Yak Breeds Research Articles

Identification of Candidate Genes Associated with Yak Body Size Using a Genome-Wide Association Study and Multiple Populations of Information.

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.

The Novel Structural Variation in the GHR Gene Is Associated with Growth Traits in Yaks (Bos grunniens)

The growth hormone receptor (GHR) is a member of the cytokine/hematopoietic factor receptor superfamily, which plays an important role in the growth and development, immunity, and metabolism of animals. This study identified a 246 bp deletion variant in the intronic region of the GHR gene, and three genotypes, including type II, type ID, and type DD, were observed. Genotype analysis of structural variation (SV) was performed on 585 individuals from 14 yak breeds, and it was found that 246 bp deletion was present in each breed. The II genotype was dominant in all yak breeds except for SB yak. The association analysis of gene polymorphisms and growth traits in the ASD yak population showed that the 246 bp SV was significantly associated with body length at 6 months (p < 0.05). GHR messenger RNA (mRNA) was expressed in all the tested tissues, with significantly higher levels in the liver, muscle, and fat than in other organs. The results of transcription activity showed that the luciferase activity of the pGL4.10-DD vector was significantly higher than that of the pGL4.10-II vector (p < 0.05). Additionally, the transcription-factor binding prediction results showed that the SV in the runt-related transcription factor 1 (Runx1) transcription-factor binding site may affect the transcriptional activity of the GHR gene, regulating yak growth and development. This study showed that the novel SV of the GHR gene could be used as a candidate molecular marker for the selection of the early growth trait in ASD yak.

Genome-Wide Landscape of mRNAs, lncRNAs, and circRNAs during Testicular Development of Yak.

Testicular development is a tightly regulated process in mammals. Understanding the molecular mechanisms of yak testicular development will benefit the yak breeding industry. However, the roles of different RNAs, such as mRNA, lncRNA, and circRNA in the testicular development of yak, are still largely unclear. In this study, transcriptome analyses were performed on the expression profiles of mRNAs, lncRNAs, and circRNAs in testis tissues of Ashidan yak at different developmental stages, including 6-months-old (M6), 18-months-old (M18), and 30-months-old (M30). A total of 30, 23, and 277 common differentially expressed (DE) mRNAs, lncRNAs, and circRNAs were identified in M6, M18, and M30, respectively. Furthermore, functional enrichment analysis showed that the common DE mRNAs during the entire developmental process were mainly involved in gonadal mesoderm development, cell differentiation, and spermatogenesis processes. Additionally, co-expression network analysis identified the potential lncRNAs related to spermatogenesis, e.g., TCONS_00087394 and TCONS_00012202. Our study provides new information about changes in RNA expression during yak testicular development, which greatly improves our understanding of the molecular mechanisms regulating testicular development in yaks.

Spatial distribution and ecological risk assessment of heavy metals in alpine grasslands of the Zoige Basin, China

Heavy metals elements are not only related to the functions of ecosystems but also affect human health. To understand the characteristics of heavy metals in the topsoil of the Zoige alpine basin, a total of 252 grass and topsoil samples were collected in May and September 2014. The results showed that only Cd and Pb highly exceeded their background values (BV); in May and September, Cd was 2.02- and 1.55-fold higher than its BV, respectively, and Pb was 2.35- and 2.17-fold above its BV, respectively. The sources of Cd and Pb were homologous. In addition, the comprehensive potential ecological risk index was less than 150, indicating that heavy metal pollution in the study area is currently low. The spatial interpolation indicated that Cd and Pb pollution might be related to tourism and transportation, but the low biological absorption coefficient for all heavy metals showed that heavy metal absorption ability of forage was low and would not impact yak breeding. Finally, the soil was lightly contaminated by Cd and Pb due to the rapid development of the animal husbandry and tourism. The spatial variation of heavy metal in the basin is dominated by structural factors, and the random factors also have an effect on spatial distribution of As, Cd, Cu and Ni. The random factors such as overgrazing can exert an influence on physical structure and the circulation of nutrient substances of meadow soil through livestock grazing and trampling, ultimately affecting the content and distribution of soil heavy metals.

Dynamic changes in the yak rumen eukaryotic community and metabolome characteristics in response to feed type.

With diversification of yak breeding, it is important to understand the effects of feed type on the rumen, especially microbiota and metabolites. Due to the unique characteristics of yak, research on rumen microbes and metabolites is limited. In this study, the effects of two diet types on rumen eukaryotic microflora and metabolites were evaluated using the Illumina MiSeq platform and liquid chromatography-mass spectrometry (LC-MS). All identified protozoa belonged to Trichostomatia. At the genus level, the relative abundance of Metadinium and Eudiplodinium were significantly (p < 0.05) higher in the roughage group than that of concentrate group, while the concentrate group harbored more Isotricha. Ascomycota, Basidiomycota, and Neocallimastigomycota were the main fungal phyla, and the Wallemia, Chordomyces, Chrysosporium, Cladosporium, Scopulariopsis, and Acremonium genera were significantly (p < 0.05) more abundant in the roughage group than the concentrate group, while the concentrate group harbored more Aspergillus, Neocallimastix, Thermoascus, and Cystofilobasidium (p < 0.05). Metabolomics analysis showed that feed type significantly affected the metabolites of rumen protein digestion and absorption (L-proline, L-phenylalanine, L-tryosine, L-leucine, L-tryptophan, and β-alanine), purine metabolism (hypoxanthine, xanthine, guanine, guanosine, adenosine, and adenine), and other metabolic pathway. Correlation analysis revealed extensive associations between differential microorganisms and important metabolites. The results provide a basis for comprehensively understanding the effects of feed types on rumen microorganisms and metabolites of yaks. The findings also provide a reference and new directions for future research.

Paternal genetic diversity, differentiation and phylogeny of three white yak breeds/populations in China

The white yak, a type of unique and valuable farm animals on the Qinghai-Tibet Plateau, are mainly distributed in Tianzhu (County of Gansu Province), Menyuan, Huzhu and Ledu (three Counties of Qinghai Province) in China. In the present study, the Y-chromosomal genetic diversity, differentiation and phylogeny of three Chinese white yak breeds/populations (Tianzhu, Huzhu and Menyuan) were comprehensively explored using five Y-SNPs (SRY4, USP9Y, UTY19, AMELY3 and OFD1Y10) and one Y-STR (INRA189) markers. The results showed that six Y-haplotypes (H1Y1, H9Y1, H10Y1, H11Y2, H12Y2 and H13Y2) were identified in 97 male yak from three white yak breeds/populations. Among these haplotypes, H1Y1, H10Y1 and H11Y2 were shared by all of breeds/populations and H12Y2 was shared by Tianzhu and Huzhu populations. However, H9Y1 and H13Y2 haplotypes were only detected in Menyuan and Tianzhu white yak populations, respectively. The Y-haplotype diversity was maximum in Huzhu white yak (0.7500 ± 0.0349), the medium in Tianzhu white yak (0.6881 ± 0.0614) and the lowest in Menyuan white yak (0.5720 ± 0.0657). The total Y-haplotype diversity of three white yak breeds/populations was 0.7567 ± 0.0233, indicating rich paternal genetic diversity in white yak. The FST values showed a moderate differentiation between Tianzhu and Menyuan (FST = 0.0763, P < 0.05) populations, but a weak differentiation between Huzhu and Tianzhu white yak breeds/populations (FST = 0.0186, P > 0.05) and Huzhu and Menyuan (FST = − 0.005, P > 0.05) populations. The clustering analysis revealed a close genetic relationship between Huzhu and Menyuan white yak, both were far from Tianzhu white yak breed. The phylogenetic analyses showed that white yak had two Y-haplogroups/lineages (Y1 and Y2) with two potential paternal origins. The findings of present study provide new insight into the basic information for the formulation of molecular breeding programs of white yak. Moreover, it also contributes to the conservation and utilization of this special animal genetic resource.

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 &lt; 0.05) and 30-months yaks (p &lt; 0.05), and withers height of 6 months yaks (p &lt; 0.05) and 18-months yaks (p &lt; 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.

Comparative transcriptome analysis in the caput segment of yak and cattleyak epididymis

Cattleyaks are equally adaptable to harsh environment as yaks, but produce far more milk and meat in terms of quality and quantity. However, male cattleyaks with active secondary sexuality are infertile and have restricted productivity and breeding of yaks. Much researches continue to be done in regard to the differences in transcriptome profiling in cattleyak epididymis with respect to yak epididymis. The caput segment of the epididymis is highly specialized for the initiation of spermatozoa maturation, synthesis and secretion. We used RNA-Seq technology to comparatively analyze differentially expressed genes (DEGs) associated with sperm maturation between the caput epididymis of yak and cattleyak. Transcriptomic profiling identified 109 DEGs in which 44 were upregulated and 65 were downregulated. 8 DEGs were validated by quantitative real-time PCR. DEGs were analyzed by GO and KEGG analysis to screen the key genes involved in sperm maturation. The upregulation of PAOX and ATP2C2 may be associated with toxicity and apoptosis resistance in cattleyak with respect to yak. However, downregulated DEFB109, DEFB121, DEFB123, DEFA1, LY6G5C, SLC13A2, CST3, CRYBA4 and ADAM28 were associated with innate immune response, sperm maturation, motility and antimicrobial functions. AMPK and Hedgehog signaling pathways were involved in the top-listed five significantly enriched pathways, and the downregulation of HNF4α and LRP2 may have contributed to infertility in cattleyak. The data provide a powerful resource, contributing to the knowledge on the molecular mechanisms underlying male cattleyak infertility.

Whole-Genome Resequencing Highlights the Unique Characteristics of Kecai Yaks.

Simple SummaryKecai 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.

Genome-Wide Association Study of Body Weight Trait in Yaks.

Simple SummaryThe yak is the largest mammal in the Qinghai–Tibetan Plateau and also supplies necessary sources of food and finance for the Tibetan people. Their body weight is a valuable trait for breeding. In the traditional breeding processes, pedigree data were used to evaluate individual genetic potency ability. However, based on the free range husbandry and random mating in domesticated yaks, the genetic improvement in yaks’ body weight is still very slow. In this study, we performed a genome-wide association study using whole genome sequencing data to detect the potential functional genes for body weight in yaks. In total three functional genes were identified as being associated with body weight. The results of this study are important for developing and improving body weight in yaks.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.

Main Factors Influencing the Gut Microbiota of Datong Yaks in Mixed Group

Simple SummaryThis study examined the differences and similarities in gut microbial diversity and ecological assembly processes of Datong yaks, including domestic males and females and wild males, which were fed together on the Qinghai-Tibet Plateau in a mixed group. The results revealed that mixed grouping could influence the gut microbiota of these three groups of yaks and improve the gut microbial diversity of domestic females. The findings of this study can help to understand the effects of mixed grouping on the gut microbiota of livestock on the Qinghai-Tibet Plateau and improve the production of Datong yaks.The Datong yak (Bos grunniens) is the first artificial breed of yaks in the world and has played an important role in the improvement of domestic yak quality on the Qinghai-Tibet Plateau. The Datong yak breeding farm in the Qinghai province of China is the main place for the breeding and feeding of Datong yaks. It hosts domestic Datong yaks and wild male yaks, mainly in mixed groups. Different managements have different effects on livestock. The gut microbiota is closely related to the health and immunity of Datong yaks, and mixed grouping can affect the composition and diversity of the gut microbiota of Datong yaks. To reveal the effects of mixed grouping on the gut microbiota of Datong yaks and wild yaks and identify the main dominant factors, we compared the gut microbial diversities of domestic males and females and wild males based on 16S rRNA V3–V4 regions using fresh fecal samples. The data showed significant differences in the gut microbial diversity of these three groups, and the α-diversity was the highest in wild males. Different factors influence the gut microbiota, and the main influencing factors were different in different groups, including sex differences, host genetics, and physical interactions. We also compared ecological assembly processes in the three groups. The results showed that mixed grouping contributed to the improvement of gut microbial diversity in domestic females. Our study provides effective and feasible suggestions for the feeding and management of the Datong yaks.

Smart Grazing in Tibetan Plateau: Development of a Ground-Air-Space Integrated Low-Cost Internet of Things System for Yak Monitoring

This paper analyzes the present situation and difficulties of yak breeding in the “Three Needy Autonomous Regions” of Sichuan Province, integrating the specific natural environments of Qinghai-Tibet Plateau. Research work focuses on the requirements of no network conditions, large-scale application, and ultralow use cost. We propose a smart grazing IoT system, in which collars and ear-tags are designed to collect the positions and physiological signs of yaks, BeiDou Satellite-Base Stations (BDS-BSs) are designed to build local area network and ultralong-distance communication, and what is more, UAV is designed to expand the communication range to hundreds of kilometers. According to the actual needs of grazing monitoring, we propose an effective data reduction method, so that BeiDou Satellite (BDS) short-message technology can be applied to the IoT communication with high efficiency and low cost. The author carried out a significant number of experiments and verification: (1) collar realized positioning and physiological signs collecting of yaks. (2) The local area network (LAN) scheme based on LoRa built a stable communication distance of more than 3 km. (3) Ultralong-distance communication scheme based on BDS short-message technology effectively solved the problem of no network and got excellent zero additional use cost. (4) A plateau mountainous grazing UAV is designed and developed to expand the communication range.

Домашний як и его гибрид в номадном стаде монголов и бурят

Goals. The article aims at characterizing a unique animal of Inner and Central Asian nomads — the domestic yak (sarlyk) and its hybrid (khainak) that have been bred by Mongols and Buryats for hundreds of years. The work provides a first ethnographic insight into statistical data on yak population dynamics in synchronous and diachronous perspectives, reviews adaptive properties of the animal instrumental in surviving in extreme conditions of highlands, its exterior, breeding and behavioral specifics, economic significance. Materials and methods. The article explores literary, field and online sources to employ the methodology of comparative analysis, in particular, the comparative-historical-genetic method. Materials about yak breeding among Turkic peoples are essentially verifying by nature. Results. When it comes to declare the five traditional types of livestock bred, Mongols and Buryats mention no yak, the latter be clustered with cattle. Mongolia’s yak population ranks second worldwide — after China. The post-Socialist era witnessed an increase in yak numbers in Mongolia paralleled by a decrease in Russia. Domestic yaks have unique adaptive properties towards low oxygen partial pressure, extreme cold, and meagre fodder resources. The incomplete domestication of animals is determined by high profitability via such extensive farming techniques. Being meat, dairy and working animals, sarlyks and khainaks were most essential to the traditional economy of nomads. In the 21st century, their products become exotic and environment friendly food items, while skin, hair, wool, undercoat and other components serve as unique raw materials for light industry, pharmacology and cosmetology. Conclusions. The 21st century Mongolia with its vast yak friendly territories witnesses a significant head increase resulting in industrial processing facilities of yak raw materials nationwide. In the 1980s, the Soviets were undertaking active purposeful efforts to develop yak breeding, while the free market period decreased both numbers of animals held by Buryats and their habitat. The situation is due to the lack of demand for yak products and the lack of infrastructure for industrial processing of raw materials. The domestic yak and its hybrid had made it possible for nomads of Inner Asia — Mongols and Buryats — to significantly extend economic boundaries of their ethnic territories and inhabit montane grasslands and shrublands.

Genomic Diversity Profiling and Breed-Specific Evolutionary Signatures of Selection in Arunachali Yak.

Arunachali yak, the only registered yak breed of India, is crucial for the economic sustainability of pastoralist Monpa community. This study intended to determine the genomic diversity and to identify signatures of selection in the breed. Previously available double digest restriction-site associated DNA (ddRAD) sequencing data of Arunachali yak animals was processed and 99,919 SNPs were considered for further analysis. The genomic diversity profiled based on nucleotide diversity, π (π = 0.041 in 200 bp windows), effective population size, Ne (Ne = 83) and Runs of homozygosity (ROH) (predominance of shorter length ROHs) was found to be optimum. Subsequently, 207 regions were identified to be under selective sweeps through de-correlated composite of multiple signals (DCMS) statistic which combined three individual test statistics viz. π, Tajima’s D and |iHS| in non-overlapping 100 kb windows. Mapping of these regions revealed 611 protein-coding genes including KIT, KITLG, CDH12, FGG, FGA, FGB, PDGFRA, PEAR1, STXBP3, olfactory receptor genes (OR5K3, OR5H6 and OR1E1) and taste receptor genes (TAS2R1, TAS2R3 and TAS2R4). Functional annotation highlighted that biological processes like platelet aggregation and sensory perception were the most overrepresented and the associated regions could be considered as breed-specific signatures of selection in Arunachali yak. These findings point towards evolutionary role of natural selection in environmental adaptation of Arunachali yak population and provide useful insights for pursuing genome-wide association studies in future.

Characterization of the complete mitochondrial genome of Tibet Gaoshan Yak (Bos grunniens)

Tibet Gaoshan Yak (Bos grunniens) is a local Yak breed that mainly produces meat in Tibet Autonomous Region, China. In this study, the complete mitochondrial genome of Tibet Gaoshan Yak was sequenced. The total length of the mitochondrial genome is 16,323 bp, and the base composition is 33.71% for A, 13.21% for G, 27.27% for T, and 25.81% for C. The genome includes 13 protein-coding genes (ND1-ND6, ND4L, COX1-COX3, ATP6, ATP8, and CYTB), two rRNA genes (12S rRNA and 16SrRNA), 22 tRNA genes, and a noncoding control region (D-loop). Phylogenetic analysis showed that Tibet Gaoshan Yak has the closest relationship with Polled Yak. The sequence analysis provided in this study will be helpful to the management of Yak breeds, the origin, and evolution of Yak, and the protection and utilization of genetic resources.

Testis transcriptome profiling identified lncRNAs involved in spermatogenic arrest of cattleyak

Cattleyaks are the crossbred offspring between cattle and yaks, exhibiting the prominent adaptability to the harsh environment as yaks and much higher growth performances than yaks around Qinghai-Tibet plateau. Unfortunately, cattleyak cannot be effectively used in yak breeding due to its male infertility resulted from spermatogenic arrest. In this study, we performed RNA sequencing (RNA-seq) and bioinformatics analysis to determine the expression profiles of long noncoding RNA (lncRNA) from cattleyak and yak testis. A total of 604 differentially expressed (DE) lncRNAs (135 upregulated and 469 downregulated) were identified in cattleyak with respect to yak. Through gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, we identified several DE lncRNAs regulating the mitotic cell cycle processes by targeting the genes significantly associated with the mitotic cell cycle checkpoint and DNA damage checkpoint term and also significantly involved in p53 signaling pathway, mismatch repair and homologous recombination pathway (P < 0.05). The reverse transcription PCR (RT-PCR) and quantitative Real-Time PCR (qRT-PCR) analysis of the randomly selected fourteen DE lncRNAs and the seven target genes validated the RNA-seq data and their true expressions during spermatogenesis in vivo. Molecular cloning and sequencing indicated that the testis lncRNAs NONBTAT012170 and NONBTAT010258 presented higher similarity among different cattleyak and yak individuals. The downregulation of these target genes in cattleyak contributed to the abnormal DNA replication and spermatogenic arrest during the S phase of mitotic cell cycle. This study provided a novel insight into lncRNA expression profile changes associated with spermatogenic arrest of cattleyak.

Effect of Gender to Fat Deposition in Yaks Based on Transcriptomic and Metabolomics Analysis.

Fat deposition in yaks plays an important part in survival, multiplication, and meat quality. In this work, the characteristic of fat deposition in male yaks (MYs) and female yaks (FYs) and the regulations of gender to yak fat deposition were explored by mRNA-Seq and non-targeted metabolomics analyses. FYs possessed a higher body fat rate (BFR) of visceral fat, fat content in longissimus dorsi (LD) and liver, and subcutaneous fat thickness (p < 0.05). The fat and cholesterol synthesis in liver and the fat transport in FY blood increased. The fat metabolism in yaks is the combined effect of carbohydrate, fatty acid, and amino acid metabolism by tricarboxylic acid (TCA) cycle, and an increase of triglyceride (TG) synthesis was accompanied by an increase of steroid synthesis. The high levels of myo-inositol and cortisol (COR) (p < 0.01) activated the calcium signaling in FY subcutaneous fat, followed by the increase of adipocyte secretion, and resulted in more leptin (LEP) secretion (p < 0.01). Then peroxisome proliferator-activated receptor (PPAR) signaling was activated by the focal adhesions and ECM–receptor interaction. Finally, the TG and steroid synthesis increased by the expression regulation of ME1, SCD, ELOVL6, DGAT2, DBI, LPL, CPT1, PLIN1, LIPA, DHCR24, and SQLE gene. The above genes can be considered as the candidate genes for yak with higher fat amount in molecular breeding in the future. This study can provide a theoretical basis for improving the meat quality and breeding of yaks.

Adaptation Mechanisms of Yak (Bos grunniens) to High-Altitude Environmental Stress.

Simple SummaryThe yak is a multipurpose domesticated animal that serves as a protein source for local herders and a sacred carrier of culture and religion. Besides their economic significance, yaks harbor special morphological, physiological, biochemical, and genetic adaptations for tolerance to high-altitude stress. Morphologically, yaks have large hearts and lungs, compact bodies, thick outer hair covering, and nonfunctional sweat glands, which help to withstand hypoxia and cold stress. A reduced heat production, decreased respiration and sweating, reduced metabolism, and efficient nitrogen utilization are the major physiological and biochemical mechanisms for yak survival at high altitudes. Furthermore, the yak has undergone long-term natural selection and developed a unique genetic architecture that favors survival in hostile environments. The yak expresses the HIF-1α pathway-related genes (ADAM17, ARG2, and MMP3) putatively involved in hypoxia response and nutrition pathways genes (CAMK2B, GENT3, HSD17B12, WHSC1, and GLUL) for nutritional assimilation at high altitudes.Living at a high altitude involves many environmental challenges. The combined effects of hypoxia and cold stress impose severe physiological challenges on endothermic animals. The yak is integral to the livelihood of the people occupying the vast, inhospitable Qinghai–Tibetan plateau and the surrounding mountainous region. Due to long-term selection, the yak exhibits stable and unique genetic characteristics which enable physiological, biochemical, and morphological adaptations to a high altitude. Thus, the yak is a representative model for mammalian plateau-adaptability studies. Understanding coping mechanisms provides unique insights into adaptive evolution, thus informing the breeding of domestic yaks. This review provides an overview of genetic adaptations in Bos grunniens to high-altitude environmental stress. Combined genomics and theoretical advances have informed the genetic basis of high-altitude adaptations.

Using weighted gene co-expression network analysis (WGCNA) to identify the hub genes related to hypoxic adaptation in yak (Bos grunniens).

As a mammal living at the highest altitude in the world, the yak has strong adaptability to the harsh natural environment (such as low temperature, scarce food, especially low oxygen) of Qinghai-Tibet Plateau (QTP) after a long process of natural selection. Here, we used Weighted Correlation Network Analysis (WGCNA), a systematic biology method, to identify hypoxic adaptation-related modules and hub genes. The research of the adaptability of yak against hypoxia is of great significance to identify the genetic characteristics and yak breeding. Based on the transcriptome sequencing data (PRJNA362606), the R package DESeq2 and WGCNA were conducted to analyze differentially expressed genes (DEGs) and construct the gene co-expression network. The module hub genes were identified and characterized by the correlation of gene and trait, module membership (kME). In addition, GO and KEGG enrichment analyses were used to explore the functions of hub genes. Our results revealed that 1098, 1429, and 1645 DEGs were identified in muscle, spleen, and lung, respectively. Besides, a total of 13 gene co-expression modules were detected, of which two hypoxic adaptation-related modules (saddlebrown and turquoise) were found. We identified 39 and 150 hub genes in these two modules. Functional enrichment analyses showed that 12 GO terms and 18 KEGG pathways were enriched in the saddlebrown module while 85 GO terms and 22 KEGG pathways were enriched in the turquoise module. The significant pathways related to hypoxia adaptation include FoxO signaling pathway, Thermogenesis pathway, and Retrograde endocannabinoid signaling pathway, etc. CONCLUSIONS: In this study, we obtained two hypoxia-related specific modules and identified hub genes based on the connectivity by constructing a weighted gene co-expression network. Function enrichment analysis of two modules revealed mitochondrion is the most important organelle for hypoxia adaptation. Moreover, the insulin-related pathways and thermogenic-related pathways played a major role. The results of this study provide theoretical guidance for further understanding the molecular mechanism of yak adaptation to hypoxia.

Body weight estimation of yak based on cloud edge computing

In stock farming, the body size parameters and weight of yaks can reasonably reflect the growth and development characteristics, production performance and genetic characteristics of yaks. However, it is difficult for herders to measure the body size and weight of yaks by traditional manual methods. Fortunately, with the development of edge computing, herders can use mobile devices to estimate the yak’s body size and weight. The purpose of this paper is to provide a machine vision-based yak weight estimation method for the edge equipment and establish a yak estimation comprehensive display system based on the user’s use of the edge equipment in order to maximize the convenience of herdsmen’s work. In our method, a set of yak image foreground extraction and measurement point recognition algorithm suitable for edge equipment were developed to obtain yak’s measurement point recognition image, and the ratio between body sizes was transmitted to the cloud server. Then, the body size and weight of yaks were estimated using the data mining method, and the body size estimation data were constantly displayed in the yak estimation comprehensive display system. Twenty-five yaks in different age groups were randomly selected from the herd to perform experiments. The experimental results show that the foreground extraction method can obtain segmentation image with good boundary, and the yak measurement point recognition algorithm has good accuracy and stability. The average error between the estimated values and the actual measured values of body height, oblique length, chest depth, cross height and body weight is 1.95%, 3.11%, 4.91%, 3.35% and 7.79%, respectively. Compared with the traditional manual measurement method, the use of mobile end to estimate the body size and weight of yaks can improve the measurement efficiency, facilitate the herdsmen to breed yaks, reduce the stimulation of manual measurement on yaks and lay a solid foundation for the fine breeding of yaks in Sanjiangyuan region.