Bos Grunniens Research Articles

Surviving winter on the Qinghai-Tibetan Plateau: Pikas suppress energy demands and exploit yak feces to survive winter

SignificanceEndothermic animals must survive periods of seasonally lowered temperature, coincident with lowered food supply. While we know much about hibernation and migration as survival strategies, the responses of nonhibernating, nonmigrating species are more opaque, yet how these animals survive such periods is important to understand their potential susceptibility to climate change. Here, we report on a 13-y study of a species of lagomorph (plateau pika) from the Qinghai-Tibetan Plateau. We show pikas suppress their metabolism in winter and exploit a novel food source (feces of its supposed competitor, the domestic yak), which may contribute to their survival. Deposition of a fat store in the fall and its progressive utilization was not part of the overwinter strategy.

Genome-wide identification of cyclin-dependent kinase (CDK) genes affecting adipocyte differentiation in cattle

BackgroundCyclin-dependent kinases (CDKs) are protein kinases regulating important cellular processes such as cell cycle and transcription. Many CDK genes also play a critical role during adipogenic differentiation, but the role of CDK gene family in regulating bovine adipocyte differentiation has not been studied. Therefore, the present study aims to characterize the CDK gene family in bovine and study their expression pattern during adipocyte differentiation.ResultsWe performed a genome-wide analysis and identified a number of CDK genes in several bovine species. The CDK genes were classified into 8 subfamilies through phylogenetic analysis. We found that 25 bovine CDK genes were distributed in 16 different chromosomes. Collinearity analysis revealed that the CDK gene family in Bos taurus is homologous with Bos indicus, Hybrid-Bos taurus, Hybrid Bos indicus, Bos grunniens and Bubalus bubalis. Several CDK genes had higher expression levels in preadipocytes than in differentiated adipocytes, as shown by RNA-seq analysis and qPCR, suggesting a role in the growth of emerging lipid droplets.ConclusionIn this research, 185 CDK genes were identified and grouped into eight distinct clades in Bovidae, showing extensively homology. Global expression analysis of different bovine tissues and specific expression analysis during adipocytes differentiation revealed CDK4, CDK7, CDK8, CDK9 and CDK14 may be involved in bovine adipocyte differentiation. The results provide a basis for further study to determine the roles of CDK gene family in regulating adipocyte differentiation, which is beneficial for beef quality improvement.

Ensiling pretreatment with two novel microbial consortia enhances bioethanol production in sterile rice straw

The present study extracts and enriches cellulolytic microbial consortia from yak (Bos grunniens) and evaluates their effects on the fermentation profile and bioethanol yield in rice straw silage. Two microbial consortia (CF and PY) with high cellulolytic activity were isolated and observed to be prone to utilize natural carbon sources. Two consortia were introduced with and without combined lactic acid bacteria (CLAB) to rice straw for up to 60 days of ensiling, and their application notably decreased the levels of structural carbohydrates and pH values of rice straw silages. Treatments that combining microbial consortia and CLAB resulted in the highest levels of lactic acid, water soluble carbohydrates, mono- and disaccharides, and lignocellulose degradation, with PY + CLAB group yielding the highest bioethanol production. The microbial consortia identified herein exhibit great potential for degrading fibrous substrates, and their combination with CLAB provides a feasible way to efficiently use rice straw for bioethanol production.

Interferon-α-A (IFN-α-A) Diversity in Domestic Yak (Bos grunniens) of Pakistan

Among the various species of livestock, the domestic yak (Bos grunniens) belongs to the class Bovidae and is specially adapted for survival at high altitudes under extreme climatic conditions. Yak is a very useful species due to the multiple products it provides, such as meat, hide, milk and other dairy products. Like other livestock species, domestic yak is also in danger of infection by microbial infections. However, multiple immunity genes encode special protein products to fight infection. One of these immunity genes is interferon-α-A (IFN-α-A), which encodes proteins that belongs to cytokines and fights viral infections. The current study analysed the genetic variation and phylogenetic analysis of the IFN-α-A gene in domestic yak, with comparisons to other mammalian species to investigate immune diversity level, with the aim of designing molecular selection strategies for better disease resistant animals.

Helminthological monitoring of introduced animals in the Steppe Research Station “Orenburg Tarpania”

At the Steppe Research Station “Orenburg Tarpania” of the Institute of Steppe of the Ural Branch of the Russian Academy of Sciences (Orenburg region, Russia), we carried out work to study acclimatization of large ungulates of inhabiting arid ecosystems to the natural conditions of the South Ural steppe sub-region. The “Orenburg Tarpania” contains introduced animal species: Przewalski’s horse, kiangs, two-humped camels, domestic yaks and an indigenous breed of downy goats. The goal of the project is to return large phytophages to their natural steppe habitat. To prevent an increase in the infection of new populations with helminths to a clinically significant level and to study the adaptation to the existing territorial helminth-faunal complex, we monitor helminth infections of animals kept in the station and in the adjacent areas. Our survey revealed parasitism of nematodes of the suborder Strongylata (families Strongylidae and Trichonematidae) and the suborder Asagidata (Ragassagis equorum) was revealed in ungulates. Parasitism of nematodes of the suborder Strongylata (genera Chabertia and Nematodirus), and protozoa of the genus Eimegia, was detected in ruminants in the Steppe Research Station. The invasion intensity in all cases ranged from low to medium, with no clinical signs. Further studies are planned to determine the degree of biological equilibrium formation in the helminth-host system of the model plot.

Microbiome and Metabolomics Reveal the Effects of Different Feeding Systems on the Growth and Ruminal Development of Yaks

The change in the feeding system can greatly improve the growth performance of the yak (Bos grunniens), an important livestock species in the plateau region. Here, we comprehensively compared the effects of different feeding systems on the growth performance and ruminal development of yaks, and investigated the effects of ruminal microorganisms and metabolites using the 16S rRNA gene sequencing and liquid chromatograph–mass spectrometer (LC-MS) technologies. We found that compared to traditional grazing feeding, house feeding significantly improved the growth performance (such as average daily gain and net meat weight) and rumen development of the yaks. At the genus level, the abundance of Rikenellaceae RC9 Gut group, Christensenellaceae R-7 group, Lachnospiraceae NK3A20 group, Ruminococcaceae UCG-014, and Prevotellaceae UCG-003 showed significant differences and was closely related to rumen development in the two distinct feeding systems. Also, metabolomics revealed that the change in the feeding system significantly affected the concentration and metabolic pathways of the related rumen metabolites. The metabolites with significant differences were significantly enriched in purine metabolism (xanthine, adenine, inosine, etc.), tyrosine metabolism (L-tyrosine, dopaquinone, etc.), phenylalanine metabolism (dihydro-3-caumaric acid, hippuric acid, etc.), and cAMP signaling pathway [acetylcholine, (-)-epinephrine, etc.]. This study scientifically support the house fattening feeding system for yaks. Also, our results provide new insights into the composition and function of microbial communities that promote ruminal development and in general growth of the yaks.

Dynamics of rumen bacterial composition of yak (Bos grunniens) in response to dietary supplements during the cold season.

This study aimed to explore the rumen bacterial community of yak in response to dietary supplements during the cold season. In addition, the rumen fermentation products were also analyzed. Twenty-one female domestic yaks were randomly divided into three groups i.e., pure grazing (GG) group, grazing plus oats hay supplement (OG) group, and grazing plus concentrate supplement group (CG). Rumen contents were collected after 90 days to assess rumen fermentation parameters and bacterial community. The GC group presented higher concentrations of ammonia nitrogen (P < 0.001), and total volatile fatty acids (TVFA) (P < 0.001), and lower rumen pH (P < 0.001) compared to other experimental groups. The CG group displayed higher proportions of propionate, butyrate, isobutyrate, and isovalerate while lower A/P ratio compared to other experimental groups. Shannon, Chao1, and ACE values were significantly lower in the OG group compared to GG and CG groups. Anosim test showed significant differences in bacterial community structure between groups but the PCA plot was not very informative to see these differences. Bacteroidetes, Proteobacteria, and Firmicutes were the three dominant phyla in all groups. The genera Oscillospira was more abundant in GG and OG groups. Higher relative abundance of Ruminococcus and Clostridium was observed in the GG group, while Ruminobacter, Corynebacterium, and Selenomonas were more abundant in the CG group. These findings will help in improving our understanding of rumen bacteria in yaks in response to changes in diet.

Effects of root extracts of three traditional Chinese herbs as dietary supplements on dry matter intake, average daily gain, rumen fermentation and ruminal microbiota in early weaned yak calves

Herbal supplements are being tested as alternatives to antibiotics in enhancing the performance of livestock. The present study evaluated the effects of herbal root extracts from three traditional Chinese medicinal herbs as dietary supplements on dry matter intake (DMI), average daily gain (ADG), rumen fermentation and ruminal microbiota in early weaned yak calves (Poephagus grunniens). Twenty, four-month old weaned yak calves (72.3 ± 3.65 kg) were divided into four groups, matched for bodyweight and sex (n = 5 per group), and received either no supplement (control group) or 80 mL/kg DMI of herbal root extracts of Angelica sinensis, Codonopsis pilosula or Glycyrrhiza uralensis. The water extract (∼170 mL) was mixed with 300 g concentrate and offered to the calves each day for 60 days following a 14-day adaptation period. Dry matter intake did not differ among treatments, but ADG was highest for calves fed Codonopsis pilosula root extract (P = 0.026). Compared with control calves, calves fed root extract of Glycyrrhiza uralensis had a higher ruminal proportion of propionate (P = 0.034), calves fed root extracts of Codonopsis pilosula and Glycyrrhiza uralensis had higher ruminal proportions of isovalerate (P = 0.032) and calves fed root extract of Glycyrrhiza uralensis had a lower acetate:propionate ratio (P = 0.027) on d 30. Calves consuming Angelica sinensis, Codonopsis pilosula and Glycyrrhiza uralensis root extract had lower ruminal NH3-N concentrations than control calves on d 60 (P < 0.05). The abundances of Bacteroidetes and Firmicutes comprised over 90 % of the total phyla in the four groups. Yak calves consuming Glycyrrhiza uralensis root extract had the highest abundance of Bacteroidetes (P = 0.009) and lowest abundance of Firmicutes (P = 0.023). Calves consuming Codonopsis pilosula root extract had the highest abundances of Proteobacteria (P = 0.035) and Actinobacteria (P = 0.007), while calves consuming the three herbal root extracts tended to have lower abundances of Kiritimatiellaeota (P = 0.082), Spirochaetes (P = 0.081) and Synergistetes (P = 0.058) than control calves. In conclusion, consuming Codonopsis pilosula root extract increased ADG in early weaned yak calves, while consuming the three herbal root extracts increased ruminal proportions of propionate and isovalerate, and altered rumen microbiota. Supplementary Codonopsis pilosula proved to be the most beneficial of the three herbal roots for the early weaned calves.

Molecular characterization, expression and functional analysis of yak IFITM3 gene

IFITM3 is interferon-induced transmembrane 3, which plays an extremely key role in anti-proliferation, anti-virus and anti-tumor diseases.In this study, the yak (Bos grunniens) IFITM3 (BgIFITM3) gene contained a 5′-untranslated region (UTR) (25 bp), a coding region (441 bp), and a 3′-UTR (115 bp). The expression of BgIFITM3 gene in liver was significantly higher than that in heart, spleen, lung and kidney (P < 0.01). BgIFITM3 protein was localized on the yak hepatocyte plasma membrane, and its expression was significantly different between 1 day and 15 months of age (P < 0.05). Moreover, the prokaryotic expression vector of BgIFITM3 protein was constructed and expressed successfully, with a molecular weight of 19.5 kDa. The activities of yak hepatocyte were significantly inhibited after treating with BgIFITM3 protein (10 and 20 μg/mL) (P < 0.01). The expression levels of ERBB-2, IRS-1, PI3KR-1, AKT-1 and MAPK-3 were significantly lower after treating with 20 μg/mL BgIFITM3 protein (P < 0.05). Besides, the activities of HepG2 cells were significantly inhibited after treating with BgIFITM3 protein (1, 10 and 20 μg/mL) (P < 0.05). While, the cloning ability and migration ability of HepG2 cells were significantly inhibited after treating with 10 μg/mL BgIFITM3 protein (P < 0.05). Finally, the mitochondria of HepG2 cells was concentrated, cristae widened, and the double film density of mitochondria was increased after treating with 10 μg/mL BgIFITM3 protein. After 10 μg/mL BgIFITM3 protein treating, the expression levels of VDAC-2, VDAC-3 and p53 genes were significantly increased, but the expression level of GPX-4 gene was significantly decreased (P < 0.01).Taken together, the BgIFITM3 protein could inhibit the proliferations of yak hepatocyte and HepG2 cells by regulating the PI3K/Akt pathway or ferroptosis-related genes, respectively. These results benefit for further study of the function of BgIFITM3 protein.

Molekularna filogenija i genetička raznolikost domaćih jakova (Bos grunniens) u Pakistanu na temelju mitohondrijskih i mikrosatelitskih markera

The complete Cytchrome b gene and partial mtDNA control region were sequenced for the Pakistani domestic yak (Bos grunniens) within the Bovidae family. A total of 300 samples were genotyped using 27 bovine microsatellite markers from the Gilgit-Baltistan and Skardu regions of Pakistan. We identified a total of 35 mutations and 9 haplotypes based on D-loop sequences, with a haplotype and nucleotide diversity of 0.9640±0.051 and 0.02172±0.00224, respectively. For the Cyt b gene, a total of 23 variable sites and six different haplotypes were observed with 0.885±0.067 haplotype and 0.00989±0.003 nucleotide diversity. Phylogenetic analysis of D-loop and Cyt b gene suggested that domestic yak sequences cluster into two highly divergent maternal lineages (lineages I and II), while three haplogroups A, C, and D were identified of the six previously known haplogroups. Haplogroups A and C were dominant and widely distributed among all investigated yak samples. All microsatellites were polymorphic and a total of 138 alleles were observed, with average polymorphic information content (PIC) of 0.56 indicating their effectiveness. The average heterozygosity was observed at 0.6071 with allele diversity of 5.1111 and gene diversity of 0.4830. The implications of these findings can be applied for yak conservation.

Whole-Transcriptome Analysis of Yak and Cattle Heart Tissues Reveals Regulatory Pathways Associated With High-Altitude Adaptation.

BackgroundThe yak (Bos grunniens) is an important livestock species that can survive the extremely cold, harsh, and oxygen-poor conditions of the Qinghai-Tibetan Plateau and provide meat, milk, and transportation for the Tibetans living there. However, the regulatory network that drive this hypoxic adaptation remain elusive.ResultsThe heart tissues from LeiRoqi (LWQY) yak and their related cattle (Bos Taurus) breeds, which are two native cattle breeds located in high altitude (HAC) and low altitude (LAC) regions, respectively, were collected for RNA sequencing. A total of 178 co-differentially expressed protein-coding transcripts (co-DETs) were discovered in each of the LAC-vs-LWQY and LAC-vs-HAC comparison groups, including NFATC2, NFATC1, ENPP2, ACSL4, BAD, and many other genes whose functions were reported to be associated with the immune-system, endocrine-system, and lipid metabolism. Two and 230 lncRNA transcripts were differentially expressed in the LAC-vs-LWQY and LAC-vs-HAC comparisons’ respectively, but no lncRNA transcripts that were co-differentially expressed. Among the 58 miRNAs that were co-differentially expressed, 18 were up-regulated and 40 were down-regulated. In addition, 640 (501 up-regulated and 139 down-regulated) and 152 (152 up-regulated and one down-regulated) circRNAs showed differential expression in LAC-vs-LWQY and LAC-vs-HAC comparison groups, respectively, and 53 up-regulated co-differentially expressed circRNAs were shared. Multiple co-DETs, which are the targets of miRNAs/lncRNAs, are significantly enriched in high-altitude adaptation related processes, such as, T cell receptor signaling, VEGF signaling, and cAMP signaling. A competing endogenous RNA (ceRNA) network was constructed by integrating the competing relationships among co-differentially expressed mRNAs, miRNAs, lncRNAs and circRNAs. Furthermore, the hypoxic adaptation related ceRNA network was constructed, and the six mRNAs (MAPKAPK3, PXN, NFATC2, ATP7A, DIAPH1, and F2R), the eight miRNAs (including miR-195), and 15 circRNAs (including novel-circ-017096 and novel-circ-018073) are proposed as novel and promising candidates for regulation of hypoxic adaptation in the heart.ConclusionIn conclusion, the data recorded in the present study provides new insights into the molecular network of high-altitude adaptation along with more detailed information of protein-coding transcripts and non-coding transcripts involved in this physiological process, the detailed mechanisms behind how these transcripts “crosstalk” with each other during the plateau adaptation are worthy of future research efforts.

Phylogeographical analysis shows the need to protect the wild yaks' last refuge in Nepal.

The wild yak Bos mutus was believed to be regionally extinct in Nepal for decades until our team documented two individuals from Upper Humla, north‐western Nepal, in 2014. The International Union for Conservation of Nature (IUCN) seeks further evidence for the conclusive confirmation of that sighting. We conducted line transects and opportunistic sign surveys in the potential wild yak habitats of Humla, Dolpa, and Mustang districts between 2015 and 2017 and collected genetic samples (present and historic) of wild and domestic yaks Bos grunniens. We also sighted another wild yak in Upper Humla in 2015. Phylogenetic and haplotype network analyses based on mitochondrial D‐loop sequences (~450 bp) revealed that wild yaks in Humla share the haplotype with wild yaks from the north‐western region of the Qinghai‐Tibetan Plateau in China. While hybridization with domestic yaks is a major long‐term threat, illegal hunting for meat and trophy put the very small populations of wild yaks in Nepal at risk. Our study indicates that the unprotected habitat of Upper Humla is the last refuge for wild yaks in Nepal. We recommend wild yak conservation efforts in the country to focus on Upper Humla by (i) assigning a formal status of protected area to the region, (ii) raising awareness in the local communities for wild yak conservation, and (iii) providing support for adaptation of herding practice and pastureland use to ensure the viability of the population.

Effects of rumen-protected methionine and lysine supplementation on milk yields and components, rumen fermentation, and the rumen microbiome in lactating yaks (Bos grunniens)

The objectives of this study were to investigate the effects of supplementing rumen-protected methionine (RPM) or lysine (RPL) alone or in combination with RPM and RPL (RPML) on milk yield and milk components, rumen fermentation characteristics, and the rumen microbiome in lactating yaks. Thirty-two multiparous lactating yaks with parity (2.13 ± 1.08 lactations), body weight (169 ± 15.0 kg), and milk yield (1.02 ± 0.13 kg/d) were blocked by milk yield and randomly assigned into one of the four treatments: control (CON; basal diet without adding rumen-protected amino acid) and the basal diet supplemented with RPM (50.0 g/d), RPL (66.7 g/d), or RPML (12.5 g/d RPM and 50.0 g/d RPL). The basal diet consisted of 600 g/kg rye hay and 400 g/kg corn-based concentrate. The dry matter intake, lactoferrin concentration, and lactose yield were greater (P < 0.05) in the RPM and RPML groups than those in the CON and RPL groups. Compared to the other three groups, the RPM supplementation increased (P < 0.01) the milk and protein yield. The milk protein content in the RPM group was greater (P < 0.01) than that in the CON and RPML groups. The RPM group had a higher milk content of alanine (P < 0.01) and aspartic acid (P = 0.01) than that in the other three treatments. The RPM group had a lower (P < 0.01) rumen pH and a higher (P = 0.02) valerate proportion than those in the other three treatments, whereas the RPML group had a higher (P = 0.03) rumen ammonia nitrogen concentration than that in the other three treatments. The relative abundances of Proteobacteria (P = 0.01) and Prevotella_1 (P = 0.02) were increased in the RPM and RPML groups, respectively. Operational taxonomic units (OTU) unique to the yaks of RPL and RPML groups belonged mainly to the phylum Bacteroidetes, whereas the majority of OTUs unique to the yaks of the RPM group belonged mainly to the phylum Firmicutes. The relative abundances of Fibrobacter and Selenomonas_1 were positively correlated with milk yield and concentration of propionate, valerate, butyrate, and total volatile fatty acids. The relative abundances of Candidatus_Saccharimonas, Ruminococcaceae_UCG-014, Rikenellaceae_RC9_gut_group, and Erysipelotrichaceae_UCG-004 were positively correlated with the content of milk protein. These results suggest that supplementation of RPM and RPL can affect rumen microbial populations, which in turn affect rumen fermentation and thus, the metabolites available for milk synthesis.

Mitogenomic diversity and phylogeny analysis of yak (Bos grunniens)

Background and aimMitochondrial genome has aseries of characteristics such as simple structure, no recombination, maternalinheritance, stable structure, fast evolution rate, and high copy number. Moreover, it is easy to be sequenced,contains high-resolution phylogenetic information, and exists in a wide rangeof taxa. Therefore, it is widely used in the study of biological phylogeny. Atpresent, phylogenetic studies focus mainly on D-loop region, cytochrome b gene,and protein-coding sequence. Phylogenetic studies using the mitochondrialcomplete sequence are rarely reported in yak. Therefore, the present studyaimed to construct phylogenetic tree using yak mitochondrial complete sequenceand compare the subsequent results with previous findings obtained usingpartial sequences.ResultsComplete mitochondrial sequences of five yakpopulations from Qinghai and Xinjiang were obtained. The mitotype diversity ofthe five populations was Xueduo yak (0.992 ± 0.015), Pamir yak (0.990 ± 0.014),Yushu yak (0.963 ± 0.033), Qilian yak (0.948 ± 0.036), and Huanhu yak (0.905 ±0.048), which showed a higher mitotype diversity compared with other breeds fromthe previous reports, including Jiulong yak, Maiwa yak, Zhongdian yak, andTianzhu yak. A total of 78 mitotypes were obtained from 111 individuals. Amongthese, Yushu yak, Huanhu yak, Xueduo yak, and Qilian yak all shared mitotypes,but the Pamir yak did not share mitotypes with these four populations.Phylogenetic analysis showed that yak populations were separable into threedistinct branches. The analysis identified a new phylogenetic branch containingboth wild and domestic yaks. The 155 mitotypes found in 206 individuals weredivided into 3 haplogroups by mitotype clustering. Thehaplogroup was not associated with the geographical distribution of yaks. Theyaks in the same population or the same ecological environment were distributedin different haplogroups. Among the threehaplogroups, haplogroup A and haplogroup B showed a star-shaped distribution ofmitotypes. The central mitotypes were widely distributed and had a highfrequency.ConclusionsThegenetic diversity of yaks in Qinghai was high. Both domestic and wild yaks clusteredinto three branches.

Structural Variants Selected during Yak Domestication Inferred from Long-Read Whole-Genome Sequencing.

Structural variants (SVs) represent an important genetic resource for both natural and artificial selection. Here we present a chromosome-scale reference genome for domestic yak (Bos grunniens) that has longer contigs and scaffolds (N50 44.72 and 114.39 Mb, respectively) than reported for any other ruminant genome. We further obtained long-read resequencing data for 6 wild and 23 domestic yaks and constructed a genetic SV map of 372,220 SVs that covers the geographic range of the yaks. The majority of the SVs contains repetitive sequences and several are in or near genes. By comparing SVs in domestic and wild yaks, we identified genes that are predominantly related to the nervous system, behavior, immunity, and reproduction and may have been targeted by artificial selection during yak domestication. These findings provide new insights in the domestication of animals living at high altitude and highlight the importance of SVs in animal domestication.

Evolution of immunogenetic components used to form ultralong VH CDR3 antibodies in Bovidae

Abstract Cattle has a restricted repository of immunoglobulin heavy chain gene segments with only one family of V, 4 J and 16 D segments functional. Among these segments are a V and D that, together, encode a heavy chain with an ultralong CDR3 region which manifests as a “stalk” supporting a “knob” domain of which only the knob has antigen binding capability. This antibody structure has boundless therapeutic potential, including for treatment of HIV and other antigens with veiled epitopes. Upon the discovery of this ultralong antibody in Bos taurus, speculation of its origin began. The components that should facilitate ultralong CDR3H antibodies appear in more species than just Bos taurus; they expand throughout the bovine subfamily as evidence by the presence of a V motif “TTVHQ” crested by an 8 base-pair (bp) duplication, and a comparatively long D segment. Several closely-related species encode the ultralong V segments gene in their germline IgH locus. Phylogenetically bookending the cluster that is genomically equipped for the ultralong cattlebody are the species Bos taurus and Bison bison with Bos mutus, indicus, and grunniens in between. The added length of the D segment is less consistent throughout the group as none of the species encode as long of segment as Bos taurus at 50 amino acids. Two species studied, Bos mutus and Bos grunniens, have 15 and 22 amino acids, respectively, encoded by their longest D segment, and Bison bison has 23. Though we do know the germline encodes the ultralong antibody, it is imperative to know if the gene rearrangement is actually expressed and employed in the mature repertoire.

Seroprevalence and Epidemiology of Toxoplasma gondii in Animals in the Qinghai-Tibetan Plateau Area, China.

Toxoplasma gondii belongs to the Apicomplexan protozoa—an obligate intracellular parasite—causing toxoplasmosis that has a worldwide distribution and is very harmful to both human health and the livestock industry. However, the information on toxoplasmosis in the Qinghai-Tibetan Plateau Area (QTPA) and the seroprevalence of T. gondii in the food-borne animals in that area has been limited. Therefore, this study focused to T. gondii and toxoplasmosis to perform an indirect ELISA test based on recombinant TgSAG2 protein to establish a comprehensive record of the seroprevalence of T. gondii infections in a wide range of animals, including Tibetan sheep (Ovis aries), yaks (Bos grunniens), cows, chicken, pigs, and horses, in the QTPA. Overall, the seropositive rates of the specific-T. gondii IgG and IgM antibodies in all investigated animals were 44.1% (1179/2673) and 18.0% (469/2612), respectively. The 14.9% (389/2612) sera were determined to be both IgG and IgM positive samples, 30.2% (789/2673) were single-IgG seropositive, and a total of 80 in 2612 animals (3.0%) were single-IgM seropositive. Moreover, for the animal species, the pig was the most prevalent animal (90.2%, 304/337) for IgG positivity, followed by Tibetan sheep (50.7%, 460/907), chickens (45.8%, 229/500), yaks (21.1%, 140/663), cows (18.5%, 38/205) and horses (13.1%, 8/61), respectively. For the IgM antibody positivity, the pig was also the most prevalent animal (41.8%, 141/337), followed by Tibetan sheep (21.2%, 191/907), cows (15.1%, 31/205), chickens (12.4%, 62/500) and yaks (6.6%, 44/663), respectively. The significant differences in the prevalent distribution of T. gondii were found in the different altitudes. In conclusion, this study found the high seroprevalence for T. gondii infections among these animal species in the QTPA, and provides new data to facilitate further research for development of control measures against T. gondii infections in the surveyed locations.

The complete mitochondrial genome and phylogenetic analysis of Yanglong yak (Bos grunniens)

In this study, we assembled the complete mitochondrial genome of Yanglong yak (Bos grunniens) from Illumina sequencing reads. The mitochondrial genome is 16,323 bp long with an A + T-biased nucleotide composition, and encodes 13 protein-coding, 22 tRNA, and two rRNA genes along with a noncoding control region. In addition, its gene order is identical to those of the previously published mitochondrial genomes of its congeners. Phylogenetic analysis indicates that this breed is closely related to Datong yak, Pamir yak, Tianjun yak, polled yak, Seron yak, Sunnan yak, a series of Domestic Yak and wild yak, followed by Jinchuan yak and Gannan yak, and slightly far away from Bison and Bos taurus.

Domestication Shapes the Community Structure and Functional Metagenomic Content of the Yak Fecal Microbiota.

Domestication is a key factor of genetic variation; however, the mechanism by which domestication alters gut microbiota is poorly understood. Here, to explore the variation in the structure, function, rapidly evolved genes (REGs), and enzyme profiles of cellulase and hemicellulose in fecal microbiota, we studied the fecal microbiota in wild, half-blood, and domestic yaks based on 16S rDNA sequencing, shotgun-metagenomic sequencing, and the measurement of short-chain-fatty-acids (SCFAs) concentration. Results indicated that wild and half-blood yaks harbored an increased abundance of the phylum Firmicutes and reduced abundance of the genus Akkermansia, which are both associated with efficient energy harvesting. The gut microbial diversity decreased in domestic yaks. The results of the shotgun-metagenomic sequencing showed that the wild yak harbored an increased abundance of microbial pathways that play crucial roles in digestion and growth of the host, whereas the domestic yak harbored an increased abundance of methane-metabolism-related pathways. Wild yaks had enriched amounts of REGs in energy and carbohydrate metabolism pathways, and possessed a significantly increased abundance of cellulases and endohemicellulases in the glycoside hydrolase family compared to domestic yaks. The concentrations of acetic, propionic, n-butyric, i-butyric, n-valeric, and i-valeric acid were highest in wild yaks. Our study displayed the domestic effect on the phenotype of composition, function in gut microbiota, and SCFAs associated with gut microbiota, which had a closely association with the growth performance of the livestock. These findings may enlighten the researchers to construct more links between economic characteristics and gut microbiota, and develop new commercial strains in livestock based on the biotechnology of gut microbiota.

Introgression, admixture, and selection facilitate genetic adaptation to high-altitude environments in cattle

Domestication and subsequent selection of cattle to form breeds and biological types that can adapt to different environments partitioned ancestral genetic diversity into distinct modern lineages. Genome-wide selection particularly for adaptation to extreme environments left detectable signatures genome-wide. We used high-density genotype data for 42 cattle breeds and identified the influence of Bos grunniens and Bos javanicus on the formation of Chinese indicine breeds that led to their divergence from India-origin zebu. We also found evidence for introgression, admixture, and migration in most of the Chinese breeds. Selection signature analyses between high-altitude (≥1800 m) and low-altitude adapted breeds (<1500 m) revealed candidate genes (ACSS2, ALDOC, EPAS1, EGLN1, NUCB2) and pathways that are putatively involved in hypoxia adaptation. Immunohistochemical, real-time PCR and CRISPR/cas9 ACSS2-knockout analyses suggest that the up-regulation of ACSS2 expression in the liver promotes the metabolic adaptation of cells to hypoxia via the hypoxia-inducible factor pathway. High altitude adaptation involved the introgression of alleles from high-altitude adapted yaks into Chinese Bos taurus taurus prior to their formation into recognized breeds and followed by selection. In addition to selection, adaptation to high altitude environments has been facilitated by admixture and introgression with locally adapted cattle populations.