Whole genome resequencing revealed genomic variants and functional pathways related to adaptation in Indian yak populations

The present study aims to identify genomic variants through a whole genome sequencing (WGS) approach and uncover biological pathways associated with adaptation and fitness in Indian yak populations. A total of 30 samples (10 from each population) were included from Arunachali, Himachali and Ladakhi yak populations. WGS analysis revealed a total of 32171644, 27260825, and 32632460 SNPs and 4865254, 4429941, and 4847513 Indels in the Arunachali, Himachali, and Ladakhi yaks, respectively. Genes such as RYR2, SYNE2, BOLA, HF1, and the novel transcript ENSBGRG00000011079 were found to have the maximum number of high impact variants in all three yak populations, and might play a major role in local adaptation. Functional enrichment analysis of genes harboring high impact SNPs revealed overrepresented pathways related to response to stress, immune system regulation, and high-altitude adaptation. This study provides comprehensive information about genomic variants and their annotation in Indian yak populations, thus would serve as a data resource for researchers working on the yaks. Furthermore, it could be well exploited for better yak conservation strategies by estimating population genetics parameters viz., effective population size, inbreeding, and observed and expected heterozygosity.

A comprehensive study on the longissius dorsi muscle of Ashdan yaks under different feeding regimes based on transcriptomic and metabolomic analyses

Yak is an important dominant livestock species at high altitude, and the growth performance of yak has obvious differences under different feeding methods. This experiment was conducted to compare the effects of different feeding practices on growth performance and meat quality of yaks through combined transcriptomic and metabolomic analyses. In terms of yak growth performance, compared with traditional grazing, in-house feeding can significantly improve the average daily weight gain, carcass weight and net meat weight of yaks; in terms of yak meat quality, in-house feeding can effectively improve the quality of yak meat. A combined transcriptomic and metabolomic analysis revealed 31 co-enriched pathways, among which arginine metabolism, proline metabolism and glycerophospholipid metabolism may be involved in the development of the longissimus dorsi muscle of yak and the regulation of meat quality-related traits. The experimental results increased our understanding of yak meat quality and provided data materials for subsequent deep excavation of the mechanism of yak meat quality.

Targeted and untargeted metabolomics reveals meat quality in grazing yak during different phenology periods on the Qinghai-Tibetan Plateau

Yak meat is more popular among consumers because of its high nutritional value, but little attention has been paid to its meat quality, which is affected by different phenology periods grass. We hypothesized that seasonal variations in grass composition influenced the ruminal bacteria community, and eventually affected the meat quality of yaks. This study aims to investigate the relationship of meat quality in grazing yak as well as the key rumen bacteria using targeted and untargeted metabolomics and 16S rRNA during different phenology periods. The main three altered metabolic pathways in grazing yak, including amino acids biosynthesis, glutathione metabolism, and fatty acids biosynthesis, were found in the grass period (GP) group compared to the regreen period (RP) and hay period (HP) groups. The GP group had higher concentrations of flavor amino acids (FAA), polyunsaturated fatty acids (PUFA), and a lower ratio of n-6/n-3 compared with the RP group. Correlation analysis results showed that Rikenellaceae_RC9_gut_group was positively correlated with fatty acids and lipid metabolites, which might be involved in lipid metabolism. Pediococcus had a positive correlation with biological peptides, which could be involved in the metabolism of bioactive compounds. In conclusion, grass in different phenology periods was associated with modified amino acids and fatty acids composition of yak meat as well as altered regulation of biological pathways, which was correlated with changes in rumen bacterial communities.

DEFB114 protein enhances host resistance to fungal infection through the NOD1/2-ATG16L1-NF-κB signaling pathway

The overuse of antibiotics has led to the enhanced resistance of many pathogenic bacteria, posing a threat to human health. Therefore, there is a need to develop green and safe alternatives to antibiotics. Beta-defensins play a crucial role in host defense against pathogens and have multifunctional properties, exerting key roles in innate and adaptive immunity, as well as non-immune processes. In this study, a 210 bp long cDNA sequence of yak DEFB114 gene was amplified and successfully expressed in a prokaryotic system. The DEFB114 protein exhibited significant inhibitory effects on the growth of Aspergillus fumigatus in vitro. When co-cultured with yak macrophages, DEFB114 protein enhanced macrophage phagocytic activity and increased nucleic acid fluorescence intensity (P < 0.05). DEFB114 protein also enhanced the activity of yak macrophages stimulated by inactivated Aspergillus fumigatus spores, increased the release of nitric oxide (NO), and promoted the expression of genes such as γ-actin, Lgals, Man2b, and Capg (P < 0.05). In mice experiments, DEFB114 protein promoted resistance against Aspergillus fumigatus infection, by regulating the NOD1/2-ATG16L1-NF-κB pathway to modulate the host immune response and exert its anti-infective effects. In summary, the yak DEFB114 protein could inhibit the growth of Aspergillus fumigatus and enhance the animal's resistance to pathogenic microorganisms, thereby having significant implications in the treatment and prevention of fungal infections.

Heme oxygenase 1 (HO1) regulates autophagy and apoptosis via the PI3K/AKT/mTOR signaling pathway of yak Sertoli cells

Successful male reproduction depends on healthy testes. Autophagy has been confirmed to be active during many cellular events associated with the testes. It is not only crucial for testicular spermatogenesis but is also an essential regulatory mechanism for Sertoli cell (SCs) ectoplasmic specialization integrity and normal function of the blood-testis-barrier. Hypoxic stress induces oxidative damage, apoptosis, and autophagy, negatively affecting the male reproductive system. Cryptorchidism is a common condition associated with infertility. Recent studies have demonstrated that hypoxia-induced miRNAs and their transcription factors are highly expressed in the testicular tissue of infertile patients. Heme oxygenase 1 (HO1) is a heat-shock protein family member associated with cellular antioxidant defense and anti-apoptotic functions. The present study found that the HO1 mRNA and protein are up-regulated in yak cryptorchidism compared to normal testes. Next, we investigated the expression of HO1 in the SCs exposed to hypoxic stress and characterized the expression of key molecules involved in autophagy and apoptosis. The results showed that hypoxic stress induced the upregulation of autophagy of SCs. The down-regulation of HO1 using siRNA increases autophagy and decreases apoptosis, while the over-expression of HO1 attenuates autophagy and increases apoptosis. Furthermore, HO1 regulates autophagy and apoptosis via the PI3K/AKT/mTOR signaling pathway. These results will be helpful for further understanding the regulatory mechanisms of HO1 in yak cryptorchidism.

Yak IGFBP3 promotes hepatocyte proliferation through PI3K-Akt signaling pathway

IGFBP3 (Insulin-like growth factor binding protein 3) constitutes a crucial constituent of the insulin-like growth factor (IGF), which are intimately associated with the organism's growth and development processes. Despite its significance, the precise function of IGFBP3 in yak liver development remains largely unexplored. In the present study, we systematically examined the expression profile of IGFBP3 in the liver tissues of yaks across various growth stages, elucidated its influence on the activity of yak hepatocytes, and probed its effects on murine liver development. A comparative analysis revealed that the expression of IGFBP3 was significantly higher in the liver tissue of 5-year-old yaks compared to their 15-month-old and 1-day-old counterparts (P < 0.01). To further validate its biological function, pET-28a-BgIGFBP3 prokaryotic expression vector was constructed. Upon exposing yak hepatocytes to varying concentrations of Bos grunniens (Bg) IGFBP3 protein, we observed augmented cellular activities and elevated colony formation rates. Moreover, our investigation revealed the upregulation of key genes within the PI3K-Akt signaling pathway, including ERBB2, IRS1, PIK3R1, AKT1, RAF1, MAP2K2, and MAPK3, in both yak hepatocyte cultures and murine models. These findings collectively indicate that BgIGFBP3 promotes the proliferation of yak hepatocytes and enhances murine liver development by modulating the PI3K-Akt signaling pathway. The functional relevance of BgIGFBP3 was substantiated through in vivo and in vitro experiments, thereby underscoring its potential as a regulatory factor in liver development processes.

Yak genome database: a multi-omics analysis platform

BACKGROUND

The yak (Bos grunniens) is a large ruminant species that lives in high-altitude regions and exhibits excellent adaptation to the plateau environments. To further understand the genetic characteristics and adaptive mechanisms of yak, we have developed a multi-omics database of yak including genome, transcriptome, proteome, and DNA methylation data.

DESCRIPTION

The Yak Genome Database ( http://yakgenomics.com/ ) integrates the research results of genome, transcriptome, proteome, and DNA methylation, and provides an integrated platform for researchers to share and exchange omics data. The database contains 26,518 genes, 62 transcriptomes, 144,309 proteome spectra, and 22,478 methylation sites of yak. The genome module provides access to yak genome sequences, gene annotations and variant information. The transcriptome module offers transcriptome data from various tissues of yak and cattle strains at different developmental stages. The proteome module presents protein profiles from diverse yak organs. Additionally, the DNA methylation module shows the DNA methylation information at each base of the whole genome. Functions of data downloading and browsing, functional gene exploration, and experimental practice were available for the database.

CONCLUSION

This comprehensive database provides a valuable resource for further investigations on development, molecular mechanisms underlying high-altitude adaptation, and molecular breeding of yak.

Sodium acetate and sodium butyrate attenuate diarrhea in yak calves by regulating gut microbiota and metabolites

Diarrhea is a severe issue in calves that causes fertility problems and economic issues worldwide. Sodium acetate/sodium butyrate (SA/SB) alleviates diarrhea in mice; however, little information is available about the preventive effect of SA/SB on diarrheic yak calves living on the Tibet plateau. Yak calves (n = 19) of age ≥4 months and weight 37 ± 2 Kg were randomly divided into control (C, n = 10) and supplement groups (S, n = 9). Yaks belonging to the supplement group were given sodium butyrate (10 g/kg) and sodium acetate (5 g/kg) for 28 days, along with normal feed, seasonal grasses, pasture, and water. The blood and fecal samples from yak calves were collected for assessment of antioxidant capacity, inflammatory cytokines, microbiome, and short-chain fatty acids (SCFAs) concentration analysis. Results of this study revealed that a lower diarrhea rate, higher weight, and net weight gain were recorded in yaks belonging to group S supplemented with SA/SB. Similarly, increased antioxidant capacity with higher levels of T-AOC, SOD, and GSH-px and decreased inflammatory reactions by decreasing both TNF-α and IL-1β concentrations were recorded in yaks of group S. The concentration of SCFAs was significantly higher (p < 0.05) in yaks from group S than group C. Microbiome analysis revealed that 8 phyla and 54 genera were significantly different (p < 0.05) in both yak groups, with increased probiotics (Akkermansia, Oscillospira), SCFAs producing genera (Oscillospira, ASF356, Anaerosporobacter and Phascolarctobacterium), and decreased inflammatory related genus (Flavonifractor, Fournierella) and harmful bacteria (Oscillibacter, Achromobacter) in group S. In conclusion, the results demonstrated that SA and SB could decrease diarrhea rates in yak calves on the plateau via increasing antioxidant ability and SCFAs, while decreasing inflammatory responses in yaks by moderating gut microbiota. The current results provide new insights for the prevention and treatment of diarrhea in yaks.

Profiling and functional analysis of circular RNAs in yaks intramuscular fat

Circular RNAs (circRNAs) are a new class of endogenous RNA regulating gene expression. However, the regulatory mechanisms of lipid metabolism in yaks involved in circRNAs remain poorly understood. The IMF plays a crucial role in the quality of yak meat, to greatly improve the meat quality. In this study, the fatty acid profiles of yak IMF were determined and circRNAs were sequenced. The results showed that the total of polyunsaturated fatty acid (PUFA) content of adult yak muscle was significantly higher than that in yak calves (p < 0.05). A total of 29,021 circRNAs were identified in IMF tissue, notably, 99 differentially expressed (DE) circRNAs were identified, to be associated with fat deposition, the most significant of which were circ_12686, circ_6918, circ_3582, ci_106 and ci_123 (A circRNA composed of exons is labelled 'circRNA' and a circRNA composed of introns is labelled 'ciRNA'). KEGG pathway enrichment analysis showed that the differential circRNAs were enriched in four pathways associated with fat deposition (e.g., the peroxisome proliferator-activated receptor signalling, fatty acid degradation, sphingolipid metabolism and sphingolipid signalling pathways). We also constructed co-expression networks of DE circRNA-miRNA using high-throughput sequencing in IMF deposition, from which revealed that ci_106 target binding of bta-miR-130b, bta-miR-148a, bta-miR-15a, bta-miR-34a, bta-miR-130a, bta-miR-17-5p and ci_123 target binding of bta-miR-150 were involved in adipogenesis. The study revealed the role of the circRNAs in the IMF deposition in yak and its influence on meat quality the findings demonstrated the circRNA differences in the development of IMF with the increase of age, thus providing a theoretical basis for further research on the molecular mechanism of IMF deposition in yaks.

DNA methylation dynamics during yak adipocyte differentiation

In mammals, epigenetic modifications involving DNA methylation are necessary for the completion of the cell differentiation process. However, the global DNA methylation landscape and its dynamics during yak adipocyte differentiation remain unexplored. Here, we performed whole-genome bisulfite sequencing (WGBS) to asses DNA methylation in yak preadipocytes and adipocytes, combining these results with those of our previous studies on changes in chromatin accessibility and gene expression during yak adipogenesis. The results showed that CG methylation levels were lower in promoter than in exon and intron, and gradually decreasing from the distal regions to transcription start site (TSS). There was a significant negative correlation between CG methylation levels located in promoter and gene expression levels. The 46 genes shared by CG differentially methylated regions (DMRs) and differential chromatin accessibility were significantly enriched in Hedgehog and PI3K-Akt signaling pathways. ATAC-seq peaks with high chromatin accessibility located in both promoter (≤ 2 kb from TSS) and distal (> 2 kb from TSS) regions corresponded to low methylation levels. Taken together, these findings demonstrated that DNA methylation and its interactions with chromatin accessibility regulate gene expression during yak adipocyte differentiation, contributing to the understanding of mechanisms of various epigenetic modifications and their interactions in adipogenesis.

Identification of circRNA-associated ceRNA networks in the longissimus dorsi of yak under different feeding systems

BACKGROUND

Yaks (Bos grunniens), prized for their ability to thrive in high-altitude environments, are indispensable livestock in the plateau region. Modifying their feeding systems holds significant promise for improving their growth and meat quality. Tenderness, a key determinant of yak meat quality and consumer appeal, is demonstrably influenced by dietary regimen. Indoor feeding regimes have been shown to enhance tenderness by lowering shear stress and optimizing pH values. CircRNAs, well-known modulators of circulatory function, also play a crucial role in skeletal muscle development across various animal species. However, their functional significance in yak skeletal muscle remains largely unexplored.

RESULTS

In this study, we identified a total of 5,534 circRNAs within the longissimus dorsi muscle, and we found 51 differentially expressed circRNAs (20 up-regulated and 31 down-regulated) between the two feeding groups. Constructing a comprehensive ceRNA network illuminated intricate regulatory mechanisms, with PGP and circRNA_0617 converging on bta-miR-2285q, mirrored by KLF15/circRNA_0345/bta-miR-20b and CTSF/circRNA_0348/bta-miR-146a. These findings shed light on the potential of circRNAs to influence yak muscle development and meat quality, offering valuable insights for future research.

CONCLUSIONS

This investigation unraveled a complex interaction network between circRNAs、mRNAs and miRNAs in yak skeletal muscle. We further elucidated the target genes regulated by these target genes within the network, offering valuable insights into the potential regulatory mechanisms governing muscle development and meat quality-related traits in yaks.

A dynamic individual yak heifer live body weight estimation method using the YOLOv8 network and body parameter detection algorithm

Live body weight (LBW) is one of the most important parameters for supervising the growth and development of livestock. The yak (Bos grunniens) is a special species of cattle that lives on the Qinghai-Tibetan Plateau. Yaks are more untamed than regular cattle breeds, thus it is more challenging to measure their LBW. In this study, a YOLOv8 yak detection and LBW estimation models were used to automatically estimate yak LBW in real-time. First, the proper posture (normal posture) and individual yak identification was confirmed and then the YOLOv8 detection model was used for LBW estimation from 2-dimensional (2D) images. Yak LBW was estimated through yak body parameter extraction and a simple linear regression between the estimated yak LBW and the actual measured yak LBW. The results showed that the overall detection performance of yak normal yak posture was described by precision, recall, and mean Average Precision 50 (mAP50) indicators, reaching 81.8, 86.0, and 90.6%, respectively. The best yak identification results were represented by precision, recall, and mAP50 values of 97.8, 96.4, and 99.0%, respectively. The yak LBW estimation model achieved better results for the 12 mo old yaks with shorter hair with R2, root mean square error (RMSE), mean absolute percentage error (MAPE), and Multiple R values of 0.96, 2.43 kg, 1.69%, and 0.98, respectively. The results demonstrate that yak LBW can be estimated and monitored in real-time using this approach. This study has the potential to be used for daily yak LBW monitoring in an unstressed manner and to save considerable labor resources for large-scale livestock farms. In the future, to reduce the limitations caused by the impacts of yak hair and light condition data sets of dairy cows and yaks of different ages will be used to improve and generalize the model.

Transcriptomics and metabolomics of blood, urine and ovarian follicular fluid of yak at induced estrus stage

To gain a deeper understanding of the metabolic differences within and outside the body, as well as changes in transcription levels following estrus in yaks, we conducted transcriptome and metabolome analyses on female yaks in both estrus and non-estrus states. The metabolome analysis identified 114, 13, and 91 distinct metabolites in urine, blood, and follicular fluid, respectively. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis highlighted an enrichment of pathways related to amino acid and lipid metabolism across all three body fluids. Our transcriptome analysis revealed 122 differentially expressed genes within microRNA (miRNA) and 640 within long non-coding RNA (lncRNA). Functional enrichment analysis of lncRNA and miRNA indicated their involvement in cell signaling, disease resistance, and immunity pathways. We constructed a regulatory network composed of 10 lncRNAs, 4 miRNAs, and 30 mRNAs, based on the targeted regulation relationships of the differentially expressed genes. In conclusion, the accumulation of metabolites such as amino acids, steroids, and organic acids, along with the expression changes of key genes like miR-129 during yak estrus, provide initial insights into the estrus mechanism in yaks.

Do microbial-gut-muscle mediated by SCFAs, microbial-gut-brain axis mediated by insulin simultaneously regulate yak IMF deposition?

Ruminant rumen plays an important role in the digestibility of cellulose, hemicellulose, starch and fat. In this study, the yaks under graze and stall feeding were chosen as the models of different rumen bacteria and intramuscular fat (IMF). The characteristics of IMF deposition, serum indexes in yaks were detected; the bacteria, metabolites in rumen was explored by 16S rRNA sequencing technology, untargeted metabolomics based on liquid chromatography-mass spectrometer and gas chromatography, respectively; the transcriptome of longissimus thoracis was identified by RNA-Sequencing analysis. Based on above results, a hypothesis that yak IMF deposition is regulated by the combined action of microbiome-gut-brain and muscle axis was proposed. The short-chain fatty acids (SCFAs) and neurotransmitters precursors like acetylcholine produced in yak rumen promoted insulin secretion via central nervous system. These insulin resulted in the high expression of SREBF1 gene by gut-brain axis; SCFAs can directly arrive to muscular tissue via blood circulation system, then activated the expression of PPARγ gene by gut-muscle axis. The expression of lipogenesis gene SCD, FABP3, CPT1, FASN and ACC2 was accordingly up-regulated. This study firstly introduce the theory of microbiome-gut-brain/muscle axis into the study of ruminant, and comprehensively expounded the regulatory mechanism of yak IMF deposition.

Differential metabolites screening in yak (Bos grunniens) seminal plasma after cryopreservation and the evaluation of the effect of galactose on post-thaw sperm motility

Sperm survival and activity depend on the provision of energy and nutrients from seminal plasma (SP). This study aimed to investigate the variations of metabolites within SP before and after freezing and subsequently explore the potential regulatory mechanisms affecting yak sperm cryodamage due to changes in metabolites in the SP. Untargeted metabolomics analysis was performed to screen for differential metabolites, followed by KEGG analysis to identify enriched signaling pathways. The combinatorial analysis of metabolomics and sperm proteomics revealed the influence of key SP metabolites on sperm proteins. Subsequently, the relevant differentially expressed proteins were verified by Western blot analysis. Finally, the mechanism underlying the positive effect of galactose on sperm motility was determined by assessing the change in ATP content in sperm before and after freezing and thawing. The data showed that a total of 425 and 269 metabolites were identified in the positive and negative ion modes, respectively. Freezing and thawing resulted in the up-regulation of 70 metabolites and the down-regulation of 29 metabolites in SP. The primary impact of freezing and thawing was observed in carbohydrate metabolism, including pyruvate metabolism, pentose phosphate pathway, galactose metabolism, the TCA cycle, and butanoate metabolism. In the combined analysis and Western blot results, a significant positive correlation was observed between galactose and Aldo-keto reductase family 1 member B1 (AKR1B1) (P < 0.05), which has the ability to convert galactose into galactol. Furthermore, the addition of galactose to thawed semen improved sperm motility by increasing AKR1B1 protein in sperm and was associated with the content of ATP. These data identify differential metabolites between fresh and frozen-thawed SP and suggest that galactose is a valuable additive for cryopreserved sperm, providing a theoretical basis for further exploration of the refrigerant formula for yak sperm cryopreservation.

Secondary Structure Analysis of Fasciola from Semi-wild Ruminants of Northeast India

PURPOSE

The objective of this study is to study the secondary structure analysis of Fasciola flukes from a rare mithun host from Manipur. Fascioliasis, a neglected tropical trematodiasis, is poorly studied in India and is widely believed to be predominantly caused by F. gigantica. Through this study, we want to assess the flukes from the rare semi-wild ruminants of Northeast India. This study is important as the mithun population is semi-wild and its population is declining in Manipur.

METHODS

Sample collected from the difficult and challenging terrain of Northeast India. The sample was collected from mithun and observed under the microscope. DNA was isolated, sequenced, and analyzed using various bioinformatics tools. The secondary structure analysis of the Internal Transcribed Spacer 2 (ITS2) region was also performed.

RESULTS

The secondary structure species tree corroborated the Bayesian inference and, hence, strengthened the phylogeny reconstructed. The annotated ITS2 sequence and RNA secondary of the Manipur isolate displayed the typical four-helix or four-domain model. Helix III reveals the presence of the UGGU motif with other deviations like UGG and GGU.

CONCLUSION

This is an in-depth analysis of the secondary structure of Fasciola species. The present study has demonstrated the usefulness of ITS2 and its secondary structures for characterizing parasites. The information on fascioliasis in the mithun's population presents itself useful with regards to their conservation strategy as their populations in both Manipur and Nagaland are dwindling.

Correlation between microbial characteristics and reproductive status of the yak uterus based on macrogenomic analysis

INTRODUCTION

This study aimed to investigate the microbial characteristics of yak uteri collected using intrauterine cotton swabs (CS) during different reproductive stages and the correlation of these microbial characteristics with reproductive status.

METHODS

We used a macrogenomic approach to analyze the functional aspects of different microorganisms in samples collected during the pre-estrus, estrus, late estrus, and diestrus stages.

RESULTS

The results revealed the presence of 1293 microbial genera and 3401 microbial species in the uteri of yaks at different reproductive stages. The dominant bacterial species varied across the different periods, with Micrococcus and Proteus being dominant during pre-estrus; Pseudomonas, Clostridium, Flavobacterium, Bacillus, and Staphylococcus during estrus; Acinetobacter, Bacillus and Proteus during late estrus; and Pseudomonas, Escherichia coli, and Proteus during diestrus.

DISCUSSION

The primary functions of these bacteria are enriched in various metabolic pathways, including carbohydrate and amino acid metabolism, intracellular transport and secretion, post-translational protein modification, and drug resistance. These findings suggest that the microbial diversity in the uterus of yaks plays a crucial role in reproductive regulation and can help prevent reproductive tract-related diseases.

Exploring the induction of endometrial epithelial cell apoptosis in clinical-type endometritis in yaks through the cyt-c/caspase-3 signaling axis

Endometritis is a significant contributor to reduced productivity in yaks in Tibet, China. The Cyt-c/Caspase-3 signaling axis plays a crucial role in the mitochondrial pathway that triggers cell apoptosis due to endogenous factors. In this study, we examined the endometrial epithelial tissue of yaks with endometritis using pathological examination, immunohistochemical analysis, TUNEL staining, qRT-PCR, and Western blot. The results indicated significant changes in the apoptotic factors of the Cyt-c/Caspase-3 signaling axis. The expression levels of Bak1, Bax, Cyt-c, Apaf-1, Caspase-9, and Caspase-3 were significantly increased (P < 0.05), while the expression level of Bcl-2 was significantly decreased. Immunohistochemistry results revealed significant increase in Bak1, Bax, Cyt-c, Apaf-1, Caspase-9, and Caspase-3 expression in the cytoplasm compared to the healthy group, except for Bcl-2, which showed a significant decrease. Pathological section analysis demonstrated that clinical endometritis in yaks led to structural damage, bleeding, congestion, and inflammatory cell infiltration in the endometrial epithelium. Our study findings indicated that clinical endometritis in yaks can modulate apoptosis of endometrial epithelial cells via the Cyt-c/Caspase-3 signaling pathway, resulting in different levels of damage. This research is pioneering in exploring cell apoptosis induced by clinical endometritis in yaks, offering novel insights and potential strategies for the future prevention and treatment of endometritis in yaks.

Metagenomic analysis for exploring the potential of Lactobacillus yoelii FYL1 to mitigate bacterial diarrhea and changes in the gut microbiota of juvenile yaks

Diarrhea in calves is a common disease that results in poor nutrient absorption, poor growth and early death which leads to productivity and economic losses. Therefore, it is important to explore the methods to reduce diarrhea in yak's calves. Efficacy of lactic acid bacteria (LAB) for improvement of bacterial diarrhea is well recognized. For this purpose, two different doses (107 CFU, 1011 CFU) of Lactobacillus yoelii FYL1 isolated from yaks were fed to juvenile yaks exposed to E. coli O78. After a trial period of ten days fresh feces and intestinal contents of the experimental yaks were collected and metagenomics sequencing was performed. It was found that feeding a high dose of Lactobacillus yoelii FYL1 decreased abundance of phylum Firmicutes in the E. coli O78 infected group whereas, it was high in animals fed low dose of Lactobacillu yoelii FYL1. Results also revealed that counts of bacteria from the family Oscillospiraceae, genus Synergistes and Megasphaera were higher in control group whereas, order Bifidobacteriales and family Bifidobacteriaceae were higher in infected group. It was observed that bacterial counts for Pseudoruminococcus were significantly (P < 0.05) higher in animals of group that were given high dose of Lactobacillus yoelii FYL1 (HLAB). Compared to infected group multiple beneficial bacterial genera such as Deinococus and Clostridium were found higher in the animals that were given a low dose of Lactobacillus yoelii FYL1 (LLAB). The abundance of pathogenic bacterial genera that included Parascardovia, Bacteroides and Methanobrevibacter was decreased (P < 0.05) in the lower dose treated group. The results of functional analysis revealed that animals of LLAB had a higher metabolism of terpenoids and polyketides compared to animals of infected group. Virus annotation also presented a significant inhibitory effect of LLAB on some viruses (P < 0.05). It was concluded that L. yoelii FYL1 had an improved effect on gut microbiota of young yaks infected with E. coli O78. This experiment contributes to establish the positive effects of LAB supplementation while treating diarrhea.

Antimicrobial activity of yak beta-defensin 116 against Staphylococcus aureus and its role in gut homeostasis

Staphylococcus aureus (S. aureus) is one of the most common food-borne poisoning microbial agent. However, the antimicrobial activity of β-defensin 116 in yak and its application in S. aureus-induced diarrheal disease have not been reported. In this study, 303 bp cDNA sequence of yak DEFB116 gene was obtained. In addition, the prokaryotic expression vector of DEFB116 protein with a molecular weight of 16 kDa was successfully constructed and expressed. The yak DEFB116 gene can encode 19 amino acids, the percentage of hydrophobic amino acids is 36 % and the total positive charge is 6, which has potential antibacterial potential. Sufficient DEFB116 protein concentration and time can destroy the integrity of the bacterial cell membrane, resulting in leakage of intracellular solutes and thus killing S. aureus. The intestinal histopathological features and the number of inflammatory cells were improved in the diarrhea mouse model under the action of DEFB116 protein. The decrease of goblet cells was reversed, the expression of mucoprotein was increased. DEFB116 protein increased the abundance of Lactobacillus johnsonii, Lactobacillus reuteri and Desulfovibrio, and inhibited the reproduction of pathogenic bacteria. These findings provide new insights into the potential future applications of yak β-defencins in the food industry and medical fields.

Single-cell RNA sequencing and UPHLC-MS/MS targeted metabolomics offer new insights into the etiological basis for male cattle-yak sterility

The variety of species can be efficiently increased by interspecific hybridization. However, because the males in the hybrid progeny are usually sterile, this heterosis cannot be employed when other cattle and yaks are hybridized. While some system-level studies have sought to explore the etiological basis for male cattle-yak sterility, no systematic cellular analyses of this phenomenon have yet been performed. Here, single-cell RNA sequencing and UPHLC-MS/MS targeted metabolomics methods were used to study the differences in testicular tissue between 4-year-old male yak and 4-year-old male cattle-yak, providing new and comprehensive insights into the causes of male cattle-yak sterility. Cattle-yak testes samples detected 6 somatic cell types and one mixed germ cell type. Comparisons of these cell types revealed the more significant differences in Sertoli cells (SCs) and [Leydig cells and myoid cells (LCs_MCs)] between yak and cattle-yak samples compared to other somatic cell clusters. Even though the LCs and MCs from yaks and cattle-yaks were derived from the differentiation of the same progenitor cells, a high degree of overlap between LCs and MCs was observed in yak samples. Still, only a small overlap between LCs and MCs was observed in cattle-yak samples. Functional enrichment analyses revealed that genes down-regulated in cattle-yak SCs were primarily enriched in biological activity, whereas up-regulated genes in these cells were enriched for apoptotic activity. Furthermore, the genes of up-regulated in LCs_MCs of cattle-yak were significantly enriched in enzyme inhibitor and molecular function inhibitor activity. On the other hand, the genes of down-regulated in these cells were enriched for signal receptor binding, molecular function regulation, positive regulation of biological processes, and regulation of cell communication activity. The most significant annotated differences between yak and cattle-yak LCs_MCs were associated with cell-to-cell communication. While yak LCs_MCs regulated spermatogenic cells at spermatogonia, spermatocyte, and spermatid levels, no such relationships were found between cattle-yak LCs_MCs and germ cells. This may suggest that the somatic niche in male cattle-yak testes is a microenvironment that is ultimately not favorable for spermatogenesis.

Transcriptomic analysis of yak longissimus dorsi muscle identifies genes associated with tenderness

Meat tenderness is an important sensory index when consumers choose meat products, which determines the value of meat products and consumers' buying intentions. Yak meat is rich in nutrition and unique in flavor, which is favored by consumers. However, its meat has the deficiencies of low tenderness and poor taste, which has a negative impact on the value of its meat products and customer satisfaction. To identify the genes affecting the yak meat tenderness, we used RNA-seq to analyze the longissimus dorsi muscle of yaks with different tenderness, screened a total of 1120 differentially expressed genes (DEGs). Meanwhile, 23 pathways were significantly enriched. By further analysis, we identified eight genes related to yak meat tenderness (WNT5A, ARID5B, SERPINE1 KLHL40, RUNX1, MAFF, RFX7 and ARID5A). Notably, SERPINE1 was involved in the significant enrichment pathways of 'complement and coagulation cascade pathway', 'HIF-1 signaling pathway' and 'AGE-RAGE signaling pathway in diabetic complications' which can regulate meat tenderness. This implies that SERPINE1 may play an important regulatory role among them. The DEGs associated with yak meat quality screened in this work will be helpful to identify potential biomarkers related to meat tenderness.

Differentially expressed transcripts study during pregnancy and postpartum anestrus of yak (Bos grunniens)

Background: Yak is the main livestock species in the plateau area, and its reproductive performance is low, usually two years or three years. A very few of yaks recover within a certain period of time after delivery and smoothly enter the next estrous cycle, while most of them enter the postpartum anestrus and show no estrus performance. However, the key biological factors and influencing mechanisms that cause postpartum anestrus in yaks are not clear. Objective: To study the expression of differential transcripts in ovaries of yak during pregnancy and postpartum anestrus. Methods: Each three yaks in pregnancy and anestrus under natural grazing conditions in Haiyan County, Qinghai Province were selected and slaughtered, and their ovaries were collected and sent to Biomarker Technologies. Oxford Nanopore Technologies single-molecule real-time electrical signal sequencing technology was used to perform full-length transcriptome sequencing. Astalavista software was used to identify the types of alternative splicing events in yak estrus and pregnancy, and TAPIS pipeline was used to identify alternative polyadenylation. Results: The results showed that there were 1751 differentially expressed transcripts (DETs) between pregnancy and anestrus in yak, of which 808 were upregulated and 943 were downregulated. GO analysis showed that the biological processes of DETs were mainly reproductive, reproductive and rhythmic processes. KEGG analysis showed that the DET cell junction-related adhesion junction protein (β-catenin) and amino terminal kinase (JNK) were involved in FAs (local adhesion). Phosphatidylinositol-3-kinase (PI3K) is involved in the PI3K/AKT/mTOR signaling pathway. Circadian rhythm output cycle failure (Clock) and brain and muscle tissue aromatic hydrocarbon receptor nuclear transporter-like protein 1 (Bmal1) are involved in circadian rhythm signaling pathway. Conclusion: This study found that β-catenin, JNK, PI3K, Clock and Bmal1 were closely related to postpartum anestrus in yak.

Quantitative proteomic analysis of cattle-yak and yak longissimus thoracis provides insights into the differential mechanisms of meat quality

In this study, proteins of cattle-yak longissimus thoracis (CYLT) and yak longissimus thoracis (YLT) were compared using tandem mass tag-labeled quantitative proteomic analysis. A total of 157 proteins were screened as differentially abundant proteins (DAPs) derived from 1551 quantitative proteins. Bioinformatics analysis revealed that the upregulated DAPs in CYLT were mainly involved in energy metabolism, oxidative stress, muscle fiber structure, and extracellular matrix (ECM), while the downregulated DAPs were mainly involved in energy metabolism and ECM function. The upregulated myoglobin, downregulation of NADH dehydrogenase, and upregulation of cytochrome oxidase indicated that CYLT initiates compensatory regulation in response to hypoxic high-altitude environments. Two differentially abundant myosins and five collagens suggested that CYLT and YLT may have distinct differences in the assembly structure of muscle fibers and connective tissue. These differences in energy metabolism and muscle structure will inevitably affect the postmortem physiology of "muscle to meat" and consequently the meat qualities. Therefore, our results will provide important clues to gain insight into the potential causes of meat quality differences between cattle-yak and yak based on high-altitude response.

Proteomic analysis of high and low-motility frozen-thawed spermatozoa in yak provides important insights into the molecular mechanisms underlying sperm cryodamage

Sperm cryodamage caused by cryopreservation limits the use of frozen yak spermatozoa in artificial insemination (AI). However, the proteomic changes involved in the cryodamage of yak spermatozoa have not been investigated to date. Therefore, this study aimed to identify proteins related to freezing tolerance. Tandem mass tag (TMT) were used in combination with liquid chromatography-tandem mass spectrometry (LC-MS/MS) for identifying differentially expressed proteins (DEPs) between high-motility (HM) and low-motility (LM) frozen-thawed yak spermatozoa. A total of 116 DEPs were identified (>1.5-fold, P < 0.05); of which, 104 proteins were upregulated in HM spermatozoa and 12 proteins were upregulated in LM spermatozoa. The results of functional annotation analysis revealed that the DEPs were mainly involved in metabolic processes. A total of 20 DEPs that were abundantly expressed in HM spermatozoa were strongly associated with carbohydrate metabolism. The results of KEGG analysis revealed that the DEPs were enriched in glycolysis/gluconeogenesis, PPAR signaling pathway, and Ras signaling pathway. In addition, many antioxidant enzymes such as superoxide dismutase (SOD1), peroxiredoxin-6 (PRDX6), and Parkinson disease protein 7 (PARK7) were upregulated in HM spermatozoa, suggesting that these enzymes affect the motility of spermatozoa by regulating the levels of reactive oxygen species (ROS) in frozen-thawed spermatozoa. Altogether, the findings of this study elucidate the mechanisms through which cryopreservation affects the movement of yak spermatozoa and offer a novel basis for refining freezing techniques and modifying cryopreservation extender components.

Transcriptomic analysis reveals differentially expressed genes and key immune pathways in the spleen of the yak (Bos grunniens) at different growth stage

Yak is one of the rare and unique cattle species on the Qinghai-Tibetan Plateau, which has strong adaptability to the extreme environment of the plateau. The spleens are important functional organs that enable animals to adapt to their external environment and are vital in the growth and development process. To further investigate changes in immune function during yak development, we compared the transcriptome profiles of spleen tissues among juvenile (1-day old), youth (15-months old), and prime (5-years old) yaks. Immunology of spleen development was evaluated based on histological analyses and global gene expression was examined by using RNA-sequencing (RNA-seq) technology. In this work, we found 6378 genes with significant differences between the spleen of juvenile yak and youth yak, with the largest difference between groups. There were 3144 genes with significant differences between the spleen of young yak and prime yak, with the smallest differences between groups. Further, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted for the functional annotation of these genes. GO and KEGG analysis showed that some of them were related to growth, disease, immune, and metabolism. However, the genetic mechanism underlying the adaptability of yak spleens at different ages to harsh plateau environments remains unknown. These findings are important for studying the mechanisms of spleen development in yaks of different age groups.

The potential mediation of hypoxia-inducible factor-1α in heat shock protein 27 translocations, caspase-3 and calpain activities and yak meat tenderness during postmortem aging

The present study aimed to characterize the influence of hypoxia-inducible factor-1α on heat shock protein 27 and cytochrome c translocation, yak meat microstructure destruction, and endogenous enzymes activities, refining the understanding of the tenderization process after slaughter. Postmortem yak longissimus thoracis et lumborum muscles were incubated with 0.9% saline or hypoxia-inducible factor-1α stabilizer dimethyloxaloylglycine at 4 °C for 6, 12, 24, 72, and 120 h. Results showed that hypoxia-inducible factor-1α activation promoted heat shock protein 27 migration and cytochrome c release, facilitating (P < 0.05) caspase-3 activity by mediating the heat shock protein 27/caspase-3 interaction but did not exert (P > 0.05) significant effects on the calpain-1 activity. Additionally, hypoxia-inducible factor-1α activation contributed to the mitochondrial apoptosis cascade, leading to a higher (P < 0.01) apoptosis rate. Therefore, these observations indicate that hypoxia-inducible factor-1α affects caspase-3 activity and tenderness of postmortem muscle through distinct regulatory mechanisms, possibly, in part, with heat shock protein 27 and cytochrome c mediation.

High genotype diversity and zoonotic potential of Enterocytozoon bieneusi in yaks (Bos grunniens) from Ganzi Tibetan Autonomous Prefecture, Sichuan Province

Enterocytozoon bieneusi is a common pathogen in humans and various animals, threatening the breeding industry and public health. However, there is limited information on the molecular characteristics of E. bieneusi in yaks, an economically important animal mainly domesticated in the Qinghai Tibet Plateau in China. In the present study, nested PCR targeting the ITS gene region was applied to investigate the positive rates and genetic diversity of E. bieneusi in 223 faecal samples of yaks from three locations in Ganzi Tibetan Autonomous Prefecture, Sichuan Province. The total positive rate of E. bieneusi was 23.8% (53/223). Significant differences in positive rates were identified among yaks from three locations (χ2 = 8.535, p = 0.014) and four age groups (χ2 = 17.259, p = 0.001), with the highest positive rates in yaks from Yajiang and aged < 6 months, respectively. Sequence analysis identified seven known (EbpC, LW1, LQ10, PigEBITS5, ESH-01, J and BEB4) and five novel (Ganzi1-5) ITS genotypes. Phylogenetic analysis showed eight genotypes (EbpC, LW1, LQ10, PigEBITS5, ESH-01, Ganzi1, Ganzi2 and Ganzi4) in group 1 and three genotypes (J, BEB4 and Ganzi3) in group 2, indicating high genotype diversity and zoonotic potential of E. bieneusi in yaks from Ganzi. Considering the increasing zoonotic genotypes in yaks in the present study compared with previous findings, interventions should be developed to reduce the potential transmission of E. bieneusi between humans and animals.

Molecular cloning and characterization of STC1 gene and its functional analyses in yak (Bos grunniens) cumulus granulosa cells

Cumulus granulosa cells (CGCs), an important type of ovarian somatic cells, carries out various functions related to oogenesis, follicular development, and steroidogenesis. Studying the biological mechanisms involved in the development and function of CGCs makes a great contribution to understanding the reproductive regulation in female animals. Stanniocalcin-1 (STC1) is an important Ca2+-regulated glycoprotein hormone that exhibits high expression levels in ovaries. In this study, we cloned the coding sequence of the yak STC1, predicted the structure of STC1 protein, detected the expression and localization of STC1 in yak ovaries, and analyzed the functions of STC1 in yak CGCs. The CDS (coding sequence) region of yak STC1 gene was found to be 744 bp and encoded 247 amino acids. Homology comparison revealed that STC1 protein was highly conserved among mammals. The STC1 mRNA displayed dynamic expression profiles in different stages of yak ovaries, and the highest expression was found in the follicular phase. Regarding localization, STC1 protein was widely distributed in various kinds of yak ovarian cells, including oocytes, mural granulosa cells, CGCs, and thecal cells. Repressing the expression of STC1 resulted in defective proliferation and survival of yak CGCs. In addition, knockdown the expression of STC1 repressed the secretion of progesterone and promoted the secretion of estrogen. Overexpression of STC1 partially rescued the proliferation of CGCs and resulted in opposite effects on the secretion of progesterone and estrogen. Several apoptosis and steroidogenesis-related genes, including BAX, BCL2, HSD3B1, HSD17B1, CYP11A1 and CYP17A1 showed altered expressions after repressing or increasing the expression of STC1 in yak CGCs. To the best of our knowledge, this study is the first to focus on the role of STC1 in yak CGCs, and the outcomes offer fresh insights into the mechanism governing yak reproduction.

Genome Analysis and Safety Assessment of Achromobacter marplatensis Strain YKS2 Strain Isolated from the Rumen of Yaks in China

Achromobacter marplatensis strain YKS2 isolated from the yak rumen has the feature of producing cellulose. This study aims to analyze the genome and safety of strain YKS2 in vivo, considering its future research and application prospects. The genome of strain YKS2 was sequenced and used for genomic in silico studies. The administration of strain YKS2 in three doses was carried out on mice for 3 days of oral and 7 days of clinical observation tests. The BW, FI, organ indices, gut microbiota, and histological appearances of organs and intestines, along with hematological parameters and serum biochemistry, were measured in mice. The chromosome size of strain YKS2 was 6,588,568 bp, with a GC content of 65.27%. The 6058 coding sequences of strain YKS2 without plasmid were predicted and annotated and have multiple functions. The mice in all groups were alive, with good mental states and functional activities. Compared with the control group, there was no significant difference in the three dose groups on BW, FI, hematological parameters (WBC, LYM, etc.), and serum biochemistry (ALB, ALT, etc.). No abnormalities were observed in the main visceral organs, intestinal tissue, and V/C value in groups. However, the IEL number of duodenum and gut microbiota diversity (Shannon's index) in the high-dose group was significantly higher than in the control group (p < 0.05). Besides, the low dose of strain YKS2 also significantly affected the bacterial abundance of Firmicutes, Actinobacteria, and desulphurizing Bacteroidetes at the phylum level. There was no significant effect at genus levels in groups. In conclusion, the study revealed the genome and potential functional genes of strain YKS2, which is beneficial to understanding the features of the A. marplatensis strain and proved strain YKS2 to be without acute toxicity to mice. However, a long-term feeding toxicity experiment in vivo should be performed to further ensure its potential application value strain in the animal industry.

Effects of vascular endothelial growth factor (VEGF) on the viability, apoptosis and steroidogenesis of yak (Bos grunniens) granulosa cells

Vascular endothelial growth factor (VEGF) is crucial for follicle development through the regulation of granulosa cell (GC) function in some mammals, but its mechanism is unclear in yak (Bos grunniens). Therefore, the objectives of this study were to investigate the effects of VEGF on the viability, apoptosis and steroidogenesis of yak GCs. First, we investigated the localization of VEGF and its receptor (VEGFR2) in yak ovaries by immunohistochemistry analysis and evaluated the effect of culture medium containing different VEGF concentrations and culture times on the viability of yak GCs by Cell Counting Kit-8. Then, optimal treatment with 20 ng/mL VEGF for 24 h was selected to analyze the effects of this compound on intracellular reactive oxygen species levels by DCFH-DA kit, cell cycle and apoptosis by flow cytometry, steroidogenesis by ELISA kit and the expression of the related genes by RT‒qPCR. The results showed that VEGF and VEGFR2 were highly coexpressed in GCs and theca cells. GCs cultured in medium containing 20 ng/mL VEGF for 24 h significantly improved cell viability, decreased ROS production, promoted the transition from G1 phase to S phase (P < 0.05), increased the expression of the CCND1 (P < 0.05), CCNE1, CDK2, CDK4, and PCNA genes (P < 0.01) and decreased the expression of the P53 gene (P < 0.05). This treatment significantly reduced GC apoptosis (P < 0.05) by promoting the expression of BCL2 and GDF9 (P < 0.01) and inhibiting the expression of BAX and CASPASE3 (P < 0.05). VEGF promoted progesterone secretion (P < 0.05) accompanied by increased expression of HSD3B, StAR and CYP11A1 (P < 0.05). Taken together, our findings highlight the beneficial influence exerted by VEGF in improving GC viability and reducing ROS production and the apoptosis rate through the modulation of related gene expression.

Identification and prevalence of fluke infection in yak and Tibetan sheep around Qinghai Lake, China

Liver flukes (Fasciola spp.) and rumen flukes (Paramphistomum spp.) are significant parasites in livestock worldwide, and Fasciola spp. are considered an important zoonotic parasite. To our knowledge, there are no reports on fluke species identification and epidemiological prevalence in yak and Tibetan sheep around Qinghai Lake, China. Therefore, this study aimed to identify the major fluke species and determine the prevalence of fluke infections among yak and Tibetan sheep in this area. A total of 307 fecal samples were collected and fluke eggs identified using morphology and molecular methods. Our study is the first to display that the predominant fluke species were F. hepatica and P. leydeni in yak and Tibetan sheep around Qinghai Lake. The overall prevalence of fluke infections in yak and Tibetan sheep was 57.7% (177/307). Specifically, the prevalences of F. hepatica and P. leydeni were 15.0% (46/307) and 31.6% (97/307), respectively, and the co-infection of both species was 11.1% (34/307). No significant difference existed in the prevalence of overall fluke infection between yak and Tibetan sheep (p < 0.05). However, F. hepatica prevalence was significantly different in yak and Tibetan sheep (p < 0.05) but not P. leydeni. The findings of this study provide useful information about the current status of natural fluke invasion in yak and Tibetan sheep around Qinghai Lake, which could be important for monitoring and controlling these parasites in the region.

Effect of slaughter age and postmortem aging time on tenderness and water-holding capacity of yak (Bos grunniens) longissimus thoracis muscle

The present study investigated the effect of slaughter age (2.43 ± 0.20, 4.15 ± 0.19, 6.62 ± 0.18, 10.59 ± 0.74 years) and postmortem aging time (1, 24, and 72 h) on the tenderness and water-holding capacity (WHC) of yak longissimus thoracis muscles to determine the most suitable age for slaughter to ensure product consistency. Under conventional postmortem aging conditions (4 °C), muscles of each age group exhibited the effect of cold shortening. Once the cold shortening occurred, the age effect on thickening muscle fiber and developing cross-links of collagen, considered to intensify the meat toughness, became less important. Owing to greater carcass weight and intramuscular fat, muscles of the older carcass (over 6-year-old) were less influenced by the cold shortening effect during the chilling process and showed lessened sarcomere contraction, delayed formation of drip loss channels, and increased level of myofibril fragmentation index (MFI) and myofiber structural disintegration, resulting in greater tenderness and WHC, especially 6-7 years group. Aging of 72 h structurally disintegrated the collagen cross-linking and integrity of muscle fibers and elevated the MFI, improving the meat tenderness. Therefore, the suitable slaughter age for yak is 6-7 years old and after 72 h aging, improved quality of yak meat can be obtained.

Effects of different cooking methods on physicochemical, textural properties of yak meat and its changes with intramuscular connective tissue during in vitro digestion

The effects of vacuum cooking (VC), traditional cooking (TC), and high-pressure cooking (HPC) on the physicochemical properties and texture of yak meat and the digestibility of yak meat and intramuscular connective tissue (IMCT) were investigated. Compared with VC treatment, TC and HPC treatment significantly increased meat cooking loss and meat hardness (P < 0.05). Meanwhile, the carbonyl content of yak meat of TC and HPC was 3.73 nmol/mg protein, and the free sulfhydryl content was 7.93 nmol/mg protein, indicating that more protein was oxidized at higher temperatures. Oxidative aggregation of proteins caused by cooking reduced meat digestibility by about 25%. However, cooking reduced the undigested residue of IMCT and promoted its digestion. Principal component analysis showed that the physicochemical, texture, oxidation, and protein digestibility of TC and HPC meat were similar but significantly different from VC meat.

BMP15 Modulates the H19/miR-26b/SMAD1 Axis Influences Yak Granulosa Cell Proliferation, Autophagy, and Apoptosis

Bone morphogenetic protein 15 (BMP15) regulates the growth and development of follicles. In particular, the long non-coding RNA H19 plays an important role in mammalian reproduction. However, the function and regulatory mechanism of the interaction of BMP15 with H19 in yak granulosa cell (GC) proliferation, autophagy, and apoptosis are poorly understood. In our study, quantitative reverse-transcription-polymerase chain reaction analysis showed that H19 were highly expressed in yak healthy follicles. H19 was induced by BMP15 protein in yak GCs. In addition, we confirmed that overexpression of H19 promoted yak GC proliferation and autophagy and inhibited apoptosis. Bioinformatic analysis and luciferase reporter assays demonstrated that H19 directly binds to miR-26b, and SMAD1 was identified as a target of miR-26b. miR-26b overexpression inhibited GC proliferation and autophagy and promoted apoptosis through decreased SMAD1 expression, which was attenuated by H19 overexpression. RNA immunoprecipitation-quantitative polymerase chain reaction and dual-luciferase assays showed that miR-26b was sponged by H19 to preserve SMAD1 expression. Furthermore, SMAD1 mRNA expression was induced and miR-26b expression was reduced after yak GCs were treated with BMP15 protein. In conclusion, our results demonstrated that the H19/miR-26b/SMAD1 axis responds to BMP15 to regulate yack GC proliferation, autophagy, and apoptosis.

TMT-based quantitative proteomics analysis reveals the differential proteins between fresh and frozen-thawed sperm of yak (Bos grunniens)

Sperm cryopreservation is one of the most effective methods for the conservation of germplasm resources and used of superior sires widely. However, the motility of yak (Bos grunniens) sperm was low after thawing and the proteomics changes in sperm cryopreservation remain unknown. Therefore, the aim of this study was to explore the differences between fresh sperm and frozen sperm of yak through the proteomic analysis and thus improve the understanding of sperm cryodamage. The Tandem Mass Tags (TMT) technology was used to screen differentially expressed proteins (DEPs) before and after freezing. Then, GO and KEGG analysis were conducted to analyze the DEPs enriched signaling pathways. Finally, the DEPs, including superoxide dismutase 1 (SOD1) and NADH ubiquinone oxidoreductase core subunit S8 (NDUFS8) were verified by the immunofluorescence technique. The results showed that there were 229 DEPs between fresh and frozen-thawed yak sperm. Compared with the fresh sperm, 120 proteins were up-regulated and 109 proteins were down-regulated in frozen-thawed sperm. The GO annotation showed that the up-regulated proteins enriched in metabolic and cytoskeleton-related processes, including lipoprotein metabolic process, lipid transport, extracellular region and intermediate filament cytoskeleton organization. In contrast, the down-regulated proteins enriched in biological processes including single fertilization, sperm capacitation and response to unfolded protein. KEGG pathway analysis indicated that freezing and thawing affected the oxidative phosphorylation pathway, the fructose and mannose metabolic pathway and the glycerolipid metabolic pathway of yak sperm. Immunofluorescence results showed that the protein expression level of SOD1 protein in the frozen group was significantly lower than that in the fresh group (P < 0.01), and the protein expression level of NDUFS8 protein was significantly higher in frozen group (P < 0.01). This study revealed the DEPs between fresh and frozen-thawed sperm and provides a theoretical basis to further explore the exertion of normal biological functions of yak sperm after freezing and thawing.

Identification and profiling of microRNAs during yak's testicular development

BACKGROUND

Normal testicular development is highly crucial for male reproduction and is a precondition for spermatogenesis that is the production of spermatozoa in the testes. MiRNAs have been implicated in several testicular biological processes, including cell proliferation, spermatogenesis, hormone secretion, metabolism and reproductive regulation. In the present study, we used deep sequencing data to study the functions of miRNAs during testicular development and spermatogenesis, by analyzing the expression patterns of small RNAs in 6-, 18- and 30-month-old yak testis tissues.

RESULTS

A total of 737 known and 359 novel miRNAs were obtained from 6-, 18- and 30-month-old yak testes. In all, we obtained 12, 142 and 139 differentially expressed (DE) miRNAs in 30- vs. 18-, 18- vs. 6-, and 30- vs. 6-month-old testes, respectively. Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of all DE miRNA target genes revealed BMP2, TGFB2, GDF6, SMAD6, TGFBR2 and other target genes as participants in different biological processes, including TGF-β, GnRH, Wnt, PI3K-Akt, MAPK signaling pathways and several other reproductive pathways. In addition, quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) was used to detect the expression of seven randomly selected miRNAs in 6-, 18- and 30-month-old testes, and the results were consistent with the sequencing data.

CONCLUSIONS

The differential expression of miRNAs in yak testes at different development stages was characterized and investigated using deep sequencing technology. We believe that the results will contribute to further understanding the functions of miRNAs in regulating the development of yak testes and improving the reproductive performance of male yaks.

Single-cell transcriptomic survey of cell diversity and functional changes in yak hearts at different altitude

The yak (Bos grunniens) is a species adapted to the hypoxic environment in the plateau area. The heart is a hypoxia-sensitive organ involved in this adaptation. Herein, we used single-cell RNA-seq technology and clustering to determine the presence of 11 cell populations in the yak heart. We analyzed gene expression differences and expression patterns in each cell subpopulation at different altitudes. The cells related to altitude changes are mainly smooth muscle cells and vascular endothelial cells. Of the four transcription factors (MEF2B, FOXP4, ARID5A, HES4) found in smooth muscle cells, only MEF2B was specifically expressed in vascular smooth muscle cells. Three key transcription factors (HNF1B, DMRTA1, ARNTL2) were also found in the cardiomyocyte module. Compared with data extracted from low-altitude yak, we observed that the high altitude yak has enhanced contraction and relaxation of vascular smooth muscle cells and an increased metabolic level of cardiomyocytes. These may be strategies for the yak to adapt to high-altitude hypoxia environments. This article is protected by copyright. All rights reserved.

High oxygen-modified packaging (HiOx-MAP) mediates HIF-1α regulation of tenderness changes during postmortem aging of yak meat

In the present study, we studied the effect of high oxygen-modified packaging (HiOx-MAP) on yak meat tenderness and the underlying mechanism. HiOx-MAP significantly increased the myofibril fragmentation index (MFI) of yak meat. In addition, western blotting showed that the expression of hypoxia-inducible factor (HIF-1α) and ryanodine receptors (RyR) in the HiOx-MAP group was reduced. HiOx-MAP increased the activity of sarcoplasmic reticulum calcium-ATPase (SERCA). The energy disperse spectroscopy (EDS) mapping showed gradually reduced calcium distribution in the treated endoplasmic reticulum. Furthermore, HiOx-MAP treatment increased the caspase-3 activity and the apoptosis rate. The activity of calmodulin protein (CaMKKβ) and AMP-activated protein kinase (AMPK) was down-regulated leading to apoptosis. These results indicated that HiOx-MAP promoted apoptosis during postmortem aging to improve the tenderization of meat.

Yak DEFB124 alleviates intestinal injury caused by Staphylococcus aureus infection

To investigate the characteristics and functions of yak β-defensin 124 (DEFB124), prokaryotic expression, analysis of gut microbiological and other methods were used in this study. The results showed that the sequence of yak DEFB124 gene was 306 bp in length and 207 bp in open reading frame, which encoded 68 amino acids. Yak DEFB124 protein was highly conserved and had the closest relationship with cattle. Yak DEFB124 protein was a secreted cationic β-defensin. The recombinant expression plasmid pET32a-DEFB124 was constructed, and an about 24 kDa protein was successfully expressed. Yak DEFB124 protein had inhibitory activity against Staphylococcus aureus (S. aureus), and its MIC value was 64 μg/mL. After treating with yak DEFB124 protein, the activities of alkaline phosphatase (AKP) and total superoxide dismutase (T-SOD) were higher (P < 0.01) in the jejunum tissue, but the activity of lysozyme (LZM) was lower (P < 0.01). The number of goblet cells in the duodenum, jejunum, and ileum of the mice in the DEFB124 group was increased (P < 0.01). Besides, the expressions of MUC2 mRNA and protein were increased (P < 0.05) after the treatment with yak DEFB124 protein. Furthermore, the relative abundance of Lactobacillus in jejunum of mice in DEFB124 group was also increased. In summary, yak DEFB124 protein could increase the number of goblet cells in mice intestine and the abundance of intestinal probiotics Lactobacillus, thereby protecting the intestinal tract and alleviating intestinal damage.

Non-denatured yak type I collagen accelerates sunburned skin healing by stimulating and replenishing dermal collagen

Sunburn is one of the most common skin lesions caused by excessive UV exposure, and its incidence is highly correlated with the risks of skin cancer. A variety of drugs including corticosteroids and NSAIDs have been developed to treat acute sunburn, however, they have raised severe concerns such as poor healing efficacy and long recovery time. We have for the first time extracted non-denatured type I collagen from yak hide, which displays a canonical triple helical structure with melting temperature of 42.7 °C. The highly pure yak collagen type I (YCI) self-assembles to form well-ordered nanofibers with periodic d-bands. YCI is highly biocompatible, and it significantly promotes the proliferation and adhesion of HFF-1 cells. The sunburn healing effects of YCI has been investigated using acute skin injury mouse model. Histological analysis shows that 4 days' treatment of YCI has resulted in the recovery of sunburned mice skin to a healthy state, indicated by pronounced acceleration of epithelization and collagen deposition. The collagen volume fraction as well as the hydroxyproline (Hyp) content of YCI-treated sunburned skin have been found to be greatly increased, confirming the enhanced regeneration of collagen. YCI creams and dressings have also shown superior healing capacity of sunburn by remarkably shortening the recovery time. Notably, the denatured collagen-targeted staining results indicated a large quantity of denatured collagen in sunburned mice, which became substantially reduced after the YCI treatment. FITC-labeled YCI has been further found to penetrate into the dermis of sunburned mice. The highly biocompatible and bioactive non-denatured YCI provides an improved treatment of sunburn, indicating very promising applications of YCI in cosmetics and dermatology.

Genome-wide identification of SNPs associated with body weight in yak

BACKGROUND

The yak is the most important livestock in the Qinghai-Tibet Plateau, and body weight directly affects the economic values of yak. Up to date, the genome-wide profiling of single-nucleotide polymorphisms (SNPs) associating with body weight has not been reported in yak. In the present study, the SNPs in 480 yaks from three breeds were analyzed using the commercial high-density (600 K) yak SNP chips.

RESULTS

The results identified 12 and 4 SNPs potentially associated with body weight in male and female yaks, respectively. Among them, 9 and 2 SNPs showed significant difference in yak body weight between different genotypes at each locus in male and female yaks, respectively. Further exploration found 33 coding genes within the 100 kbp upstream or downstream to the SNP loci, which might be potentially affected by the variation of SNPs. Among them, G protein-coupled receptor kinase 4 (GRK4) might be potentially affected by the SNP AX-174555047, which has been reported to affect the functioning of two body-weight associated hormones (parathyroid hormone, PTH, and adrenomedullin, ADM). Determination of PTH and ADM levels in yak revealed positive relationship between PTH level and body weight, negative relationship between ADM level and body weight along with the variation of AX-174555047 mutation.

CONCLUSIONS

These results suggested that the SNP AX-174555047 might potentially affect body weight through mediating GRK4 expression and then PTH and ADM functioning. Thus, the SNP AX-174555047 might be used as a biomarker for molecular breeding of yak. More investigations are required to validate this point.

Construction of transcriptome atlas of white yak hair follicle during anagen and catagen using single-cell RNA sequencing

BACKGROUND

As the direct organ of villus, hair follicles have obvious seasonal cycles. The hair follicle cycle is orchestrated by multiple cell types that together direct cell renewal and differentiation. But the regulation property of hair follicle cells from anagen to catagen in yak is still unknown.

RESULTS

In this study, single-cell RNA sequencing was performed on 24,124 single cells of the scapular skin from white yak. Based on tSNE cluster analysis, the cell types of IFE-DC, epidermal cell lines, fibroblasts, keratinocytes, IRS, DS, INFU, and other cells in yak hair follicles during anagen and catagen were successfully identified, and the gene expression profiles were described. The GO enrichment analysis indicated the different cells characteristic genes to be mainly enriched in the epidermal development, epithelial cell differentiation and wound healing pathways. The pseudotime trajectory analysis described the differentiation trajectory of the epidermal lineage and dermal lineage of the hair follicle during anagen and catagen. Moreover, the dynamic changes of the genes like LHX2, KRT25, and KRT71 were found to be highly expressed in HS and IRS, but not in the IFE-DC, INFU, and keratinocyte during differentiation.

CONCLUSIONS

Our results analyzed the time-varying process of gene expression in the dermal cell lineage and epidermal cell lineage of hair follicles during anagen and catagen during fate differentiation was expounded at the single cell level, revealing the law of fate specialization of different types of cells. In addition, based on the enrichment analysis, the transcriptional regulatory factors involved in the different cell fates were also revealed. These results will help to enhance our understanding of yak hair follicle cycle and promote the development and utilization of yak villus.

Whole transcriptome analyses and comparison reveal the metabolic differences between oxidative and glycolytic skeletal muscles of yak

Mammalian skeletal muscle is composed of various muscle fibers that exhibit different physiological and metabolic features. Muscle fiber type composition has significant influences on the meat quality of livestock. In this study, we comprehensively analyzed the whole transcriptome profiles of the oxidative muscle biceps femoris (BF) and the glycolytic muscle obliquus externus abdominis (OEA) of yak. A total of 1436 mRNAs, 1172 lncRNAs, and 218 circRNAs were differentially expressed in the oxidative muscles compared with the glycolytic muscles. KEGG annotation showed that differentially expressed mRNAs regulated by lncRNA and circRNA were mainly involved in PPAR signaling pathway, citrate cycle (TCA cycle), and PI3K-Akt signaling pathway, which reflect the different metabolic properties between oxidative and glycolytic muscles. In addition, regulatory networks associated with muscle fiber type conversion and mitochondria energy metabolism in muscles were constructed. Our study provides new evidence for a better understanding of the molecular mechanisms underlying skeletal muscle fiber determination and meat quality traits of yak.

Combined transcriptome and proteome analysis of yak PASMCs under hypoxic and normoxic conditions

Background

Yaks are animals that have lived in plateau environments for generations. Yaks can adapt to the hypoxic plateau environment and also pass this adaptability on to the next generation. The lungs are the most important respiratory organs for mammals to adapt to their environment. Pulmonary artery smooth muscle cells play an important role in vascular remodeling under hypoxia, but the genetic mechanism underpinning the yak's ability to adapt to challenging plateau conditions is still unknown.

Methods

A tandem mass tag (TMT) proteomics study together with an RNA-seq transcriptome analysis were carried out on pulmonary artery smooth muscle cells (PASMCs) that had been grown for 72 hours in both normoxic (20% O2) and hypoxic (1% O2) environments. RNA and TP (total protein) were collected from the hypoxic and normoxic groups for RNA-seq transcriptome sequencing and TMT marker protein quantification, and RT-qPCR validation was performed.

Results

A total of 17,711 genes and 6,859 proteins were identified. Further, 5,969 differentially expressed genes (DEGs) and 531 differentially expressed proteins (DEPs) were identified in the comparison group, including 2,924 and 186 upregulated genes and proteins and 3,045 and 345 down-regulated genes and proteins, respectively. The transcriptomic and proteomic analyses revealed that 109 DEGs and DEPs were highly positively correlated, with 77 genes showing the same expression trend. Nine overlapping genes were identified in the HIF-1 signaling pathway, glycolysis / gluconeogenesis, central carbon metabolism in cancer, PPAR signaling pathway, AMPK signaling pathway, and cholesterol metabolism (PGAM1, PGK1, TPI1, HMOX1, IGF1R, OLR1, SCD, FABP4 and LDLR), suggesting that these differentially expressed genes and protein functional classifications are related to the hypoxia-adaptive pathways. Overall, our study offers abundant data for further analysis of the molecular mechanisms in yak PASMCs and their adaptability to different oxygen concentrations.

The uniqueness and superiority of energy utilization in yaks compared with cattle in the highlands: A review

Yaks living on the Qinghai-Tibetan Plateau for a long time have evolved a series of mechanisms to adapt to the unique geographical environment and climate characteristics of the plateau. Compared with other ruminants, yaks have higher energy utilization and metabolic efficiency. This paper presents possible mechanisms responsible for the efficient energy utilization, absorption and metabolism resulting from the unique evolutionary process of yaks. It is hoped that the information discussed in this review will give a better insight into the uniqueness and superiority of yaks in regards to energy metabolism and utilization compared with cattle and open new avenues for the targeted regulation of energy utilization pathways of other ruminants.

Effect of rapamycin treatment on oocyte in vitro maturation and embryonic development after parthenogenesis in yaks

Autophagy plays an important role in mammalian oocyte maturation and early embryonic development and rapamycin is well known for inducing autophagy. Although previous studies have reported the effects of rapamycin on oocytes in vitro maturation (IVM) in different species, few studies have been reported on the role of rapamycin in yak oocytes IVM and embryonic development. Therefore, the objective of this study was to examine the effect of rapamycin treatment on yak oocytes IVM and early embryonic development. Specifically, immature yak oocytes during IVM or parthenogenetic (PA) embryos were treated with different rapamycin concentrations to select an optimal dose. Then evaluated its effect on maturation rates, cleavage, and blastocyst formation rates, mitochondrial membrane potential, ROS levels. Related genes and proteins expression in matured oocytes and blastocysts were also evaluated. The results show that 10 nM rapamycin treatment during IVM significantly improved oocyte maturation rates of oocytes and blastocyst formation rates. Treatment with 10 nM rapamycin reduced ROS level but increased mitochondrial membrane potential. Correspondingly, mRNA and protein expressions of LC3, Beclin-1, and Bcl-2 up-regulated while Bax down-regulated in matured yak COCs. When parthenogenetic embryos were treated with different rapamycin concentrations, 10 nM rapamycin treatment showed higher 8-cell and blastocyst formation rates. Also, CDX2, POU5F1, SOX2, and Nanog levels in blastocysts were upregulated. In summary, our findings demonstrate that rapamycin treatment improves oocytes maturation probably by increasing mitochondrial membrane potential, reducing ROS levels, and regulating the apoptosis in mature yak oocytes. Rapamycin treatment also improves embryonic developmental competence in the yak.

Changes in arterial blood vessels and VEGF and Ang-1 expression in pregnant and non-pregnant yak uterine caruncle

We investigated the structural features of arterial blood vessels in yak uterine caruncle and the effects of the expression of vascular regulation-related factors on angiogenesis in pregnant and non-pregnant yak uterus. Three-dimensional specimens of the uterine artery of non-pregnant and pregnant yaks were produced to observe and measure the distribution characteristics and number of arterial vessels in the uterus and caruncle in the two periods. The uterine caruncle structure was observed and analyzed by hematoxylin-eosin staining. The expression features of vascular endothelial growth factor (VEGF) and angiopoietin-1 (Ang-1) in the uterine caruncle were detected with immunohistochemistry, quantitative real-time PCR (qRT-PCR), and western blotting. The length and number of blood vessels in the caruncle were increased, the degree of curvature was decreased, and the folding was more complicated during pregnancy as compared with that during non-pregnancy. The immunohistochemical results demonstrated that VEGF and Ang-1 were mainly expressed strongly in the mucosal epithelial cytoplasm. The glandular lumen of the uterine gland, lymphocytes, and the media and adventitia of blood vessels are widely distributed, and they are all positive. VEGF and Ang-1 mRNA and protein levels were highest in pregnancy, followed by that in the luteal phase and in the follicular phase, and three stages were significantly different (p < 0.05). These findings provide an anatomical reference and theoretical basis for improving the diagnosis and treatment of yak reproductive disorders and other diseases in high-altitude and low-oxygen environments.

Plant community-mediated effects of grazing on plant diseases

Grazing is one of the most important management practices for grasslands. To date, most studies on how grazing affects plant diseases have focused on a single plant species, ignoring plant community characteristics and phylogeny. We used data from a 6-year yak grazing experiment (0, 1, 2, and 3 yak(s) ha^- 1 treatment) in an alpine meadow ecosystem of Qinghai-Tibetan Plateau, from which we tested grazing effects on foliar fungal diseases at both population and community levels. By measuring plant community variables (including richness, evenness, phylogenetic diversity, and composition) and disease severity, we evaluated the relative importance of plant community-mediated effects of yak grazing on community pathogen load with a multi-model inference approach. We found significant differences in pathogen load among different grazing treatments; we recorded the highest and lowest pathogen loads in the 1 yak ha^- 1 treatment and in the 3 yaks ha^- 1 treatment, respectively. Pielou's evenness index and community proneness (i.e., an estimate of the capacity of plant communities to support diseases) best explained variation in pathogen load, indicating that plant community-mediated effects (through evenness and proneness) of yak grazing determined pathogen load. Our study provides empirical evidence that grazing influences foliar fungal disease prevalence through plant community evenness and composition, which demonstrates the necessity of incorporating host plant community characteristics into disease load prediction frameworks.

Comparative analysis of gut microbiota in healthy and diarrheic yaks

BACKGROUND

Yak (Bos grunniens) mainly inhabiting Tibet Plateau, displayed a high incidence of diarrhea due to harsh living environment and nutritional deficit. Gut microbial community has been reported to be closely related to many diseases including diabetes, obesity and inflammatory bowel disease, but information regarding diarrheic influence on gut microbiota in yaks remains scarce. Here, this study was performed to investigate the gut bacterial and fungal alternations of diarrheic yaks.

RESULTS

Results revealed that the gut bacterial and fungal communities of diarrheic yaks showed a distinct decline in alpha diversity, accompanied by significant shifts in taxonomic compositions. Specifically, diarrhea caused a distinct increase in the relative abundance of 1 phylum and 8 genera as well as a distinct decrease in 3 phyla and 30 genera. Fungal taxonomic analysis indicated that the relative richness of 1 phylum and 2 genera dramatically increased, whereas the relative richness of 2 phylum and 43 genera significantly decreased during diarrhea. Surprisingly, 2 bacterial genera and 5 fungal genera even cannot be detected in the gut microbiota of diarrheic yaks.

CONCLUSIONS

In summary, this study indicated that the gut bacterial and fungal compositions and diversities of yaks altered significantly during diarrhea. Moreover, these findings also contribute to understanding the gut microbial composition and diversity of yaks and developing strategies to alleviate and prevent diarrhea from gut microbial perspective.