Concentrated supplementary feeding is an effective strategy for addressing nutritional deficiencies in yaks during the cold-season grazing period. However, limited research has investigated whether long-term implementation may alter the gut microbiota and metabolite profiles of yaks, potentially posing health risks to the host. This study investigated the regulatory role of Lactobacillus fermentum in host metabolism through the gut microbiota, employing a “nutrition-gut-metabolism” perspective. Eighty healthy male Pamir yaks with similar body conditions were randomly divided into four groups (n = 20 per group), including Control (Con), Medium Energy (ME), High Energy (HE), and Medium Energy plus Lactobacillus fermentum (MEJ). Body weight was recorded every 30 days during the 150-day trial. Jejunal tissues and contents from nine yaks per group were collected for subsequent analyses. Key findings revealed that the HE group showed significantly increased crypt depth and elevated relative abundance of Clostridium_sensu_stricto_1 (P < 0.05). In contrast, the MEJ group reversed the decline in villus height and width observed in the ME group, while significantly enhancing muscularis thickness. Notably, MEJ yaks exhibited higher abundance of Paeniclostridium, Romboutsia and Treponema (P < 0.05) and markedly increased short-chain fatty acids concentrations (P < 0.001). Metabolomic analysis identified upregulated pathways, including D-amino acid metabolism and Neuroactive ligand-receptor interaction. Furthermore, comparative analyses pinpointed five critical microbial taxa (e.g., vadinBE97, Lachnospiraceae_UCG-008) and 18 key metabolites (e.g., 15-Deoxyprostaglandin J2, Lasalocid A) associated with these effects. In conclusion, Lactobacillus fermentum supplementation improved yak growth performance and mitigates metabolic risks linked to excessive energy intake. These findings provided a theoretical foundation for optimizing yak feeding strategies and advancing precision nutrition in ruminant production.

Hexi cattle are a local cattle population endemic to the Hexi Corridor in Gansu Province, China, and exhibit strong adaptability to the region's arid continental environment. However, comprehensive genomic investigations of this population are still lacking. In the present study, we integrated population genomic analyses with a genome-wide association study (GWAS) to dissect the genetic architecture of Hexi cattle. Whole-genome resequencing data were generated for 264 Hexi cattle, and public genomic datasets from six representative cattle breeds were obtained from the NCBI database for comparative analysis. Multiple analytical approaches-including principal component analysis (PCA), linkage disequilibrium (LD) decay analysis, neighbor-joining (NJ) phylogenetic tree construction, and ADMIXTURE analysis-were adopted to evaluate population structure and evolutionary relationships. A mixed linear model was then used to identify significant SNPs associated with five major body conformation traits in six-month-old cattle: body weight (BW), withers height (WH), hip height (HH), heart girth (HG), and abdominal girth (AG). Our results confirm the admixed nature of Hexi cattle, whose genome is derived primarily from Simmental cattle and secondarily from Mongolian cattle. A total of 69 trait-associated significant SNPs were identified and functionally annotated. Specifically, TBC1D31, DERL1 and MCPH1 were linked to BW; FSCN3 and PLBD1 to WH; MCPH1 to HH; NPAS3, TBC1D31, DERL1 and MCPH1 to HG; and SOX5, NTAQ1, FAM83A, TBC1D31, DERL1, CDH11, CPLX4 and ADAM18 to AG. This study deepens our understanding of the genetic basis of growth traits in Hexi cattle and offers valuable molecular resources for future selective breeding, genetic improvement, and long-term conservation of this indigenous cattle population.

We investigated the expression profiles and functions of CircRNAs in the longissimus dorsi muscle of Datong yaks at different developmental stages, with the aim of clarifying their regulatory roles in skeletal muscle development. Samples of longissimus dorsi muscle were collected from Datong yaks at three developmental stages: 90-day-old fetuses, 6-month-old juveniles, and 3-year-old adults. High-throughput RNA sequencing was performed to identify CircRNAs. Differential expression analysis, along with GO and KEGG enrichment analyses, was conducted. A competing endogenous RNA (ceRNA) regulatory network was subsequently constructed to screen for core CircRNAs. A total of 17,027 CircRNAs were identified, with 6821 being differentially expressed. These differentially expressed CircRNAs showed significant enrichment in skeletal muscle development-related functions, such as sarcomere and calcium ion homeostasis, and were involved in key pathways, including the FoxO (Forkhead box O) and calcium signaling pathways. Construction of the ceRNA network revealed 20 core CircRNAs (e.g., CircRNA_10402 and CircRNA_15445), which may modulate the expression of 84 mRNAs by competing for binding with 42 miRNAs. This study preliminarily reveals the dynamic regulatory network of CircRNAs during skeletal muscle development in Datong yaks, providing new theoretical insights for understanding the molecular mechanisms underlying yak muscle development and for molecular breeding.

High-altitude ruminants face environmental stressors such as low temperature, hypoxia, and short grazing seasons, which challenge energy acquisition and nutrient absorption. The gastrointestinal tract (GIT) plays a central role in metabolic adaptation. In this study, we collected contents from the rumen, reticulum, omasum, abomasum, duodenum, jejunum, cecum, and rectum of Pamir yaks. Microbial composition and metabolic functions across GIT regions were investigated through volatile fatty acid (VFA) determination and 16S rRNA gene sequencing. The results showed that the total VFA concentrations were highest in the forestomach and lowest in the small intestine, with the hindgut showing intermediate levels. Microbial diversity was highest in the reticulum and lowest in the jejunum. At the phylum level, Firmicutes, Bacteroidota, and Proteobacteria were the dominant bacterial taxa. At the genus level, Prevotella, Rikenellaceae_RC9_gut_group, UCG-005, Muribaculaceae, and Christensenellaceae_R-7_group were the predominant genera. Functional predictions revealed that the forestomach exhibited a notable enrichment in metabolic pathways associated with carbohydrate, amino acid, and nucleotide metabolism. In contrast, the abomasum and small intestine showed significant enrichment in pathways related to nucleotide and nucleotide-sugar metabolism, protein synthesis, and DNA repair. The hindgut demonstrated enrichment in butyrate metabolism and immune-related pathways. This study highlights the spatial heterogeneity of VFAs, microbial communities, and functional potentials in the GIT, providing theoretical insights into the adaptive mechanisms of energy metabolism in high-altitude ruminants.IMPORTANCEThis study systematically characterized microbial community composition and volatile fatty acid (VFA) metabolic profiles across different segments of the gastrointestinal tract in plateau ruminants. The results revealed potential metabolic adaptation strategies to extreme conditions such as hypoxia, low temperature, and limited forage availability. The forestomach was identified as the primary site of energy acquisition and showed a marked enrichment of VFA-producing bacteria. Microbial diversity in the small intestine was relatively low, but metabolic pathways associated with nutrient absorption remained highly active. The hindgut exhibited distinct microbial colonization patterns and signs of potential metabolic compensation. Collectively, these findings provided important theoretical insights into nutritional regulation, ecological adaptation, and microecological intervention strategies in plateau ruminants. They also filled a critical gap in high-altitude animal microbiome research and offer significant scientific and practical implications.

Average daily gain (ADG) is a core quantitative trait determining the economic benefits of Ashidan yak, a polled new breed adapted to cold barn feeding on the Qinghai-Tibet Plateau. Unraveling its complex genetic architecture is crucial for early molecular breeding selection. In this study, high-depth whole-genome resequencing (WGS) data from 474 Ashidan yaks were used to conduct combined evaluation of genome-wide association study (GWAS) and genomic selection (GS). During GWAS analysis, sex and measurement batch were included as fixed effects, while birth weight and principal components (PC1-PC3) were incorporated as covariates. Multi-model association analysis using GLM, MLM, and FarmCPU was performed on 3.36 million LD-pruned SNPs. The genomic inflation factors (λ ≈ 1.0) for MLM and FarmCPU confirmed effective elimination of population stratification. A total of 11 genome-wide significant SNP loci and 7 key candidate genes including PDE10A, RAD51B, BCAS3 and KCNH8 were identified via the FarmCPU model. Functional enrichment analysis indicated that these gene clusters are significantly involved in cAMP signaling pathway, regulation of ion channel activity, as well as extracellular matrix remodeling of blood vessels and skeletal muscle cells. For genomic selection, a single-trait GBLUP model was constructed using 22.87 million high-density raw SNPs to fully capture polygenic minor effects. Moderately high narrow-sense genomic heritability of ADG was estimated at h2 = 0.3233 (p < 0.05). The average independent prediction accuracy across the 10-fold cross-validation reached an average of R = 0.14 ± 0.07. To evaluate marker prioritized genomic evaluation without data leakage, a strict 10-fold cross-validation scheme was implemented, where the top 1% high-priority variant set (~228,000 SNPs) was screened independently within each training fold. The resulting unbiased prediction accuracy reached R = 0.1328 ± 0.1566 (with an average RMSE of 0.3793 ± 0.0066 and a regression slope of 0.4183 ± 0.5055). Comparing this with the unselected whole-genome baseline (R = 0.14 ± 0.07) indicates that naive marker selection based solely on GBLUP effect size in small reference cohorts is influenced by sampling variance, highlighting the need to integrate multi-omics functional annotations for future custom breeding array development. This study provides quantitative insights into the polygenic architecture of ADG in yaks, offering baseline data for genomic selection and custom array development for indigenous livestock on the Qinghai-Tibet Plateau.

In livestock, understanding the genetic basis of adaptation to the environment is essential for enhancing resilience to climate change and sustaining productivity in diverse environments. Indigenous Ethiopian cattle represent an ideal model for such studies, as they have evolved across a wide range of environments from the cool, oxygen-limited highlands to the hot, pathogen-rich lowlands. These environmental gradients imposed intense selective pressures, shaping their genomic landscape. In this study, we performed the first comprehensive analysis of X-linked adaptive signatures in Ethiopian indigenous cattle using whole-genome sequencing data. Population structure analysis revealed clear genetic differentiations between Abigar and Barka cattle, while the remaining populations showed substantial shared ancestry and admixtures. Pairwise fixation index ( F_ST) estimates, runs of homozygosity (ROH) patterns, and linkage disequilibrium (LD) decay further supported historical isolation and stronger selection pressure in Barka, contrasting with the greater diversity and faster LD decay in Gojjam Highland cattle. Complementary selection signature detections ( F_ST , XP-EHH, and iHS ) revealed population-specific and shared genomic regions under selection on the X chromosome. Notably, signals associated with high-altitude adaptation were detected near the RBM3, RPS4X, and TSC22D3 loci. Additional signals were observed in genes related to thermoregulation and oxidative stress response (EDA, SUV39H1, and HDAC8), as well as immune regulation (IRAK1, BDA20, and IL1RAPL1), suggesting adaptation to hot and pathogen-rich environments. Functional enrichment analysis highlighted genes involved in extracellular matrix organization and immune signaling pathways, underscoring their roles in environmental adaptation. This study provides the first genome-wide evidence of X-linked adaptive divergence in the Ethiopian cattle. The findings highlight the contribution of the X chromosome to heat tolerance, hypoxia adaptation, and immune resilience, offering valuable genomic insights for breeding programs aimed at enhancing productivity and climate adaptability in tropical cattle.

Yaks (Bos grunniens), native to the high-altitude environments of the Qinghai-Tibet Plateau, are crucial livestock for local herders, providing milk, meat, and other resources. However, traditional grazing practices are becoming increasingly unsustainable due to overgrazing and land degradation. This study investigates the impact of different feeding systems on yak skeletal muscle development and meat quality, focusing on the role of long non-coding RNAs (lncRNAs) in regulating these processes. Using a multi-omics approach, we constructed a comprehensive competing endogenous RNA (ceRNA) network comprising lncRNAs, miRNAs, and mRNAs. Differentially expressed lncRNAs were identified and their regulatory functions assessed. We identified a total of 2,009 lncRNA transcripts in yak skeletal muscle. Differential expression analysis between grazing (Group G) and indoor-fed (Group HF) yaks revealed 157 differentially expressed lncRNAs (DElncs) (77 upregulated and 80 downregulated), 51 differentially expressed miRNAs (DEmiRs), and 1,003 differentially expressed mRNAs (DEMs). Functional enrichment analysis demonstrated that these differentially expressed transcripts were significantly enriched in energy metabolism and muscle development pathways, specifically AMPK, Insulin, and FoxO signaling. Based on these datasets, we constructed a muscle-specific ceRNA network. Notably, specific regulatory axes were identified, such as lncRNA TCONS_00010840 competing for miRNAs to regulate the expression of TRIM63, a key gene implicated in muscle atrophy and meat tenderness. Our findings suggest that intensive feeding modulates yak muscle growth and tenderness through IncRNA-mediated pathways involved in metabolic adaptation and extracellular matrix remodeling. The identified TCONS_00010840-miR − 30b − 5p- TRIM63 and TCONS_00013998-ADAMTS2 regulatory nodes represent potential molecular targets for improving yak meat quality. These results provide a theoretical framework for future functional studies into the molecular breeding of yaks.

The balance between grass and livestock has exacerbated the problem of high-quality development in the yak industry, and the nutritional regulation of enzyme preparations has become a research hotspot. The purpose of this study was to assess and contrast the effects of feeding with various concentrations of enzyme preparations of yaks, including the production performance, meat quality, fatty acid composition of the longissimus dorsi muscle, and gene expression. Adding 0.20% enzyme preparation to the diet can significantly increase the average daily gain (ADG), and reduce the dry matter intake (DMI) and feed conversion rate (FCR), but has no significant effect on the meat quality of yak. In addition, the liver transcriptome and muscle metabolize showed that the addition of enzyme preparations caused differential expression of fatty acid metabolism-related genes in the liver, which may affect the metabolism of fatty acids in the liver and thus alter the fatty acid composition in the longissimus dorsi muscle of yak. The results of this study emphasize that adding enzyme preparations can improve the production performance of yaks without affecting their meat quality, thereby enhancing the economic benefits of yak breeding.

This study investigates whether fecal microbiota transplantation (FMT) can alleviate gut microbiota dysbiosis induced by a high-fat diet (HFD) through modulation of fatty acid metabolism, competition for nutrients, production of short-chain fatty acids (SCFAs), and restoration of mucus layer integrity. To elucidate the mechanisms by which FMT regulates colonic microbial function and host metabolic responses, 80 male Bal b/c mice were randomly assigned to four experimental groups (n = 20 per group): Normal Diet Group (NDG), High-Fat Diet Group (HDG), Restrictive Diet Group (RDG), and HDG recipients of NDG-derived fecal microbiota (FMT group). The intervention lasted for 12 weeks, during which body weight was monitored biweekly. At the end of the experiment, tissue and fecal samples were collected to assess digestive enzyme activities, intestinal histomorphology, gene expression related to gut barrier function, and gut microbiota composition via 16S rRNA gene sequencing. Results showed that mice in the HDG exhibited significantly higher final body weight and greater weight gain compared to those in the NDG and RDG (p < 0.05). Notably, FMT treatment markedly attenuated HFD-induced weight gain (p < 0.05), reducing it to levels comparable with the NDG (p > 0.05). While HFD significantly elevated the activities of α-amylase and trypsin (p < 0.05), FMT supplementation effectively suppressed these enzymatic activities (p < 0.05). Moreover, FMT ameliorated HFD-induced intestinal architectural damage, as evidenced by significant increases in villus height and the villus height-to-crypt depth ratio (V/C) (p < 0.05). At the molecular level, FMT significantly downregulated the expression of pro-inflammatory cytokines (IL-1β, IL-1α, TNF-α) and upregulated key tight junction proteins (Occludin, Claudin-1, ZO-1) and mucin-2 (MUC2) relative to the HDG (p < 0.05). 16S rRNA analysis demonstrated that FMT substantially increased the abundance of beneficial genera such as Lactobacillus and Bifidobacterium while reducing opportunistic pathogens including Romboutsia (p < 0.05). Furthermore, alpha diversity indices (Chao1 and ACE) were significantly higher in the FMT group than in all other groups (p < 0.05), indicating enhanced microbial richness and community stability. Functional prediction using PICRUSt2 revealed that FMT-enriched metabolic pathways (particularly those associated with SCFA production) and enhanced gut barrier-related functions. Collectively, this study deepens our understanding of host–microbe interactions under HFD-induced metabolic stress and provides mechanistic insights into how FMT restores gut homeostasis, highlighting its potential as a therapeutic strategy for diet-induced dysbiosis and associated metabolic disorders.

Yaks (Bos grunniens) have evolved distinctive metabolic adaptations that enable survival under the prolonged cold and nutrient-deficient conditions of the Qinghai-Tibetan Plateau. Adipose tissue plays a pivotal role in maintaining energy homeostasis. The proliferation and differentiation of preadipocytes are critical for the development of adipose tissue in bovines. MicroRNAs (miRNAs) are small regulatory molecules that participate in many cell biological processes, including development, differentiation, apoptosis, and metabolism. However, the expression profiles and functional roles of miRNAs in yak lipid metabolism remain largely unknown. To elucidate the molecular mechanisms underlying yak adipogenesis, we performed miRNA sequencing during yak preadipocyte differentiation and identified stage-specific expression profiles. Data analysis indicated that 252 (day 12 vs day 0), 167 (day 12 vs day 2), and 103 (day 2 vs day 0) miRNAs were differentially expressed in three stages, respectively. Further analysis identified 13 differentially co-expressed miRNAs across the three stages. Among the differentially co-expressed miRNAs, bta-miR-181a_R-1 was markedly upregulated during adipogenic differentiation. Functional assays revealed that bta-miR-181a_R-1 dramatically increased triglyceride accumulation and the expression of adipogenic marker genes (PPARγ, FABP4, and C/EBPα, P < 0.05), whereas it did not significantly affect preadipocyte proliferation. Mechanistically, bta-miR-181a_R-1 directly targeted sirtuin 1 (SIRT1), resulting in enhanced acetylation of forkhead box O1 (FoxO1) and promotion of lipid deposition via the FoxO signaling pathway. These findings reveal a novel miR-181a_R-1/SIRT1/FoxO1 regulatory axis that promotes yak adipocyte differentiation, providing new insights into miRNA-mediated adipogenesis in ruminants and a potential molecular basis for improving fat deposition in high-altitude livestock.

Fast-twitch and slow-twitch muscle fibers not only differ in metabolic characteristics and physiological functions but also significantly influence the texture of livestock meat. RNA editing represents an important post-transcriptional regulatory process that can influence both gene expression and the resulting protein function. However, studies on RNA editing events in yak muscle remain limited. This study systematically identified RNA editing events in yak biceps femoris (BF, n = 3) and obliquus externus abdominis (OEA, n = 3) using transcriptomic data, discovering 17,713 unique editing sites, most located in non-coding regions. Within coding regions, 3350 sites were detected, with 1195 resulting in non-synonymous amino acid substitutions. Further analysis revealed that 785 sites potentially affected miRNA binding sites, suggesting RNA editing may participate in miRNA-mediated gene regulation. Tukey’s post hoc test (p < 0.05) identified 242 sites (involving 170 genes) with significantly different editing levels between BF and OEA. KEGG pathway analysis indicated that genes with differential RNA editing were predominantly associated with pathways involved in muscle fiber type transitions, including the MAPK and calcium signaling pathways. Collectively, this study maps the RNA editing landscape in yak muscle tissue and identifies distinct, fiber-type-specific RNA editing patterns between oxidative and glycolytic muscle fibers, including differences in editing levels and site distributions, supporting a potential association between RNA editing and muscle fiber type transformation.

Yak milk is recognized for its superior nutritional quality, yet the biological basis underlying its high milk protein content remains poorly understood, particularly the regulatory mechanism of the small intestine. This study compared the major nutrients and AA composition of raw milk among yaks, cattle-yaks, and cows, revealing the characteristics of high protein and rich AA in yak milk. We annotated 16 major cell types from a total of 27,026 cells by constructing the first single-cell transcriptome atlas of yak small intestine. Among them, intestinal stem cells and tuft cells exhibited strong proliferation and differentiation potential, contributing to the maintenance of efficient protein absorption. Our multistrategy GWAS framework, by integrating genomics and single-cell RNA sequencing data, further identified candidate genes associated with milk protein content (SCP2, ETV6, ACSS2, and WWOX), which are mainly involved in AA utilization and energy regulation. Notably, WWOX was consistently identified across multiple analyses. It may enhance protein absorption efficiency in the small intestine, thereby providing sufficient substrates for milk protein synthesis and ultimately increasing milk protein content in yaks. In summary, these findings demonstrate that functional specialization of the small intestine contributes to enhanced milk protein content in yaks and highlight the importance of integrating phenotypic, cellular, and genetic data to understand complex traits. This work provides a novel perspective on the regulation of milk protein and offers potential targets for genetic improvement of milk quality in yaks and other ruminants.

Cattle have evolved genetic adaptations to a diverse range of agroecological zones, such as plateaus and arid zones. However, little is known about its genetic basis of adaptation to harsh environments within a short period of time after domestication. Here, we analyzed whole-genome sequence data from three indigenous cattle breeds (Anxi, Qaidam and Zhangmu) in northwest China and five worldwide cattle breeds (Angus, Holstein, Jersey, Gir and N’Dama) to explore their genetic composition and identify selective sweeps in the Chinese cattle breeds. Analyses of phylogenetic and population structure revealed that three indigenous cattle breeds share genomic components from Bos taurus and Bos indicus. A novel set of candidate genes was identified through comparative genomic analyses of cattle from contrasting environments based on SNP and copy number variation (CNV) data. These candidate genes are potentially associated with adaptive phenotypes, including high-altitude adaptability (e.g., ANGPT1, PPARGC1A, RORA), cold climate adaptation (e.g., TSHR, PRKG, OXCT1), and dryland adaptation (e.g., PLEKHA7, NFATC1, PLCB1). This study unravels the unique adaptive diversity of three Chinese indigenous cattle breeds, providing a valuable resource for future research on sustainable livestock breeding strategies to response to climate change.

Body weight and withers height are critical indicators of growth in animals, influencing husbandry practices. In this study, we measured the body weight and withers height of Gannan yaks at different ages (0, 6, 18, 30, 42, 54, 66, and 78 months). Four nonlinear growth models (Logistic, Gompertz, von Bertalanffy, and Brody) were evaluated. The Brody model was identified as the best fit for both body weight and withers height. Females exhibited lower A values and higher K values than males, suggesting earlier onset of puberty. The absolute growth rate (AGR) for males ranged from 16.979 to 0.809 kg/month, while for females, it ranged from 7.202 to 0.588 kg/month. The relative growth rate (RGR) ranged from 74.00 to 0.18% for males and 27.12 to 0.25% for females. Regarding withers height, the AGR and RGR for males ranged from 3.749 to 0.0409 cm/month and 6.69 to 0.034%, respectively. For females, these values ranged from 3.765 to 0.0294 cm/month and 7.02 to 0.026%. Females exhibited fasterGA from birth to 78-months, while males had higher GA in withers height until 17 months, after which females surpassed malesA. Overall, males can achieve larger mature sizes, but females exhibited faster early GA.

The yak, an ideal model for studying high-altitude hypoxia adaptation, possesses unique gastrointestinal tract (GIT) adaptability. However, understanding of cellular-level mechanisms underlying host-metabolite-microbe within GIT that are crucial for growth in extreme environments remains significantly limited. Therefore, this study constructs the first comprehensive multi-tissue cellular atlas of the yak GIT, encompassing 54 distinct cell types. Cross-species and cross-tissue comparative analyses combined with large-scale population genetic data identify HNF4A and SREBF2 as GIT-specific transcription factors targeting the key gene MYO6, revealing unique transcriptional patterns and the significant influence of epithelial cells on yak body weight in GIT. Alongside the characterization of microorganisms and metabolites along the GIT, the important microorganism Bacillus infection has cell-type specificity, and affects the accumulation of key products such as Succinate and lactic acid through the interaction between different epithelial cell metabolic activities and microorganisms and the communication between different cell types (key receptors SLC27A5, PPARA), thereby affecting glycolysis and TCA cycle and other processes to strengthen the adaptability of yak GIT in extreme environments. This work provides novel insights into the unique gastrointestinal adaptations of yaks to extreme environments and holds significant implications for understanding precision breeding in yaks and mammal gastrointestinal responses to hypoxia.

Body weight (BW) is a crucial indicator of animal growth and development, significantly influencing animal husbandry practices. Previous research has identified several genes associated with BW in certain yak breeds. However, the genetic basis of BW in Gannan yaks has not been reported. In this study, 309 yaks from six breeds across five provinces in China were sampled. This collection included 247 54-month-old female Gannan yaks, along with 20 Xizang yaks, 15 Muli yaks, 10 Pamir yaks, 9 Bazhou yaks, and 8 Zhongdian yaks. Body weight measurements were recorded for the Gannan yaks. Initial analyses of runs of homozygosity (ROH), nucleotide diversity, and linkage disequilibrium (LD) decay among the six yak breeds revealed that Gannan yaks exhibited the lowest ROH, the highest nucleotide diversity, and the fastest LD decay, indicating rich genetic diversity. Subsequently, a genome-wide association study (GWAS) identified 19 BW-related genes in the Gannan yaks, with PMAIP1, GABBR1, LRPPRC, and PPP1R11 identified as key genes. Genome-wide scanning of Group 1 and Group 2 (detailed in section 2.4) identified 90 genes, and Gene Ontology (GO) analysis highlighted FGF2, SHH, and WNT11 as significantly associated with growth, development, and metabolism. Three overlapping genes were identified between GWAS and genome-wide scans. Further analyses, including nucleotide diversity, LD analysis of significant GWAS sites, allele frequency analysis, and SNP association studies, suggested that DRC1 and SELENOI are novel candidate genes for BW in Gannan yaks. These findings provide a molecular foundation for the genetic improvement of Gannan yaks.

Yaks are a rare and unique animal species inhabiting the Qinghai–Tibet Plateau; they are renowned for their remarkable ability to thrive in harsh environments. Milk-derived exosomes, tiny vesicles containing various biological molecules, play crucial roles in numerous pathological and physiological processes, including cell growth, development, and immune regulation. This study delved into the microRNA expression profiles of yak milk-derived exosomes collected from both high- and low-altitude populations using small RNA sequencing. These miRNAs were found to be implicated in pathways associated with mammary gland inflammation, virus infection regulation, and heat stress response. Functional enrichment analyses, utilizing GO and KEGG databases, revealed that the target genes of these differentially expressed miRNAs are enriched in signaling pathways crucial for Th17 cell differentiation and the Ras-MAPK signaling pathway. In conclusion, this research illuminates the adaptive mechanisms of yaks through the differential expression of miRNAs in their milk-derived exosomes across varying environmental conditions. These findings provide a valuable foundation for future investigations into yak resilience and the potential of milk-derived exosomes as tools for disease management and immune modulation.

Animal growth and development are regulated by the growth hormone receptor (GHR). To elucidate the transcriptional regulation mechanism of the yak GHR gene, we cloned its proximal promoter region and performed bioinformatic analyses. Deletion constructs were generated to produce fragments of the proximal promoter, and the fragment exhibiting the highest activity was identified using a dual-luciferase reporter assay system. Moreover, the functionality of the transcription factor binding sites was confirmed via site-directed mutagenesis and electrophoretic mobility shift assay (EMSA). Bioinformatics analysis revealed two transcriptional initiation sites were located in the upstream regulation region at positions - 277/ - 327 and - 1734/ - 1784 bp, and CpG islands were located at - 552/ - 654 and - 82/ - 289 bp upstream. We identified the - 160 to + 27 bp region as the minimal core promoter of the yak GHR gene. The transcription factor KLF5, which is involved in muscle growth and development, was predicted to bind the proximal minimum core promoter region of the GHR gene. Using site-directed mutagenesis and EMSA, we demonstrated that KLF5 is a critical transcription regulator of the GHR gene. Our findings establish a theoretical basis for investigating the regulatory mechanisms of GHR gene expression.

Fatty acid synthase (FAS) is a fundamental metabolic enzyme that catalyzes the synthesis of endogenous fatty acids; TACR3, also known as tachykinin receptor 3 or NK3R, is an important G-protein-coupled receptor that is primarily responsible for responding to neuropeptides such as neurokinin B (NKB) and plays a crucial role in embryonic development, organ formation, and cell differentiation. This study aimed to explore the association between the single-nucleotide polymorphisms (SNPs) of the FAS and TACR3 genes and the milk quality of Gannan yak and to determine them as potential molecular marker loci for the milk quality of yaks. The genotyping of 162 Gannan yaks was performed using liquid-phase chip technology. Association analyses were conducted between the obtained SNP loci genotypes and milk composition traits, including milk protein, casein, non-fat solids, and acidity. Comparative sequence analysis of two genes (FAS and TACR3) across multiple species revealed that the yak FAS gene exhibited the highest homology with Bos taurus and Bos indicus, while the yak TACR3 gene showed the greatest sequence similarity to Bos taurus. Hardy-Weinberg equilibrium tests were performed on four SNP loci, and the equilibrium indices of the four loci were 0.799, 0.368, 0.689, and 0.948 (p > 0.05), indicating that all of these loci are in Hardy-Weinberg equilibrium state. g.13,276T>C (FAS) was significantly correlated with lactose content traits (p < 0.05); g.74,382C>G (FAS) was significantly correlated with casein, protein, total solids, non-fat solids, and acidity traits (p < 0.05); g.40,529A>G (TACR3) was significantly correlated with protein, non-fat solids, citric acid, and acidity traits (p < 0.05). The influence of g.40,555C>T (TACR3) on these traits did not reach a significant level (p > 0.05). This study suggests that two genes can serve as potential candidate genes affecting the quality of Gannan yak milk, providing reference genes for improving the quality of Gannan yak milk.

The rumen is a critical organ that facilitates nutrient digestion in ruminant animals. However, the biological mechanisms by which rumen microbiota and its metabolites enable Lactobacillus to modulate rumen structure and maintain functional homeostasis under fattening feeding conditions remain poorly understood. In this study, 80 male Pamir yaks were selected, and a 170-day data collection phase was implemented. Correlation phenotypic data and multi-omics analyses (rumen microbial sequencing and rumen epithelial metabolomics) were conducted to investigate the regulatory effects of Lactobacillus supplementation on rumen microbiota and metabolic processes in a concentrate-based rearing yak model. The results demonstrated that feeding a high-energy diet may impair yak ruminal histomorphology, microbiota composition, and function while negatively modulating rumen microbiota–metabolic profiles associated with specific ruminal microbial communities and functions. Lactobacillus intervention treatment optimized the yak ruminal microbiome composition (mucous layer maturation was promoted, Prevotella and Ruminococcus abundance were reduced, and Fibrobacter and Muribaculaceae abundance were increased), thereby altering metabolite concentrations involved in various metabolic pathways under a high-energy feeding pattern (fatty acid metabolism pathways were upregulated). These alterations elucidated the beneficial impacts of the Lactobacillus supplementation strategy on yak ruminal health without compromising the high-energy intensive rearing pattern. Furthermore, the regulated ruminal microbiome metabolites may serve as potential biomarkers for future investigations into the functional impacts of Lactobacillus intervention treatment on healthy feeding strategies for yaks.