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Long non-coding RNAs (lncRNAs) have been extensively studied in recent years. Numerous lncRNAs have been identified in mice, rats, and humans, some of which play important roles in muscle formation and development. However, little is known about lncRNA regulators that affect muscle development in yak (Bos grunniens). LncRNA expression during skeletal muscle development in yak was analyzed by RNA sequencing at three development stages: 3 years (group A), 6 months (group M), and 90-day-old fetuses (group E). A total of 1180 lncRNAs were identified in the three development stages. Compared with group E, 154 were upregulated and 130 were downregulated in group A. Compared with group A, 31 were upregulated and 29 were downregulated in group M. Compared with group E, 147 were upregulated and 149 were downregulated in group M (padj < 0.001, |log2FC| > 1.2). In addition, functional annotation analysis based on gene ontology (GO) and the Kyoto protocol encyclopedia of genes and genomes (KEGG) database showed that differentially expressed lncRNAs (DElncRNAs) were cis–trans target genes. The results showed that DElncRNAs were mainly involved in PI3K-Akt signaling pathway, focal adhesion, MAPK signaling pathway, apoptosis, and p53 signaling pathway. Furthermore, RTL1, IGF2, MEF2C, Pax7, and other well-known muscle development regulators were included in a co-expression network of differentially expressed target genes and lncRNAs. These data will help to further clarify the function of lncRNAs in the different stages of skeletal muscle developmental in yak. [ABSTRACT FROM AUTHOR]

In the present study, we report the complete mitochondrial genome of Niangya yak (Bos grunniens) and its phylogenetic inferences. The complete mitochondrial DNA is a circular molecule with 16,322 bp length consisting of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a non-coding control region(D-loop). Both ND6 and 7 tRNAs (tRNA-Pro, tRNA-Glu, tRNA-Tyr, tRNA-Cys, tRNA-Asn, tRNA-Ala and tRNA-Gln) are encoded on the light strand, and the remaining genes are encoded on the heavy strand. The overall nucleotide composition is A(33.73%), T(27.28%), C(25.80%), G(13.19%) respectively. The content of C + G is 38.99%. Given that yak is indispensable for the Tibetan people, it is important to understand the genetic status of the population for further systematic genetics, evolutionary significance and protection of genetic resources. Therefore, to understand the evolutionary history of Niangya yak, the complete mitochondrial genome of Niangya yak was sequenced and compared with the mitochondrial genome of closely related Bos species. [ABSTRACT FROM AUTHOR]

Sibu yak is famous for its excellent breed in Tibet and has become a magic way for local herdsmen to get rich. The Sibu yak, however, has been identified as an endangered bovine species. In this study, the complete mitochondrial genome of Sibu yak (Bos grunniens) was sequenced. The complete mitochondrial genome is a circular molecule with 16,324 bp in length, including 2 rRNA genes, 13 protein-coding genes, 22 tRNA genes, and a non-coding control region (D-loop). The entire nucleotide composition is A(33.70%), T(27.27%), C(25,81%), G(13.21%), respectively. Except that ND6 and 7 tRNAs （tRNA-Glu,tRNA-Pro,tRNA-Cys, tRNA-Tyr, tRNA-Ala, tRNA-Asn, and tRNA-Gln) are encoded on the light strand, the remaining genes are encoded on the heavy strand. As a valuable resource, we have compared it to related Bos species to understand the evolutionary history of Sibu yak. [ABSTRACT FROM AUTHOR]

Yak is an ancient breed and Bazhou Yak is also one of China's unique yak breed resources. In the present study, its complete mitochondrial genome was assembled from Illumina sequencing data and we identified the complete mitochondrial genome of the Bazhou yak (Bos grunniens). The complete mitochondrial DNA is a circular molecule with 16,325 bp length consisting of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a non-coding control region (D-loop). The overall nucleotide composition is A (33.69%), T (27.30%), C (25.79%), and G (13.22%), respectively. The content of C + G is 39.01%. Phylogenetic analysis of the mitochondrial genomes of 15 related species by MEGA7.0 showed that the genetic relationship of Bazhou yak is closer to Datong yak and polled yak. [ABSTRACT FROM AUTHOR]

Maiwa yak is a unique local strain of yak breed resource in China. The complete mitochondrial genome was identified in this work. The mitochondrial DNA is a circular molecule with 16,324 bp in length, including 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a non-coding control region(D-loop). The overall nucleotide ratio is A (33.70%), G (13.22%), T (27.26%), C (25.82%) with a C + G content of 39.04%. Phylogenetic analysis of mitochondrial genomes of 17 close species using MEGA7.0 showed that Maiwa yak is most related to Pali yak and polled yak. [ABSTRACT FROM AUTHOR]

DNA methylation modifications are implicated in many biological processes. As the most common epigenetic mechanism DNA methylation also affects muscle growth and development. The majority of previous studies have focused on different varieties of yak, but little is known about the epigenetic regulation mechanisms in different age groups of animals. The development of muscles in the different stages of yak growth remains unclear. In this study, we selected the longissimus dorsi muscle tissue at three different growth stages of the yak, namely, 90-day-old fetuses (group E), six months old (group M), and three years old (group A). Using RNA-Seq transcriptome sequencing and methyl-RAD whole-genome methylation sequencing technology, changes in gene expression levels and DNA methylation status throughout the genome were investigated during the stages of yak development. Each group was represented by three biological replicates. The intersections of expression patterns of 7694 differentially expressed genes (DEGs) were identified (padj < 0.01, |log2FC| > 1.2) at each of the three developmental periods. Time-series expression profile clustering analysis indicated that the DEGs were significantly arranged into eight clusters which could be divided into two classes (padj < 0.05), class I profiles that were downregulated and class II profiles that were upregulated. Based on this cluster analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that DEGs from class I profiles were significantly (padj < 0.05) enriched in 21 pathways, the most enriched pathway being the Axon guidance signaling pathway. DEGs from the class II profile were significantly enriched in 58 pathways, the pathway most strongly enriched being Metabolic pathway. After establishing the methylation profiles of the whole genomes, and using two groups of comparisons, the three combinations of groups (M-vs.-E, M-vs.-A, A-vs.-E) were found to have 1344, 822, and 420 genes, respectively, that were differentially methylated at CCGG sites and 2282, 3056, and 537 genes, respectively, at CCWGG sites. The two sets of data were integrated and the negative correlations between DEGs and differentially methylated promoters (DMPs) analyzed, which confirmed that TMEM8C, IGF2, CACNA1S and MUSTN1 were methylated in the promoter region and that expression of the modified genes was negatively correlated. Interestingly, these four genes, from what was mentioned above, perform vital roles in yak muscle growth and represent a reference for future genomic and epigenomic studies in muscle development, in addition to enabling marker-assisted selection of growth traits. [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]

Yak (Bos grunniens) is an important domestic animal living in high-altitude plateaus. Due to inadequate disease prevention, each year, the yak industry suffers significant economic losses. The identification of causal genes that affect blood- and immunity-related cells could provide preliminary reference guidelines for the prevention of diseases in the population of yaks. The genome-wide association studies (GWASs) utilizing a single-marker or haplotype method were employed to analyze 15 hematological traits in the genome of 315 unrelated yaks. Single-marker GWASs identified a total of 43 significant SNPs, including 35 suggestive and eight genome-wide significant SNPs, associated with nine traits. Haplotype analysis detected nine significant haplotype blocks, including two genome-wide and seven suggestive blocks, associated with seven traits. The study provides data on the genetic variability of hematological traits in the yak. Five essential genes (GPLD1, EDNRA,APOB, HIST1H1E, and HIST1H2BI) were identified, which affect the HCT, HGB, RBC, PDW, PLT, and RDWSD traits and can serve as candidate genes for regulating hematological traits. The results provide a valuable reference to be used in the analysis of blood properties and immune diseases in the yak. [ABSTRACT FROM AUTHOR]