolism. A total of 16 genes are well known to be related to lipid metabolism (e.g., APOA1, FABP1, EHHADH, FADS2, SLC27A5, ACADM, CPT1B, ACOX2, HMGCS2, PLIN5, ACAA1, IGF1, FGFR4, ALDH9A1, ECHS1, LAMA2). A total of 11 of the above genes were significantly enriched in the PPAR signaling pathway. The reliability of the transcriptomic data was verified using qRT-PCR. Our findings provide new insights into the mechanisms regulating yak meat quality. It shows that fattening improves the expression of genes that regulate lipid deposition in yaks and enhances meat quality. This finding will contribute to a better understanding of the various factors that determine yak meat quality and help develop strategies to improve yield and quality.

A single-nucleotide polymorphism (SNP) is a genome-level trait that arises from a variation in a single nucleotide, leading to diversity in DNA sequences. SNP screening is commonly used to provide candidate genes for yak breeding efforts. Integrin Subunit Alpha 9 (ITGA9) is an integrin protein. It plays an important role in cell adhesion, signalling, and other processes. The aim of this study was to discuss the association between genetic polymorphisms in the ITGA9 gene and milk quality traits and to identify potential molecular marker loci for yak breeding quality. We genotyped 162 yaks using an Illumina Yak cGPS 7K liquid chip and identified the presence of polymorphisms at nine SNP loci in the ITGA9 gene of yaks. The results showed that the mutant genotypes in the loci g.285,808T>A, g.306,600T>C, and g.315,413C>T were positively correlated with the contents of casein, protein, total solids (TS), and solid nonfat (SNF) in yak milk. In other loci, heterozygous genotypes had a positive correlation with nutrient content in yak milk. Then, two ITGA9 haplotype blocks were constructed based on linkage disequilibrium, which facilitated a more accurate screening of ITGA9 as a candidate gene for yak milk quality improvement. In conclusion, we identified SNPs and haplotype blocks related to yak milk quality traits and provided genetic resources for marker-assisted selection in yak breeding.

The yak is a vital livestock resource on the Qinghai–Tibet Plateau, renowned for its strong disease resistance and high-quality meat. However, various diseases pose significant threats to its health and lead to substantial economic losses. Current feeding management practices, along with available drugs and vaccines, have demonstrated limited effectiveness in preventing and controlling infectious diseases. Additionally, challenges such as drug resistance and the safety of animal products persist. Therefore, enhancing the disease-resistant breeding capacity of yaks is crucial. In this study, we examined 192 yaks by measuring the concentrations of 10 immune indicators in serum by using the ELISA method and conducting whole-genome resequencing, which identified 19,182,942 SNP loci. Through genome-wide association analysis, we detected 323 significant SNPs located near or within 125 candidate genes, most of which are associated with disease and significantly enriched in the TGF-β signaling pathway. Overall, our study identified a series of novel variants and candidate genes associated with disease resistance traits in yaks, providing important information for the molecular breeding of disease resistance in yaks. These results not only contribute to a deeper understanding of the function of disease resistance genes in yaks but also hold great potential for accelerating precision disease resistance breeding in yaks.