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Simple Summary: Yaks are a major economic source for people in the Tibetan Plateau region. Yaks are rich in nutrients, but their low fat content is not conducive to the large-scale promotion of yak meat, so the study of the mechanism of yak lipid deposition is beneficial to the marketing of yak meat. In this paper, the results of transcriptome sequencing analysis of yak liver showed that it could be determined that the expression levels of genes associated with partial lipid deposition were significantly up-regulated during yak fattening. In addition, this study found that the tenderness of yak meat improved during this process. Fattening significantly affects fat deposition in yaks, which may be realized through its effects on lipid metabolic pathways. Therefore, studying the mechanism of lipid deposition in yaks and fattening yaks will improve the quality of yak meat. Yak meat is nutritionally superior to beef cattle but has a low fat content and is slow-growing. The liver plays a crucial role in lipid metabolism, and in order to determine whether different feeding modes affect lipid metabolism in yaks and how it is regulated, we employed RNA sequencing (RNA-seq) technology to analyze the genome-wide differential gene expression in the liver of yaks maintained under different raising systems. A total of 1663 differentially expressed genes (DEGs) were identified (|log2FC| ≥ 0 and p-value ≤ 0.05), including 698 down-regulated and 965 up-regulated genes. According to gene ontology (GO) and KEGG enrichment analyses, these DEGs were significantly enriched in 13 GO terms and 26 pathways (p < 0.05). Some DEGs were enriched in fatty acid degradation, PPAR, PI3K-Akt, and ECM receptor pathways, which are associated with lipid metabolism. A total of 16 genes are well known to be related to lipid metabolism (e.g., APOA1, FABP1, EHHADH, FADS2, SLC27A5, ACADM, CPT1B, ACOX2, HMGCS2, PLIN5, ACAA1, IGF1, FGFR4, ALDH9A1, ECHS1, LAMA2). A total of 11 of the above genes were significantly enriched in the PPAR signaling pathway. The reliability of the transcriptomic data was verified using qRT-PCR. Our findings provide new insights into the mechanisms regulating yak meat quality. It shows that fattening improves the expression of genes that regulate lipid deposition in yaks and enhances meat quality. This finding will contribute to a better understanding of the various factors that determine yak meat quality and help develop strategies to improve yield and quality. [ABSTRACT FROM AUTHOR]

Simple Summary: Yaks can grow in extremely harsh natural environmental conditions, such as high altitude, low temperature, and hypoxia, and hair plays an important role. As an appendage of the skin, hair follicles involve the specialization of various types of cells and intercellular communication during morphogenesis. Here, we used single-cell RNA sequencing technology to identify 11 cell types from the scapular skin of yaks, constructed a transcription map of the main cells of hair follicles in the skin, and described the heterogeneity of DP cells and dermal fibroblasts in the hair follicle cycle. Our findings provide a molecular landscape of the fate determination process of dermal cell lineages. Our research provides valuable resources for further exploration of the molecular pathways involved in hair follicles. The morphogenesis of hair follicle structure is accompanied by the differentiation of skin tissue. Mammalian coats are produced by hair follicles. The formation of hair follicles requires signal transmission between the epidermis and dermis. However, knowledge of the transcriptional regulatory mechanism is still lacking. We used single-cell RNA sequencing to obtain 26,573 single cells from the scapular skin of yaks at hair follicle telogen and anagen stages. With the help of known reference marker genes, 11 main cell types were identified. In addition, we further analyzed the DP cell and dermal fibroblast lineages, drew a single-cell map of the DP cell and dermal fibroblast lineages, and elaborated the key genes, signals, and functions involved in cell fate decision making. The results of this study provide a very valuable resource for the analysis of the heterogeneity of DP cells and dermal fibroblasts in the skin and provide a powerful theoretical reference for further exploring the diversity of hair follicle cell types and hair follicle morphogenesis. [ABSTRACT FROM AUTHOR]

Simple Summary: The methylation level of testicular tissue in young yaks and adult yaks was determined, and the N6-methyladenosine (m6A) level was significantly increased after sexual maturity. Functional enrichment analysis of differentially methylated mRNAs screened between the two groups after sequencing showed that they mainly regulated cell development, spermatogenesis, and testicular endocrine function. Functional analysis of the differentially expressed genes screened between the two groups showed that they were involved in the biological processes of mitosis, meiosis, and flagellated sperm motility. Finally, several genes related to spermatogenesis were screened for further verification. Studying the mechanism of spermatogenesis is key to exploring the reproductive characteristics of male yaks. Although N6-methyladenosine (m6A) RNA modification has been reported to regulate spermatogenesis and reproductive function in mammals, the molecular mechanism of m6A in yak testis development and spermatogenesis remains largely unknown. Therefore, we collected testicular tissue from juvenile and adult yaks and found that the m6A level significantly increased after sexual maturity in yaks. In MeRIP-seq, 1702 hypermethylated peaks and 724 hypomethylated peaks were identified. The hypermethylated differentially methylated RNAs (DMRs) (CIB2, AK1, FOXJ2, PKDREJ, SLC9A3, and TOPAZ1) mainly regulated spermatogenesis. Functional enrichment analysis showed that DMRs were significantly enriched in the adherens junction, gap junction, and Wnt, PI3K, and mTOR signaling pathways, regulating cell development, spermatogenesis, and testicular endocrine function. The functional analysis of differentially expressed genes showed that they were involved in the biological processes of mitosis, meiosis, and flagellated sperm motility during the sexual maturity of yak testis. We also screened the key regulatory factors of testis development and spermatogenesis by combined analysis, which included BRCA1, CREBBP, STAT3, and SMAD4. This study indexed the m6A characteristics of yak testicles at different developmental stages, providing basic data for further research of m6A modification regulating yak testicular development. [ABSTRACT FROM AUTHOR]

Simple Summary: Yak are an important source of produce and living materials for plateau herdsmen. However, the population of yak is small and their reproductive capacity is low, so it is very important to improve their reproductive potential. The epididymis is an important place for sperm maturation and storage, but the differential expression of the cauda epididymis before and after sexual maturity in yak has not been characterized. In this study, the key genes regulating epididymal cauda development and sperm maturation were screened by RNA-seq and proteomics. These results ultimately provide a theoretical basis for how to improve the reproductive potential of yak. Epididymis development is the basis of male reproduction and is a crucial site where sperm maturation occurs. In order to further understand the epididymal development of yak and how to regulate sperm maturation, we conducted a multi-omics analysis. We detected 2274 differential genes, 222 differential proteins and 117 co-expression genes in the cauda epididymis of yak before and after sexual maturity by RNA-seq and proteomics techniques, which included TGFBI, COL1A1, COL1A2, COL3A1, COL12A1, SULT2B1, KRT19, and NPC2. These high abundance genes are mainly related to cell growth, differentiation, adhesion and sperm maturation, and are mainly enriched via extracellular matrix receptor interaction, protein differentiation and absorption, and lysosome and estrogen signaling pathways. The abnormal expression of these genes may lead to the retardation of epididymal cauda development and abnormal sperm function in yak. In conclusion, through single and combined analysis, we provided a theoretical basis for the development of the yak epididymal cauda, sperm maturation, and screening of key genes involved in the regulation of male yak reproduction. [ABSTRACT FROM AUTHOR]

Simple Summary: Exosomes are multivesicular bodies produced and secreted by living cells as membranous vesicles with a diameter of about 30–150 nm, density of 1.13–1.19 g/mL, and a typical "cup dish" shape. Exosomes carry proteins, miRNA, lncRNA, circRNA, and mRNA and their degradation fragments are involved in intracellular signal transduction important for regulation of cellular activities. Of these, miRNAs play an important role in the regulation of gene expression in important biological processes such as cell division, tissue development, and immune response. In this study, milk quality was determined and exosome miRNAs from yak and Jeryak milk sampled in June and December were characterized by sequencing. Differentially expressed miRNAs (DEMs) and pathways related to lactation performance were identified. In summary, this study provides data that can be used to develop alternative strategies for improving the lactation performance of yaks and Jeryaks. The Jeryak is the hybrid offspring of yaks and Jersey cattle and exhibit improved milk and meat yields. Biomolecules carried within milk exosomes are important for cell growth, development, immune regulation, and various pathophysiological processes. Previous studies showed that miRNAs regulate mammary gland development, lactation, and milk quality. This study explored the relationship between milk exosomes miRNAs and lactation performance. A comparison of the milk content showed that yak milk was of a better quality compared to Jeryak milk (casein, fat, TS, SNF, lactose). Milk collected in December was superior to that collected in June for both yak and Jeryak, except for lactose concentrations. Exosomes were extracted by density gradient centrifugation and miRNA expression profiles in milk exosomes from three yaks and three Jeryaks collected in June and December were detected by small RNA sequencing. In all, 22, 120, 78, and 62 differentially expressed miRNAs (DEMs) were identified in Jun_ JY vs. Jun_ Y (P1: Jeryak in June vs. Yak in June), Jun_ JY vs. Dec_ JY (P2: Jeryak in June vs. Jeryak in December), Dec_ JY vs. Dec_ Y (P3: Jeryak in December vs. Yak in December), and Jun_ Y vs. Dec_ Y (P4: Yak in June vs. Yak in December) groups. These DEMs were enriched in functions and signaling pathways related to lactation performance. In conclusion, these findings are a reference tool to study the molecular basis of lactation performance. [ABSTRACT FROM AUTHOR]

Simple Summary: The SOX6 (sex determining region Y-box 6) gene belongs to one of the transcription factors in the SRY (sex-determining region Y) family, which affects sex determination, embryonic and nervous system development, bone and various organ formation. In the previous study, the whole-genome sequencing was used to detect multiple genes located in the copy number variation region, including SOX6 gene. In this study, we identified the correlation between the growth traits and CNV of SOX6 in 311 Ashidan yaks. The results showed that 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), suggesting the SOX6-CNV affect growth traits in yaks, and could be new markers for the selection of yak breeding. 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. [ABSTRACT FROM AUTHOR]

Simple Summary: Yaks are among the largest high-altitude mammals in the world, and they are ideally adapted to the harsh environmental conditions of the plateau regions. Yaks are thus central to the lives of herdsmen and other local populations in these high-altitude areas. Copy number variations (CNVs) are an important cause of genomic variation in livestock and identifying advantageous CNVs can aid in livestock breeding efforts. In this study, an association between CNVs in the MICALL2 and MOGAT2 genes and Ashidan yak growth traits was confirmed, providing a theoretical foundation for Ashidan yak breeding and meat production efforts. 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. [ABSTRACT FROM AUTHOR]

Simple Summary: Kecai yaks are an important genetic resource in Gansu Province, China. These yaks, produced through the crossbreeding of Gannan yaks and wild yaks, exhibit excellent production performance and high fecundity. Despite these beneficial characteristics, the genetic characteristics, population structure, and other properties of Kecai yaks have not been effectively characterized to date. Accordingly, this study was developed to explore the genetic diversity and population structure of Kecai yaks through whole-genome resequencing. These analyses ultimately revealed the status of Kecai yaks as an independent group within the overall Chinese yak population. Kecai yaks are regarded as an important genetic resource in China owing to their high fecundity and flavorful meat. However, the genetic characteristics of Kecai yaks have not been effectively characterized to date, and the relationship between Kecai yaks and other yak breeds remains to be fully characterized. In this paper, the resequencing of the Kecai yak genome is performed leading to the identification of 11,491,383 high-quality single nucleotide polymorphisms (SNPs). Through principal component, phylogenetic, and population genetic structure analyses based on these SNPs, Kecai yaks were confirmed to represent an independent population of yaks within China. In this study, marker and functional enrichment analysis of genes related to positive selection in Kecai yak was carried out, and the results show that such selection in Kecai yaks is associated with the adaptation to alpine environments and the deposition of muscle fat. Overall, these results offer a theoretical foundation for the future utilization of Kecai yak genetic resources. [ABSTRACT FROM AUTHOR]

Simple Summary: Single-cell sequencing technology can reflect cell population heterogeneity at the single-cell level, leading to a better understanding of the role of individual cells in the microenvironment. Over the past few years, single-cell sequencing technology has not only made more new discoveries in the study of cellular heterogeneity of other rare cells such as stem cells, but has also become the most powerful research method for embryonic development, organ differentiation, cancer occurrence, and cell mapping. In this review, we outline the use of scRNA-seq in hair follicles. In particular, by focusing on landmark studies and the recent discovery of novel subpopulations of hair follicles, we summarize the phenotypic diversity of hair follicle cells and their links to hair follicle morphogenesis. Enhancing our understanding of the progress of hair follicle research will help to elucidate the regulatory mechanisms that determine the fate of different types of cells in the hair follicle, thereby guiding hair loss treatment and hair-producing economic animal breeding research. Single-cell sequencing technology can fully reflect the heterogeneity of cell populations at the single cell level, making it possible for us to re-recognize various tissues and organs. At present, the sequencing study of hair follicles is transiting from the traditional ordinary transcriptome level to the single cell level, which will provide diverse insights into the function of hair follicle cells. This review focuses on research advances in the hair follicle microenvironment obtained from scRNA-seq studies of major cell types in hair follicle development, with a special emphasis on the discovery of new subpopulations of hair follicles by single-cell techniques. We also discuss the problems and current solutions in scRNA-seq observation and look forward to its prospects. [ABSTRACT FROM AUTHOR]

Simple Summary: As a domestic animal living in the Qinghai-Tibet Plateau at high altitudes from 2000 to 5000 m, the growth rate of the yak is slow under extremely harsh natural environmental conditions, such as high altitude, low temperatures, and low oxygen. Compared with conventional selection, using molecular markers in breeding to improve yak growth traits is more efficient. Many studies have indicated that CNV mutations can significantly affect the phenotypic traits of livestock and poultry. This study explored the association between the growth traits and CNVs of SOX5 and SOX8 in 326 Ashidan yaks. Our results showed that CNVs and the CNV combination of SOX5 and SOX8 were significantly associated with withers height and chest girth (p < 0.05), suggesting these mutations could be new markers for the selection of yak growth traits. Copy number variation (CNV) is a structural variant with significant impact on genetic diversity. CNV has been widely used in breeding for growth traits, meat production or quality, and coat color. SRY-like box genes (SOXs) are a class of transcription factors that play a regulatory role in cell fate specification and differentiation. SOX5 and SOX8 belong to subgroups D and E of the SOXs, respectively. Previous studies have shown that SOX5 and SOX8 are essential in the development of bones. In this study, we explored the association between the growth traits and CNVs of SOX5 and SOX8 in 326 Ashidan yaks and detected mRNA expression levels in different tissues. Our results illustrated that CNVs of SOX5 and SOX8 were significantly associated with withers height at 18 months of age and chest girth at 30 months of age (p < 0.05). The CNV combination of SOX5 and SOX8 was significantly associated with withers height at 18 months of age (p < 0.01). SOX5 expression in the lung was significantly higher than in the heart, spleen, kidney, and muscle (p < 0.05). SOX8 expression in the lung was significantly higher than in the liver and muscle (p < 0.05). Our results provide evidence that the CNVs of SOX5 and SOX8 genes could be used as new markers for the selection of yak growth traits. [ABSTRACT FROM AUTHOR]

Simple Summary: In mammals, the testis-specific serine/threonine kinase (TSSK) is essential for spermatogenesis and male fertility. This study aimed to analyze the possible alternative spliceosomes of the TSSK4 gene in the yak testis tissue using PCR amplification and cloning techniques. A total of six alternative spliceosomes were obtained, of which there were only two alternative spliceosomes in the yak testis before sexual maturity and four alternative spliceosomes in the yak testis after sexual maturity. In mammals, the testis-specific serine/threonine kinase (TSSK) is essential for spermatogenesis and male fertility. TSSK4 belongs to the family of the testis-specific serine/threonine-protein kinase (TSSK), with a crucial role in spermatogenesis. This study aimed to analyze the variable spliceosome of the TSSK4 gene in the yak for understanding the regulatory function of the TSSK4 spliceosome in yak testis development using PCR amplification and cloning techniques. The GST pull-down was used for pulling down the protein interacting with TSSK4, and then the protein interacting with TSSK4 was identified using LC–MS/MS. The results of the PCR amplification demonstrated multiple bands of the TSSK4 gene in the yak. The cloning and sequencing yielded a total of six alternative spliceosomes, which included only two alternative spliceosomes before sexual maturity and four alternative spliceosomes after sexual maturity. The sub-cells of the alternative spliceosomes were found to localize in the nucleus before sexual maturity and in the cytoplasm after sexual maturity. The LC–MS/MS analysis of the alternative spliceosome with the highest expression after sexual maturity yielded a total of 223 interacting proteins. The enrichment analysis of the 223 interacting proteins revealed these proteins participate in biological processes, cell composition, and molecular functions. The KEGG analysis indicated that the TSSK4-interacting protein participates in the estrogen signaling pathways, tight junctions, endoplasmic reticulum protein processing, and other signaling pathways. This study cloned the six alternative spliceosomes of the TSSK4 gene laying the foundation for studying the function of each spliceosome in the future. [ABSTRACT FROM AUTHOR]

Simple Summary: In order to study the influence of RNA editing sites on lactation and mammary gland development process in yaks, we comprehensively characterized the RNA editome of the yak mammary gland during the lactation period and dry period by using the transcriptome and genome sequencing data. The results revealed 82,872 nonredundant RNA editing sites, 14,159 of which were differentially edited between the lactation period and dry period. Enrichment analysis showed that the genes harboring differential editing sites were mainly associated with mammary gland development-related pathways, such as MAPK pathway, PI3K-Akt pathway, FoxO signaling pathway, GnRH signaling pathway, and focal adhesion pathway. Our findings offer some novel insights into the RNA editing function in the mammary gland of yaks. The mammary gland is a complicated organ comprising several types of cells, and it undergoes extensive morphogenetic and metabolic changes during the female reproductive cycle. RNA editing is a posttranscriptional modification event occurring at the RNA nucleotide level, and it drives transcriptomic and proteomic diversities, with potential functional consequences. RNA editing in the mammary gland of yaks, however, remains poorly understood. Here, we used REDItools to identify RNA editing sites in mammary gland tissues in yaks during the lactation period (LP, n = 2) and dry period (DP, n = 3). Totally, 82,872 unique RNA editing sites were identified, most of which were detected in the noncoding regions with a low editing degree. In the coding regions (CDS), we detected 5235 editing sites, among which 1884 caused nonsynonymous amino acid changes. Of these RNA editing sites, 486 were found to generate novel possible miRNA target sites or interfere with the initial miRNA binding sites, indicating that RNA editing was related to gene regulation mediated by miRNA. A total of 14,159 RNA editing sites (involving 3238 common genes) showed a significant differential editing level in the LP when compared with that in the DP through Tukey's Honest Significant Difference method (p < 0.05). According to the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, genes that showed different RNA editing levels mainly participated in pathways highly related to mammary gland development, including MAPK, PI3K-Akt, FoxO, and GnRH signaling pathways. Collectively, this work demonstrated for the first time the dynamic RNA editome profiles in the mammary gland of yaks and shed more light on the mechanism that regulates lactation together with mammary gland development. [ABSTRACT FROM AUTHOR]

Simple Summary: In this study, yak's TLR4 gene alternative spliceosomes were investigated using PCR amplification and cloning with an aim to improve disease-resistance in yaks and promote efficient utilization of yak's resources. qRT-PCR was used to evaluate the expression levels of two alternatively spliced TLR4 transcripts in seven distinct yak tissues. To predict the function of proteins expressed by each TLR4 spliceosome, TLR4 protein structure and function were analyzed bioinformatically. Besides, two alternative spliceosomes of yak's TLR4 gene were also identified, which were in line with predicted variants of the TLR4 gene in NCBI. These two alternative spliceosomes of the TLR4 gene were expressed in each tissue; however, the expression levels of these spliceosomes were significantly different in different tissue. We also observed that deletion of exon-2 in TLR4 affected the function of the corresponding protein. This study will lay a theoretical foundation for future studies on the role of two variants of yak's TLR4 gene in disease resistance. Besides, data from this study could be analyzed further to explore the molecular mechanism associated with disease-resistance in the yak. In this study, the yak's TLR4 gene alternative spliceosomes were investigated using PCR amplification and cloning to improve disease-resistance in yak and promote efficient utilization of yak's resources. qRT-PCR was used to determine the expression levels of two alternatively spliced transcripts of the TLR4 gene in seven distinct tissues. To predict the function of proteins expressed by each TLR4 spliceosome, bioinformatic analysis of yak's TLR4 protein structure and function was performed, which led to the identification of two alternative spliceosomes of yak's TLR4 gene. The TLR4-X1 sequence length was 2526 bp, and it encoded full-length TLR4 protein (841 amino acids). The sequence length of the exon-2 deleted TLR4-X2 sequence was 1926 bp, and it encoded truncated TLR4 protein (641 amino acids). TLR4-X2 sequence was consistent with the predicted sequence of the TLR4 gene in GenBank. Each tissue showed significantly different expression levels of these two alternative spliceosomes. As per the bioinformatic analysis of the structure and function of TLR4 protein, deletion of exon-2 in the TLR4 gene resulted in frameshift mutations of the reading frame in the corresponding protein, which altered its ligand-binding and active sites. Besides, biological property such as substrate specificity of truncated TLR4 protein was also altered, leading to altered protein function. This study has laid a theoretical foundation for exploring the role of two variants of the TLR4 gene in yak's disease resistance. Besides, this study's data could be analyzed further to explore the molecular mechanism associated with disease-resistance in the yak. [ABSTRACT FROM AUTHOR]

Simple Summary: Genomic selection is a new technology in animal breeding after the selection according to the best linear unbiased prediction (BLUP) value and marker assisted selection. Genomic selection has gradually been used in practical applications over recent years following the advent of high-density single nucleotide polymorphism (SNP) chips for livestock and poultry. Yak are a critical species on the Qinghai–Tibet Plateau, which is of great significance to herders. The early selection of yak could save feeding costs and shorten the generation interval. In the present study, we estimated the accuracy of genomic prediction compared with different classical models for yak early growth traits. The results of cross-validation indicated that the average predictive accuracy ranged from 0.147 to 0.391. The average correlation coefficient between prediction and true phenotype was 0.4. Genomic selection is a promising breeding strategy that has been used in considerable numbers of breeding projects due to its highly accurate results. Yak are rare mammals that are remarkable because of their ability to survive in the extreme and harsh conditions predominantly at the so-called "roof of the world"—the Qinghai–Tibetan Plateau. In the current study, we conducted an exploration of the feasibility of genomic evaluation and compared the predictive accuracy of early growth traits with five different approaches. In total, four growth traits were measured in 354 yaks, including body weight, withers height, body length, and chest girth in two early stages of development (weaning and yearling). Genotyping was implemented using the Illumina BovineHD BeadChip. The predictive accuracy was calculated through five-fold cross-validation in five classical statistical methods including genomic best linear unbiased prediction (GBLUP) and four Bayesian methods. Body weights at 30 months in the same yak population were also measured to evaluate the prediction at 6 months. The results indicated that the predictive accuracy for the early growth traits of yak ranged from 0.147 to 0.391. Similar performance was found for the GBLUP and Bayesian methods for most growth traits. Among the Bayesian methods, Bayes B outperformed Bayes A in the majority of traits. The average correlation coefficient between the prediction at 6 months using different methods and observations at 30 months was 0.4. These results indicate that genomic prediction is feasible for early growth traits in yak. Considering that genomic selection is necessary in yak breeding projects, the present study provides promising reference for future applications. [ABSTRACT FROM AUTHOR]

Simple Summary: The serum, fatty acid and transcriptome profiles in the subcutaneous fat of yaks were measured to explore the effect of long-term energy stress (ES) on fat metabolism during the cold season. The study indicated that under long-term ES during the cold season, the amount of fat in yaks was less, and fat mobilization was one of the main ways by which energy was obtained in yaks. Yaks regulated fat metabolism in subcutaneous fat primarily through adenosine 5′-monophosphate-activated protein kinase (AMPK) signaling. Glucose (GLU) intake, fat catabolism, fatty acid synthesis and fatty acid oxidation in the subcutaneous fat of yaks were all inhibited, which resulted in the fat mobilization of yaks slowing as much as possible under long-term ES. In addition, the energy expenditures in fat cells were inhibited by regulating phosphatidylinositol 3' -kinase (PI3K)-serine/threonine-protein kinase (Akt) andmammalian target of rapamycin (mTOR) signaling, and the limited energy obtained from GLU and fat was consumed by muscle and organs as much as possible. These factors led to an energy balance in yaks under long-term ES. The fat stored in yaks can be expended for as long as possible, and yaks can survive for as long as necessary under long-term ES. Long-term energy stress (ES) during the cold season is a serious problem for the breeding of yaks. In this paper, the response of fat metabolism in yaks to long-term ES during the cold season was studied. Gas chromatography (GC) analysis showed that the percentage of saturated fatty acids (SFAs) in the subcutaneous fat of the yaks in the ES group was 42.7%, which was less than the 56.6% in the CO group (p < 0.01) and the percentage of polyunsaturated unsaturated fatty acids (PUFAs) in the subcutaneous fat of the yaks in the ES group was 38.3%, which was more than the 26.0% in the CO group (p < 0.01). The serum analysis showed that fatty acid oxidation in yaks was increased under long-term ES. In the subcutaneous fat of yaks under long-term ES, the gene expression levels of glycerol-3-phosphate acyltransferase 4 (GPAT4), hormone-sensitive lipase (HSL), patatin-like phospholipase domain-containing protein 2 (PNPLA2), acyl-CoA dehydrogenase (ACAD), acyl-coenzyme A thioesterase 8 (ACOT8), facilitated glucose transporter (GLUT4), 3-oxoacyl-[acyl-carrier-protein] synthase (OXSM), oestradiol 17-beta-dehydrogenase 8 (HSD17B8) and malonate-Co-A ligase ACSF3 (ACSF3) were downregulated (q < 0.05), whereas the gene expression levels of aquaporin-7 (AQP7), long-chain-fatty-acid-CoA ligase (ACSL), elongation of very long chain fatty acids protein (ELOVL) and fatty acid desaturase 1 (FADS1) were upregulated (q < 0.05), indicating the inhibition of fat catabolism, fat anabolism, fatty acid oxidation, glucose (GLU) intake and SFA synthesis and the promotion of glycerinum (GLY) transportation and PUFA synthesis. Additional findings showed that the gene expression levels of leptin (LEP), adenosine 5′-monophosphate-activated protein kinase (AMPK) and phosphatidylinositol 3-kinase (PI3K) were upregulated (q < 0.05), whereas the gene expression levels of malonyl-CoA decarboxylase (MCD), sterol regulatory element-binding protein 1 (SREBF1), mammalian target of rapamycin (mTOR) and serine/threonine-protein kinase (AKT) were downregulated (q < 0.05), indicating that fat metabolism in the subcutaneous fat of yaks under ES was mainly regulated by AMPK signaling and mTOR and PI3K-AKT signaling were also involved. Energy consumption was inhibited in the subcutaneous fat itself. This study can provide a theoretical basis for the healthy breeding and genetic breeding of yaks. [ABSTRACT FROM AUTHOR]

Simple Summary: Yak (Bos grunniens) provides life materials for herdsmen in high-plateau areas. Improving their low fertility is necessary to meet the demands of the development of the yak industry. The testis is an important organ for male fertility, its development is controlled by a large number of genes. Using real-time reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) to explore the quantitative expression of genes can provide insights for illuminating the molecular mechanisms of testis development, but the RT-qPCR data are influenced by the stability of reference genes (RGs). Unfortunately, no available RGs can normalize the gene expression in yak testis development. In this study, the expression stability of 13 candidate genes in yak testis at different developmental stages was evaluated using five different pieces of software. The results showed that the TATA box-binding protein (TBP) and ubiquitously expressed transcript protein (UXT) exhibited high stability across various developmental stages, TBP and hydroxymethylbilane synthase (HMBS) were the most stably expressed genes in immature stages, and mitochondrial ribosomal protein L39 (MRPL39) and TBP exhibited the most stable expression across mature stages. This study provided suitable RGs for gene expression studies in yak testis development. Testis has an important function in male reproduction. Its development is regulated by a large number of genes. The real-time reserve transcriptase-quantitative polymerase chain reaction (RT-qPCR) is a useful tool to evaluate the gene expression levels. However, unsuitable reference genes (RGs) can cause the misinterpretation of gene expression levels. Unfortunately, the ideal RGs for yak testis development are yet to be studied. In this study, 13 commonly used RGs were selected to identify the most stable RGs in yak testis at four different developmental stages, including two immature stages (6 months and 18 months) and two mature stages (30 months and 6 years). This study used GeNorm, NormFinder, BestKeeper, ∆Ct, and RefFinder programs to evaluate the stability of 13 candidate genes. The results of RefFinder showed that the stabilities of TATA box-binding protein (TBP) and ubiquitously expressed transcript protein (UXT) were ranked the top two across all developmental stages. TBP and hydroxymethylbilane synthase (HMBS) were stably expressed in immature stages, while mitochondrial ribosomal protein L39 (MRPL39) and TBP had higher stability than other candidate genes in mature stages. This study provided valuable information for gene expression studies to assist further investigation on the molecular mechanisms in underlying yak testis development. [ABSTRACT FROM AUTHOR]

Simple Summary: Previous studies revealed that luteinizing hormone βeta polypeptide (LHB) plays an essential role in fertilization. Therefore, we aimed to confirm the importance of LHB in the testis of yak and to determine their association with male yak fertility. Histomorphological analysis of the testes is essential for predicting the fertilizing ability of the bull. To the best our knowledge, this is the first study to evaluate the micro anatomical changes and histometric alternation in testes of Datong yak. These findings could help to predict the sperm production capacity and to understand the specific molecular mechanisms of LHB during spermatogenesis. Histological examination of testes is essential for understanding infertility, sex development, and growth. Therefore, to understand the histomorphology of testes at different developmental stages, we performed hematoxylin and eosin staining of Yak testis. Our results revealed that the diameters of spermatogenic cells and their nuclei were significantly larger (p < 0.05) in the testis at six years compared to at six and 18 months. No significant difference was noted between 30 months and six years. The study was designed to compare the expression profile of LHB in Datong yak. The expression pattern of LHB was explored using quantitative PCR, semi-quantitative PCR, molecular bioinformatic, and Western blot analysis. Our observations indicated that expression of LHB was significantly higher (p < 0.05) in the testis of Datong yak. Western blotting indicated that the molecular mass of LHB protein was 16 kDa in yak. The protein encoded by yak LHB included conserved cysteine-knot domain regions. The high expression of LHB in testis indicated that LHB may be vital for the development of male gonads and the fertility of Datong yak. [ABSTRACT FROM AUTHOR]

Simple Summary: The Ashidan yak is a new cultivated breed which has polled characteristics and a mild temperament. Improving milk yield is an important aspect of a breeding program for this breed. The mammary gland undergoes dramatic physiological and metabolic changes during the transition from lactation to dry periods, which involves the expression and regulation of a great number of genes. Quantification of gene expression levels by real-time quantitative polymerase chain reaction (RT-qPCR) is important to reveal the molecular mechanisms of mammary gland development and lactation. The accuracy of RT-qPCR is strongly influenced by the expression stability of reference genes, however, a systematic approach for selecting reference genes used for analyzing gene expression of the Ashidan yak has not been developed. In this study, we selected reference genes and analyzed their expression stability at different physiological stages (lactation and dry period). We found the hydroxymethylbilane synthase gene (HMBS) and the tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide gene (YWHAZ) were the most stable genes of the mammary gland of the Ashidan yak. These results help to improve the accuracy of gene expression analysis and provide a basis for future functional studies of target gene expression in the mammary gland of the Ashidan yak. Investigating the critical genes related to milk synthesis is essential for the improvement of the milk yield of the yak. Real-time quantitative polymerase chain reaction (RT-qPCR) is a reliable and widely used method to measure and evaluate gene expression levels. Selection of suitable reference genes is mandatory to acquire accurate normalization of gene expression results from RT-qPCR. To select the most stable reference genes for reliable normalization of mRNA expression by RT-qPCR in the mammary gland of the Ashidan yak, we selected 16 candidate reference genes and analyzed their expression stability at different physiological stages (lactation and dry period). The expression stability of the candidate reference genes was assessed using geNorm, NormFinder, BestKeeper, Delta Ct, and RefFinder methods. The results showed that the hydroxymethylbilane synthase gene (HMBS) and the tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide gene (YWHAZ) were the most stable genes across all treatment samples. The reliability of selected reference genes was validated by normalizing relative expression of the lactation-related 60S ribosomal protein L35 gene (RPL35). The relative expression of RPL35 varied considerably according to the different reference genes. This work provides valuable information to further promote research in the molecular mechanisms involved in lactation and mammary gland development and provides a foundation for the improvement of the milk yield and quality of the Ashidan yak. [ABSTRACT FROM AUTHOR]

Simple Summary: The domesticated yak is among the most important livestock species on the Qinghai-Tibet Plateau. Breeders have the task of developing varieties that provide growth performance and disease resistance. Traditional breeding processes rely on complete family pedigree information and large numbers of data records. However, there are inevitably records that are missing, including incomplete pedigrees and long-term data tracking, resulting in prolonged breeding cycles, reduced breeding efficiency, and the lack of economic benefit. Genome selection (GS), also known as whole genomic selection (WGS), can significantly reduce the selection cycle of quantitative traits and accelerate genetic progression while displaying appropriate prediction accuracy (PA). It combines a reference population and single nucleotide polymorphism (SNP) loci rather than pedigrees to estimate the effect of all SNPs. Then breeding values of target traits are predicted. The key for GS is genomic prediction (GP) and an assessment of PA. The aim of this study was to explore the possibility of applying GP to important economic traits in the domesticated yak, thus providing theoretical support for its molecular breeding. A reference population was constructed consisting of 354 polled yaks, measuring four growth traits and eight hematological traits related to resistance to disease (involved in immune response and phagocytosis). The Illumina bovine HD 770k chip was used to obtain SNP information of all the individuals. With these genotypes and phenotypes, GBLUP, Bayes B and Bayes Cπ methods were used to predict genomic estimated breeding values (GEBV) and assess prediction capability. The correlation coefficient of the association of GEBV with estimated breeding value (EBV) was used as PA for each trait. The prediction accuracy varied from 0.043 to 0.281 for different traits. Each trait displayed similar PAs when using the three methods. Lymphocyte counts (LYM) exhibited the highest predictive accuracy (0.319) during all GP, while chest girth (CG) provided the lowest predictive accuracy (0.043). Our results showed moderate PA in most traits such as body length (0.212) and hematocrit (0.23). Those traits with lower PA could be improved by using SNP chips designed specifically for yak, a better optimized reference group structure, and more efficient statistical algorithms and tools. [ABSTRACT FROM AUTHOR]

Simple Summary: IZUMO1 (IZUMO sperm-egg fusion) is a crucial member of the immunoglobulin superfamily, and it plays a vital part in egg sperm interaction, fusion, and in spermatogenesis. Previous studies identified the fundamental role of the IZUMO1 gene in meiosis of bovine spermatogenesis and spermatogenic cell development and fertility. The current study confirmed the significant expression of the IZUMO1 gene with testicular development and its potential role in fertilization of Datong yak. This research explained the biological role of IZUMO1 in yak reproduction; therefore in the future it might provide a novel prospect to apply data on reproduction and to understand the further regulatory mechanisms of the IZUMO1 gene during spermatogenesis of different mammalian species. The IZUMO1 gene has promising benefits for the national development of novel non-hormonal contraceptives and in the treatments of fertility. Understanding the function of IZUMO1, its mRNA, and protein expression is critical to gain insight into spermatogenesis and promote sperm-egg fusion during reproduction of Datong yak. Therefore, we estimated the IZUMO1 gene expression in different ages of Datong yak by using semi quantitative PCR, qPCR, and western blotting. The results of the qPCR, semi-quantitative PCR and western blotting revealed that the expression level of IZUMO1 mRNA was significantly (p < 0.05) higher in the testis of 30 months and 6 years old followed by 18 and 6 months old Datong yak, respectively. We also predicted secondary and tertiary protein structure of IZUMO1 by using bioinformatics software that the revealed presence of a signal peptide, Izumo domain, immunoglobulin (Ig) like domain, and transmembrane region. Moreover, immunostaining analysis also elucidated that IZUMO1 was more prominent in the testis of 30 months and 6 years old yak, which represented that the IZUMO1 gene expression might be higher during the peak breeding ages (6 to 7 years) of the yak, and play a potential role in spermatogenesis, fertility, and testicular development. [ABSTRACT FROM AUTHOR]

Simple Summary: Yak is always in a malnutrition condition under pure grazing in the cold season. Many studies have suggested that provision of supplementary feed to yak cannot only be an effective approach to avoid weight loss, but also improve productivity. Growth hormone (GH) and insulin-like growth factor 1 (IGF-1) could improve yak productivity. In current work, we evaluated the effects of different energy feedstuffs on the serum concentration of GH, IGF-1, and relative hepatic expression of their associated binding proteins and receptors, as well as growth performance of yak. The results indicated that average daily gain (ADG), body weight (BW), feed conversion ratio, serum IGF-1 concentration, and relative expression of IGF-1 and IGFBP-3 were increased with an increase in dietary energy level, while serum GH concentration and hepatic growth hormone (GHR) expression were decreased. Serum IGF-1 concentration, relative hepatic expression of IGF-1, and insulin-like growth factor binding protein 3 (IGFBP-3) showed positive correlation with ADG, but serum GH concentration and GHR expression were negatively correlated with ADG. Yak offered with medium energy diet (NEg: 6.2 MJ/kg) displayed better growth by gaining 0.883 kg/d and showing a superior feed conversion ratio during experiment. The objective of this study was to investigate the effects of different dietary energy levels on serum concentrations of growth hormone (GH) and insulin-like growth factor 1 (IGF-1), as well as gene expression of their associated binding proteins and receptors in yak. Fifteen adult male yaks with BW of 276.1 ± 3.5 kg were allotted in three dietary groups and were fed with low (LE), medium (ME), and high energy (HE) level diet having different NEg of 5.5 MJ/kg, 6.2 MJ/kg, 6.9 MJ/kg, respectively. The effects of these treatments on ADG, BW, ADFI, and feed conversion ratio were significant (p < 0.05) throughout the experimental period. Serum GH concentration decreased (p < 0.05) with an increase in dietary energy level on d 30 and d 60. While IGF-1 concentration was higher (p < 0.05) in ME group, as compared to LE and HE groups on d 60. The expression level of growth hormone receptor (GHR) was decreased (p < 0.001) and IGF-1 was increased with the increase in the dietary energy level. The relative expression of insulin-like growth factor binding protein 3 (IGFBP-3) was higher (p < 0.001) in ME and HE groups, except the LE group. In conclusion, our findings provide a first insight into the combined effect of GH and IGF-1 in controlling the metabolism and productivity of yak. It also showed that medium energy level diet contributed to promote growth performance of yak during the cold season. [ABSTRACT FROM AUTHOR]

Simple Summary: Associating copy number variations (CNVs) with growth and gene expression are a powerful approach for identifying genomic characteristics that contribute to phenotypic and genotypic variation. A previous study using next-generation sequencing illustrated that the KLF6 gene resides within CNV regions (CNVRs) of yak populations that overlap with quantitative trait loci (QTLs) of meat quality and growth. As a result, this research aimed to assess the prevalence of KLF6 CNVs in five Chinese domestic yak breeds and to determine their association with growth and gene expression level. These results confirmed the significant function of KLF6 CNVRs in determining the mRNA expression levels of this gene in Bos grunniens skeletal muscles and the expression of this gene affects quantitative growth traits in yak populations through the negative relationship between DNA copy numbers and gene expression. This work provides the first observation of the biological role of KLF6 CNVs in Chinese Datong yak breeds and might therefore provide a novel opportunity to utilize data on CNVs in designing molecular markers for the selection of animal breeding programs for larger populations of various yak breeds. Copy number variation (CNV) is a significant marker of the genetic and phenotypic diversity among individuals that accounts for complex quantitative traits of phenotype and diseases via modulating gene dosage and disrupting coding regions in the genome. Biochemically, Kruppel-like factor 6 (KLF6) genes plays a significant role in the regulation of cell differentiation and proliferation and muscle development. The aim of this study was to detect the distributions of KLF6 copy number variations (CNVs) in five breeds of domestic yak and to explore their effect on growth traits and gene expression. The data were analyzed by real-time quantitative PCR (qPCR). Our results elucidated that a decreased CNV in the KLF6 gene is more highly associated (p < 0.05) with various growth traits than increased or normal CNVs in six-month-old and five-year-old Datong yak. Nevertheless, negative correlations between the DNA copy number and KLF6 gene expression were observed in the skeletal muscle of adult Datong yak. These results suggest that CNVs of the KLF6 gene could be crucial genomic markers for growth phenotypes of Chinese Datong yak breeds and this finding constitutes the first evidence of the biological role of KLF6 CNVs in Chinese Datong yak breeds. [ABSTRACT FROM AUTHOR]