Whole-transcriptome analysis of longissimus dorsi muscle in cattle-yaks reveals the regulatory functions of ADAMTS6 gene in myoblasts.

Cattle-yak, which is the hybrid F1 generation of cattle and yak, demonstrates better production performance compared to yak. However, there is limited research on the molecular mechanisms responsible for the muscle development of cattle-yak. To address this knowledge gap, a comprehensive transcriptomic survey of the longissimus dorsi muscle in cattle-yak was conducted. Three transcript types, namely lncRNAs, miRNAs, and circRNAs, along with protein-coding genes were characterized at two developmental stages (6 m, 18 m) of cattle-yak. The results revealed significant enrichment of these transcripts into pathways related to myoblast differentiation and muscle development signaling. Additionally, the study identified the TCONS00024465/circHIPK3-bta-miR-499-ADAMTS6 regulatory network, which may play a crucial role in the muscle development of cattle-yak by combining the transcriptome data of yak and constructing the ceRNA co-expression network. HEK 293 T cells were used to validate that TCONS00024465 and circHIPK3 are located upstream of bta-miR-499, and can competitively bind to bta-miR-499 as ceRNA. The study also verified that ADAMTS6 regulates skeletal muscle development by inhibiting myoblast proliferation, promoting myoblast differentiation, and positively regulating the apoptosis of myoblasts. Taken together, this study provides new insights into the advantages of cattle-yak production performance and offers a molecular basis for further research on muscle development.

Proteomic Analysis Reveals the Effects of Different Dietary Protein Levels on Growth and Development of Jersey-Yak.

Jersey-yak is a hybrid offspring of Jersey cattle and yak (Bos grunniens). Changing the feeding system of Jersey-yak can significantly improve its growth performance. In this study, tandem mass tag (TMT) proteomics technology was used to determine the differentially expressed proteins (DEPs) of the longissimus lumborum (LL) muscle of Jersey-yak fed different protein levels of diet. The results showed that compared with the traditional grazing feeding, the growth performance of Jersey-yaks was significantly improved by crude protein supplementation after grazing. A total of 3368 proteins were detected in these muscle samples, of which 3365 were quantified. A total of 434 DEPs were identified. Through analyses, it was found that some pathways related to muscle growth and development were significantly enriched, such as Rap1 signaling pathway, mTOR signaling pathway, and TGF-beta signaling pathway. A number of DEPs enriched in these pathways are related to muscle cell development, differentiation, and muscle development, including integrin subunit alpha 7 (ITGA7), myosin heavy chain 8 (MYH8), and collagen type XII alpha 1 chain (COL12A1). In conclusion, the results of this study provide insights into the proteomics of different feeding patterns of Jersey-yak, providing a stronger basis for further understanding the biological mechanism of hybrid varieties.

Comparative Study on Nutritional Characteristics and Volatile Flavor Substances of Yak Milk in Different Regions of Gannan.

This study aimed to investigate the nutritional properties of yak milk in various areas of Gannan. The milk composition analyzer, automatic amino acid analyzer, and flavor analyzer were used to detect the conventional nutrients, amino acids, and volatile flavor substances of 249 yak milks in Meiren grassland, Xiahe grassland, and Maqu grassland (hereinafter referred to as Meiren yak, Xiahe yak, and Maqu yak) in the Gannan area. The results showed that the fat content of Meiren yak milk was significantly higher than that of Maqu yak and Xiahe yak (p < 0.05). The protein content of Meiren yak milk was significantly higher than that of Xiahe yak (p < 0.05), but not significantly different from that of Maqu yak (p > 0.05). The casein content in the milk of Maqu yak was significantly higher than that of Meiren yak and Xiahe yak (p < 0.05). There was no significant difference in the lactose content of yak milk in the three regions (p > 0.05). The content of glutamic acid in the milk of Meiren yak, Xiahe yak, and Maqu yak was noticeably high, which was 1.03 g/100 g, 1.07 g/100 g, and 1.10 g/100 g, respectively. The total amino acid (TAA) content was 4.78 g/100 g, 4.87 g/100 g, and 5.0 g/100 g, respectively. The ratios of essential amino acids (EAA) and total amino acids (TAA) in the milk of Meiren yak, Xiahe yak, and Maqu yak were 42.26%, 41.27%, and 41.39%, respectively, and the ratios of essential amino acids (EAA) and nonessential amino acids (NEAA) were 73.19%, 70.28%, and 70.61%, respectively. In the yak milk samples collected from three different regions, a total of 34 volatile flavor compounds were detected, including 10 aldehydes, five esters, six ketones, four alcohols, two acids, and seven others. The main flavor substances qualitatively obtained from Meiren yak milk were ethyl acetate, n-valeraldehyde, acetic acid, heptanal, and n-hexanal. Xiahe yak milk mainly contains ethyl acetate, isoamyl alcohol, n-valeraldehyde, heptanal, and ethyl butyrate. Maqu yak milk mainly contains ethyl acetate, n-valeraldehyde, isoamyl alcohol, heptanal, ethyl butyrate, and n-hexanal. Principal component analysis showed that the flavor difference between Xiahe yak and Maqu yak was small, while the flavor difference between Xiahe yak, Maqu yak, and Meiren yak was large. The findings of this research can serve as a foundation for the future advancement and application of yak milk.

Effects of dietary crude protein levels in the concentrate supplement after grazing on rumen microbiota and metabolites by using metagenomics and metabolomics in Jersey-yak.

Introduction: The crude protein level in the diet will affect the fermentation parameters, microflora, and metabolites in the rumen of ruminants. It is of great significance to study the effect of crude protein levels in supplementary diet on microbial community and metabolites for improving animal growth performance. At present, the effects of crude protein level in supplementary diet on rumen fermentation parameters, microbial community, and metabolites of Jersey-Yak (JY) are still unclear. Methods: The purpose of this experiment was to study the appropriate crude protein level in the diet of JY. The rumen fermentation indexes (volatile fatty acids and pH) were determined by supplementary diets with crude protein levels of 15.16 and 17.90%, respectively, and the microbial community and metabolites of JYs were analyzed by non-target metabonomics and metagenome sequencing technology, and the changes of rumen fermentation parameters, microbial flora, and metabolites in the three groups and their interactions were studied. Results and Discussion: The crude protein level in the supplementary diet had significant effects on pH, valeric acid, and the ratio of acetic acid to propionic acid (p < 0.05). The protein level had no significant effect on the dominant microflora at the phylum level (p > 0.05), and all three groups were Bacteroides and Firmicutes. The results of metabolite analysis showed that the crude protein level of supplementary diet significantly affected the metabolic pathways such as Bile secretion and styrene degradation (p < 0.05), and there were different metabolites between the LP group and HP group, and these different metabolites were related to the dominant microbial to some extent. To sum up, in this experiment, the effects of crude protein level in supplementary diet on rumen microorganisms and metabolites of JY and their relationship were studied, which provided the theoretical basis for formulating a more scientific and reasonable supplementary diet in the future.

Multi-omics revealed the effects of dietary energy levels on the rumen microbiota and metabolites in yaks under house-feeding conditions.

Yak (Bos grunniens) is a unique large ruminant species in the Qinghai-Tibetan Plateau (QTP). Changing the energy levels of their rations can significantly improve their growth performance. Therefore, studying the effects of dietary energy levels on the rumen microflora and metabolites of yak is crucial for enhancing the development of the yak industry. Currently, there is a lack of understanding regarding the impact of feeding energy diets on rumen fermentation parameters, microbial functions, and metabolites. This study was designed to determine the appropriate energy level for feeding yak. Three test diets with metabolizable energy levels of 7.57 MJ/kg, 9.44 MJ/kg, and 11.9 MJ/kg were used and the concentration of volatile fatty acids (VFA) in rumen fluid was measured. The microbial communities, functions, and metabolites in yaks were studied by 16S rRNA sequencing, metagenome, and LC-MS non-targeted metabolomics to investigate the relationships among rumen fermentation parameters, microbial diversity, and metabolites. Ration energy levels significantly affect total VFA, acetate, propionate, butyrate, iso-valerate, valerate, and acetate/propionate (p < 0.05). At the phylum level, the dominant phyla in all three treatment groups were Bacteroidota, Firmicutes, and Actinobacteriota. At the genus level, the abundance of the unclassified_o__Bacteroidales, norank_f_Muribaculaceae, Lachnospiraceae_NK4A136_group, and Family _XIII_AD3011_group showed significant differences (p < 0.05) and were significantly correlated with differential metabolites screened for phosphatidylcholine [PC(16:0/0:0), PC(18:3/0:0)], uridine 3'-monophosphate, and adenosine monophosphate, etc. CAZymes family analysis showed that GHs and CEs differed significantly among the three groups. In addition, differential metabolites were mainly enriched in the pathways of lipid metabolism, nucleotide metabolism, and biosynthesis of other secondary metabolites, and the concentrations of differential metabolites were correlated with microbial abundance. In summary, this study analyzed the effects of ration energy levels on rumen microorganisms and metabolites of yaks and their relationships. The results provided a scientific basis for the selection of dietary energy for yaks in the house feeding period in the future.

Copy Number Variation of the SOX6 Gene and Its Associations with Growth Traits in Ashidan Yak.

Copy number variation (CNV) is a fundamental type of structural variation of the genome affecting the economic traits of livestock. The SOX6 gene (sex-determining region Y-box 6), as a transcription factor, has multiple functions with regard to sex determination, embryonic growth, the nervous system development, as well as bone, and various organ formation. This study employed quantitative real-time fluorescence quota PCR (qPCR) for detecting the SOX6-CNV of the 311 Ashidan yaks and analyzed the correlation of the SOX6-CNV with four phenotypes (including body weight, withers height, body length, and chest girth) of the yaks aged 6, 12, 18, and 30 months using ANOVA and multiple comparisons. Furthermore, the SOX6 gene expression was identified in seven different tissues of the yaks. The experiment results demonstrated the expression of SOX6 in each tissue, and the kidney and muscle tissue were found to have higher relative expression levels. Based on the processing by IBM SPSS software, SOX6-CNV was significantly correlated with the chest girth of the 6-months old yaks (p < 0.05) and 30-months yaks (p < 0.05), and withers height of 6 months yaks (p < 0.05) and 18-months yaks (p < 0.05), as well as the normal type of CNV, was chosen for yak breeding. In conclusion, SOX6 might be prominently involved in promoting growth and development of yaks, suggesting that the SOX6 gene can be used in breeding yaks by molecular marker-assisted selection (MAS). The study also offered some important insights into the references and clues for the genetic breeding of yaks.

Transcriptome-Wide Study of mRNAs and lncRNAs Modified by m6A RNA Methylation in the Longissimus Dorsi Muscle Development of Cattle-Yak.

Cattle-yak is a hybrid F1 generation of cattle and yak, which has a history of more than 3000 years and has shown better production performance and higher economic benefits than those of yaks. However, up to now, there has been no study on the transcriptome-wide m6A methylation profile of bovine skeletal muscle and its potential biological function during muscle development. Here, we observed significant changes in the expression levels of muscle-related marker genes and methylation-related enzymes during the development of cattle-yak, and the overall m6A content in the Longissimus dorsi muscle of 18-month-old cattle-yak decreased significantly. A total of 36,602 peaks, 11,223 genes and 8388 lncRNAs were identified in the two groups, including 2989 differential peaks (427 up-regulated peaks and 2562 down-regulated peaks), 1457 differentially expressed genes (833 up-regulated genes and 624 down-regulated genes) and 857 differentially expressed lncRNAs (293 up-regulated lncRNAs and 564 down-regulated lncRNAs). GO and KEGG analysis revealed that they were significantly enriched in some muscle-related pathways (Wnt signaling pathway and MAPK signaling pathway) and high-altitude adaptation-related pathway (HIF-1 signaling pathway). Moreover, m6A abundance was positively correlated with gene expression levels, while it was negatively correlated with lncRNA expression levels. This indicates that m6A modification played an important role in the Longissimus dorsi muscle development of cattle-yak; however, the regulation mechanism of m6A-modified mRNA and lncRNA may be different. This study was the first report of transcriptome-wide m6A-modified mRNAs and lncRNAs atlas in the Longissimus dorsi muscle development of cattle-yak, one which will provide new perspectives for genetic improvement in bovines.

Copy Number Variations in the MICALL2 and MOGAT2 Genes Are Associated with Ashidan Yak Growth Traits.

Copy number variations (CNVs) are a result of genomic rearrangement affecting DNA regions over 1 kb in length, and can include inversions, translocations, deletions, and duplications. The molecule interacting with CasL-like protein 2 (MICALL2) gene is primarily associated with mitochondrial protein targeting and exhibits predicted stress fiber colocalization. The monoacylglycerol O-acyltransferase 2 (MOGAT2) gene encodes an enzyme responsible for catalyzing diacylglycerol synthesis from 2-monoacylglycerol and fatty acyl-CoA. For this study, blood samples were obtained from 315 yaks, and the body weight, body length, withers height, and chest girth of these animals were measured at 6, 12, 18, and 30 months of age. Genomic DNA was harvested from the collected blood samples, and CNVs in these samples were detected by qPCR. The resultant data were compared using ANOVAs, revealing significant associations between MICALL2 gene CNVs and body weight at 6 months of age (p < 0.05), body length and chest girth at 30 months of age (p < 0.05), and withers height at 18 months of age (p < 0.01) in Ashidan yaks. Similarly, MOGAT2 CNVs were significantly associated with body weight at 6 and 30 months of age (p < 0.05), and with withers height at 18 months of age (p < 0.01) in these Ashidan yaks. MICALL2 and MOGAT2 gene expression was further analyzed in yak tissue samples, revealing that MICALL2 was most highly expressed in the adipose tissue, whereas MOGAT2 was most highly expressed in the lung. These results thus confirmed the relationship between CNVs in the MICALL2 and MOGAT2 genes and Ashidan yak growth traits, providing a valuable gene locus that can be leveraged for future marker-assisted yak breeding efforts.

Copy number variation (CNV) of the AHR gene in the Ashidan yak and its association with growth traits.

Copy number variation (CNV) is a principal genomic structure variation affecting the gene expression through the dose-effect and change of gene regulatory region. It plays an important role in regulating the various complex traits of vertebrates. The aromatic hydrocarbon receptor (AHR) is a member of ligand-dependent transcription factors which belong to the alkaline helix-loop-helix PASS family. It is used as a conservative environmental sensor during biological evolution. This study, tracked the growth data (body weight, withers height, body length, chest girth) of 332 yaks in four stages (6, 12, 18, and 30 months) were tracked. The CNV of the yaks was analyzed using real-time quantitative PCR, and the correlation between CNV of AHR and yak growth traits was analyzed using the SPSS and R software. The AHR gene expression profiles were assessed in different tissues of the 18-month-old yak. The statistical analysis indicated the AHR-CNV of the Ashidan yak to significantly correlate with the body length (P < 0.05), and was found to be correlated with the withers height at 18 months old (P < 0.01) with extreme significance. To sum up, this study for the first time discussed the relationship between AHR-CNV and the growth traits of the Ashidan yak. The results indicated that the AHR gene might become a new molecular marker in the breeding yak.

LncRNA LUADT1 inhibits cell apoptosis in diabetic retinopathy by regulating miR-383/peroxiredoxin 3 axis.

This study aimed to investigate the involvement of long non-coding RNA (lncRNA) lung adenocarcinoma transcript 1 (LUADT1) LUADT1 in diabetic retinopathy (DR). We found LUADT1 may interact with miR-383 by RNA interaction prediction. QPCR analysis showed that lncRNA LUADT1 was downregulated, and miR-383 was upregulated in DR. However, correlation analysis revealed no significant correlation between them. In retinal pigment epithelial cells (RPEpiC, h1RPE7 from Sigma-Aldrich), overexpression of LUADT1 and miR-383 failed to affect the expression of each other. However, LUADT1 overexpression led to increased and miR-383 overexpression led to decreased expression level of peroxiredoxin 3 (PRX3). Cell apoptosis analysis showed that LUADT1 and PRX3 overexpression resulted in the decreased cell apoptosis. MiR-383 played an opposite role and reduced the effects of LUADT1 and PRX3 overexpression. Therefore, LUADT1 regulates PRX3 by serving as the endogenous sponge of miR-383 in DR to regulate cell apoptosis.

Comprehensive Analysis of mRNA, lncRNA, circRNA, and miRNA Expression Profiles and Their ceRNA Networks in the Longissimus Dorsi Muscle of Cattle-Yak and Yak.

Cattle-yak, as the hybrid offspring of cattle (Bos taurus) and yak (Bos grunniens), demonstrates obvious heterosis in production performance. Male hybrid sterility has been focused on for a long time; however, the mRNAs and non-coding RNAs related to muscle development as well as their regulatory networks remain unclear. The phenotypic data showed that the production performance (i.e., body weight, withers height, body length, and chest girth) of cattle-yak was significantly better than that of the yak, and the economic benefits of the cattle-yak were higher under the same feeding conditions. Then, we detected the expression profiles of the longissimus dorsi muscle of cattle-yak and yak to systematically reveal the molecular basis using the high-throughput sequencing technology. Here, 7,126 mRNAs, 791 lncRNAs, and 1,057 circRNAs were identified to be differentially expressed between cattle-yaks and yaks in the longissimus dorsi muscle. These mRNAs, lncRNA targeted genes, and circRNA host genes were significantly enriched in myoblast differentiation and some signaling pathways related to muscle development (such as HIF-1 signaling pathway and PI3K-Akt signaling pathway). We constructed a competing endogenous RNA (ceRNA) network and found that some non-coding RNAs differentially expressed may be involved in the regulation of muscle traits. Taken together, this study may be used as a reference tool to provide the molecular basis for studying muscle development.

Relation of serum and vitreous nesfatin-1 concentrations with diabetic retinopathy.

OBJECTIVE: Nesfatin-1, belonging to adipokine family, serves as an anti-inflammatory mediator. We performed this investigation to evaluate the relation between serum and vitreous nesfatin-1 concentrations with diabetic retinopathy (DR). METHODS: This study was performed in a population of 189 diabetic patients and 48 control subjects. Diabetic patients were then divided into diabetic patients without DR, non-proliferative diabetic retinopathy (NPDR) patients, and proliferative diabetic retinopathy (PDR) patients. RESULTS: Serum and vitreous nesfatin-1 concentrations were significantly lower in the diabetic patients than in the controls. NPDR patients had reduced vitreous nesfatin-1 concentrations compared with patients without DR. In addition, there were significantly lower serum and vitreous nesfatin-1 concentrations in PDR patients compared with the other three groups. Pearson correlation analysis showed that serum nesfatin-1 was negatively correlated with body mass index and fasting plasma glucose in diabetic patients. CONCLUSION: Serum and vitreous nesfatin-1 concentrations were negatively correlated with DR.