Background: The yak is a symbol of the Qinghai-Tibet Plateau and provides important basic resources for human life on the plateau. Domestic yaks have been subjected to strong artificial selection and environmental pressures over the long-term. Understanding the molecular mechanisms of phenotypic differences in yak populations can reveal key functional genes involved in the domestication process and improve genetic breeding. Material and method: Here, we re-sequenced 80 yaks (Maiwa, Yushu, and Huanhu populations) to identify single-nucleotide polymorphisms (SNPs) as genetic variants. After filtering and quality control, remaining SNPs were kept to identify the genome-wide regions of selective sweeps associated with domestic traits. The four methods (π, XPEHH, iHS, and XP-nSL) were used to detect the population genetic separation. Results: By comparing the differences in the population stratification, linkage disequilibrium decay rate, and characteristic selective sweep signals, we identified 203 putative selective regions of domestic traits, 45 of which were mapped to 27 known genes. They were clustered into 4 major GO biological process terms. All known genes were associated with seven major domestication traits, such as dwarfism (ANKRD28), milk (HECW1, HECW2, and OSBPL2), meat (SPATA5 and GRHL2), fertility (BTBD11 and ARFIP1), adaptation (NCKAP5, ANTXR1, LAMA5, OSBPL2, AOC2, and RYR2), growth (GRHL2, GRID2, SMARCAL1, and EPHB2), and the immune system (INPP5D and ADCYAP1R1). Conclusions: We provided there is an obvious genetic different among domestic progress in these three yak populations. Our findings improve the understanding of the major genetic switches and domestic processes among yak populations.

The yak is the largest meat-producing mammal around the Tibetan Plateau, and it plays an important role in the economic development and maintenance of the ecological environment throughout much of the Asian highlands. Understanding the genetic components of body weight is key for future improvement in yak breeding; therefore, genome-wide association studies (GWAS) were performed, and the results were used to mine plant and animal genetic resources. We conducted whole genome sequencing on 406 Maiwa yaks at 10 × coverage. Using a multiple loci mixed linear model (MLMM), fixed and random model circulating probability unification (FarmCPU), and Bayesian-information and linkage-disequilibrium iteratively nested keyway (BLINK), we found that a total of 25,000 single-nucleotide polymorphisms (SNPs) were distributed across chromosomes, and seven markers were identified as significantly (p-values < 3.91 × 10⁻⁷) associated with the body weight trait,. Several candidate genes, including MFSD4, LRRC37B, and NCAM2, were identified. This research will help us achieve a better understanding of the genotype–phenotype relationship for body weight.

Known as the “ship of the plateau”, through thousands of years evolution and cruelty environments selection containing low oxygen and strong ultraviolet radiation, yaks have adapted plateau environments and supplied important goods and materials for the people in the Qinghai‐Tibet Plateau. This study aimed to identify differentially expressed (DE) genes and novel long non‐coding RNAs (lncRNAs) of yaks for the Plateau adaptation and their underlying co‐expression and regulatory network. We carried out RNA‐seq analysis for cerebral and cerebellar tissue specimens of Bos taurus , Bos grunniens × Bos Taurus , and Bos grunniens . Furthermore, 12,072 pseudo lncRNAs were predicted using three software. In total, 4,257 significant DE transcripts were identified using the Ballgown R package (P<0.01), of which 1021 were protein‐coding genes, 14 were known lncRNAs, and 661 were novel lncRNAs. Using WGCNA, a co‐expression network of DE mRNAs and lncRNAs comprising 5 modules was generated to determine functional associations clusters. This study reveals a valuable sub‐network comprising 8 hub genes, one known lncRNA, and 5 novel lncRNAs in the major module. These hub genes are associated with blood pressure regulation, generation of reactive oxygen species, and metabolism. The analysis of co‐expressed genes thus provides a basis for the regulatory mechanisms in PA in Yaks and for the detection of additional genes between crossbreed and parent populations.

Yaks have evolved several breeds or genetic resources owing to their geographical and ecological environment, and investigating the genetic construction of body size among breeds is key for breeding. Here, a genome-wide association study (GWAS) was performed for five body size traits in 31 yak breeds and genetic resources. The information from clustering individuals according to their habitats was used for kinship grouping in the compressed mixed linear model (CMLM). We named this approach the pCMLM method. A total of 3,584,464 high-quality single nucleotide polymorphisms (SNPs) were obtained, and six markers were found to be significantly associated with height by pCMLM. Four candidate genes, including FXYD6, SOHLH2, ADGRB2, and OSBPL6, were identified. Our results show that when CMLM cannot identify optimal clustering groups, pCMLM can provide sufficient associated results based on population information. Moreover, this study provides basic information on the gene localization of quantitative traits of body size among yak breeds.

Methionine is an amino acid necessary for the growth and development of all animals. Glutathione produced during methionine metabolism can reduce damage to cells caused by oxidative stress. Supplementing restricted amino acids in animals by scientific means will be beneficial to protein synthesis, which will affect the growth and development of animals and will bring huge economic benefits when applied to actual production and life. In this study, we collected three muscle tissues from 24 male Maiwa yaks, which were fattened for three months with different methionine concentrations in their diet. RNA-seq was performed to obtain expression reads. A total of 1116 editing sites were identified by at least two software; the editing site types were mainly T-to-C and A-to-G mutations. We found two significant RNA editing sites presenting high-risk editing types. One was located on the MSRA gene that regulates the reduction of methionine, and the other can make changes to the properties of encoded proteins. This provides further understanding of the mechanism of yak muscle tissue and regulation of gene expression after the addition of methionine to daily rations.