Xuezhi Ding

Genetic Diversity and Phylogenetic Evolution of Tibetan Sheep Based on mtDNA D-Loop Sequences.

The molecular and population genetic evidence of the phylogenetic status of the Tibetan sheep (Ovis aries) is not well understood, and little is known about this species’ genetic diversity. This knowledge gap is partly due to the difficulty of sample collection. This is the first work to address this question. Here, the genetic diversity and phylogenetic relationship of 636 individual Tibetan sheep from fifteen populations were assessed using 642 complete sequences of the mitochondrial DNA D-loop. Samples were collected from the Qinghai-Tibetan Plateau area in China, and reference data were obtained from the six reference breed sequences available in GenBank. The length of the sequences varied considerably, between 1031 and 1259 bp. The haplotype diversity and nucleotide diversity were 0.992±0.010 and 0.019±0.001, respectively. The average number of nucleotide differences was 19.635. The mean nucleotide composition of the 350 haplotypes was 32.961% A, 29.708% T, 22.892% C, 14.439% G, 62.669% A+T, and 37.331% G+C. Phylogenetic analysis showed that all four previously defined haplogroups (A, B, C, and D) were found in the 636 individuals of the fifteen Tibetan sheep populations but that only the D haplogroup was found in Linzhou sheep. Further, the clustering analysis divided the fifteen Tibetan sheep populations into at least two clusters. The estimation of the demographic parameters from the mismatch analyses showed that haplogroups A, B, and C had at least one demographic expansion in Tibetan sheep. These results contribute to the knowledge of Tibetan sheep populations and will help inform future conservation programs about the Tibetan sheep native to the Qinghai-Tibetan Plateau.

Genome-wide Association Study Identifies Loci for the Polled Phenotype in Yak.

The absence of horns, known as the polled phenotype, is an economically important trait in modern yak husbandry, but the genomic structure and genetic basis of this phenotype have yet to be discovered. Here, we conducted a genome-wide association study with a panel of 10 horned and 10 polled yaks using whole genome sequencing. We mapped the POLLED locus to a 200-kb interval, which comprises three protein-coding genes. Further characterization of the candidate region showed recent artificial selection signals resulting from the breeding process. We suggest that expressional variations rather than structural variations in protein probably contribute to the polled phenotype. Our results not only represent the first and important step in establishing the genomic structure of the polled region in yak, but also add to our understanding of the polled trait in bovid species.

Efficiency of in vitro embryo production of yak (Bos grunniens) cultured in different maturation and culture conditions

A study was conducted to evaluate the potential of immature oocytes from the ovaries of yak. The effects of maturation times (23–30 h), hormones (FSH, LH, E2), sera (fetal calf serum, FCS, or oestrous cow serum, ECS) and culture system (co-culture with granulosa cell, GC, or with bovine oviduct epithelia cells, BOEC, tissue culture medium, TCM, 199 absence co-culture cell, and synthetic oviduct fluid with amino acids, SOFaa) on the in vitro development of in vitro matured and fertilised yak oocytes were examined. Immature oocytes surrounded with compacted cumulus cell were cultured for 23–30 h in TCM 199 supplemented with 10% FCS and hormones. In vitro fertilisation (IVF) was performed with frozen-thawed, caffeine and heparin treated spermatozoa from Datong yak. Oocytes were incubated with 1×106/ml spermatozoa for 16–18 h and then cultured in co-culture system with GC or BOEC and/or SOFaa for 7–8 days, respectively. Cleavage and development to blastocysts were recorded on days 2 and 8, respectively, after the start of culture. 27–28 h was superior to other culture times and addition hormones (FSH, LH, E2) were superior to absence either of them for oocyte maturation. The best maturation of oocyte in TCM 199 with 5.0 mg/L LH, 0.5 mg/L FSH, 1 mg/L E2. FCS was superior to ECS for development to blastocysts. Co-culture with GC was superior to SOFaa and TCM 199 absence co-culture cell for cleavage, development to blastocysts. The results show that choice of culture conditions has marked effect on the development of in vitro matured and fertilised yak oocytes. The present results indicate that the co-culture with GCs is the most important factor for IVF to development into blastocysts of yak oocytes matured in vitro.

MicroRNA-200a regulates adipocyte differentiation in the domestic yak Bos grunniens

The domestic yak (Bos grunniens) is a culturally important animal that lives at high altitude and is farmed by Tibetan herders for its meat, milk, and other animal by-products. Within the animal, adipose tissue is an important store and source of energy and is used to maintain adequate body temperature during the extended cold seasons. Exploring the biomolecular role of microRNAs (miRNAs) in the regulation of growth, development, and metabolism of yak adipocytes may provide valuable insights into the physiology of adipogenesis in the yak. This study investigated whether and how miR-200a (a miRNA recently reported to promote adipogenesis in ST2 bone marrow stromal cells) regulates adipocyte differentiation in the yak. Expression levels of miR-200a gradually increased during day 0 to day 8 of adipocyte differentiation, and transfection of adipocytes with miR-200a enhanced lipid accumulation and triglyceride content compared to control (un-transfected) adipocytes. We additionally verified (using qRT-PCR analysis) that miR-200a increased the expression of adipocyte-specific genes involved in lipogenic transcription (PPARγ, ELVOL, and C/EBPα), fatty acid synthesis (ACC, ACS, SCD, and FAS), and fatty acid transport (DGAT, LPL, and FABP4). We also found that transfection of adipocytes with miR-200a resulted in suppression of the levels of noncanonical Wnt signaling transcription factors (Wnt5a, TAK1, and NLK). These results indicate that miRNA-200a plays an important role in promoting yak adipocyte differentiation that may operate via the suppression of noncanonical Wnt signaling.

The complete mitochondrial genome sequence of the Datong yak (Bos grunniens)

Abstract Datong yak is a famous artificially cultivated breed in China. In the present work, we report the complete mitochondrial genome sequence of Datong yak for the first time. The total length of the mitogenome is 16,323 bp long, containing 13 protein-coding genes, 22 tRNA genes, two rRNA genes and one non-coding region (D-loop region). The gene order of Datong yak mitogenome is identical to that observed in most other vertebrates. The overall base composition is 33.71% A, 25.8.0% C, 13.21% G and 27.27% T, with an A + T content of 60.98%. The complete mitogenome sequence information of Datong yak can provide useful data for further studies on molecular breeding and taxonomic status.

The complete mitochondrial genome of the Qinghai Plateau yak Bos grunniens (Cetartiodactyla: Bovidae)

Abstract The Qinghai Plateau yak Bos grunniens (Cetartiodactyla: Bovidae) is an important primitive local breed in the Qinghai-Tibetan Plateau and adjacent regions. In this study, its complete mitochondrial genome sequence has been assembled and characterized from high-throughput Illumina sequencing data. This genome is 16 322 bp in length, and contains 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a non-coding D-loop or control region. The nucleotide composition is asymmetric (33.73% A, 25.79% C, 13.19% G, and 27.29% T) with an overall A + T content of 61.02%. The gene arrangement and the composition are similar to most other vertebrates. These data would contribute to our better understanding its population genetics and evolutionary history.

Characterization of the complete mitochondrial genome sequence of wild yak (Bos mutus)

Abstract Wild yak is a special breed in China and it is regarded as an important genetic resource for sustainably developing the animal husbandry in Tibetan area and enriching region’s biodiversity. The complete mitochondrial genome of wild yak (16,322 bp in length) displayed 37 typical animal mitochondrial genes and A + T-rich (61.01%), with an overall G + C content of only 38.99%. It contained a non-coding control region (D-loop), 13 protein-coding genes, two rRNA genes, and 22 tRNA genes. Most of the genes have ATG initiation codons, whereas ND2, ND3, and ND5 genes start with ATA and were encoded on H-strand. The gene order of wild yak mitogenome is identical to that observed in most other vertebrates. The complete mitochondrial genome sequence of wild yak reported here could provide valuable information for developing genetic markers and phylogenetic analysis in yak.

Novel SNP of EPAS1 gene associated with higher hemoglobin concentration revealed the hypoxia adaptation of yak (Bos grunniens)

Abstract Endothelial PAS domain protein 1 gene (EPAS1) is a key transcription factor that activates the expression of oxygen-regulated genes. In this study, in order to better understand the effects of EPAS1 gene on hematologic parameters in yak, we firstly quantified the tissue expression patterns for EPAS1 mRNA of yak, identified polymorphism in this gene and evaluated its association with hematologic parameters. Expression of EPAS1 mRNA was detected in all eight tissues (heart, liver, lung, spleen, pancreas, kidney, muscles and ovary). The expressions of EPAS1 in lung and pancreas were extremely higher than other tissues examined. Three novel single nucleotide polymorphisms (SNPs) (g.83052 C>T, g.83065 G>A and g.83067 C>A) within the EPAS1 were identified and genotyped in Pali (PL), Gannan (GN) and Tianzhu White (TZW) yak breeds. Significant higher frequencies of the AA and GA genotypes and A allele of the g.83065 G>A were observed in the PL and GN breeds than that in the TZW breed (P A polymorphism was significantly associated with hemoglobin (HGB) concentration in yaks (P

Comparative Proteomic Analysis of Yak Follicular Fluid during Estrus

The breeding of yaks is highly seasonal, there are many crucial proteins involved in the reproduction control program, especially in follicular development. In order to isolate differential proteins between mature and immature follicular fluid (FF) of yak, the FF from yak follicles with different sizes were sampled respectively, and two-dimensional gel electrophoresis (2-DE) of the proteins was carried out. After silver staining, the Image Master 2D platinum software was used for protein analysis and matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS) was performed for differential protein identification. The expression level of transferrin and enolase superfamily member 1 (ENOSF1) was determined by Western blotting for verification analysis. The results showed that 2-DE obtained an electrophoresis map of proteins from mature and immature yak FF with high resolution and repeatability. A comparison of protein profiles identified 12 differently expressed proteins, out of which 10 of them were upregulated while 2 were downregulated. Western blotting showed that the expression of transferrin and ENOSF1 was enhanced with follicular development. Both the obtained protein profiles and the differently expressed proteins identified in this study provided experimental data related to follicular development during yak breeding seasons. This study also laid the foundation for understanding the microenvironment during oocyte development.

Comparative iTRAQ proteomics revealed proteins associated with horn development in yak

BackgroundThe practice of dehorning yak raises animal safety concerns, which have been addressed by selective breeding to obtain genetically hornless yak. The POLLED locus in yak has been studied extensively; however, little is known regarding the proteins that regulate horn bud development.MethodsA differential proteomic analysis was performed to compare the skin from the horn bud region of polled yak fetuses and the horn bud tissue of horned yak fetuses using isobaric tags for relative and absolute quantitation (iTRAQ) technology coupled with 2D LC-MS/MS.ResultsOne hundred differentially abundant proteins (DAPs) were identified. Of these, 29 were up-regulated and 71 were down-regulated in skin from the horn bud region of polled fetuses when compared to the horn bud tissue of horned fetuses. Bioinformatics analyses showed that the up-regulated DAPs were mainly associated with metabolic activities, while the down-regulated DAPs were significantly enriched in cell adhesion and cell movement activities.ConclusionsWe concluded that some important proteins were associated with cell adhesion, cell motility, keratinocyte differentiation, cytoskeleton organization, osteoblast differentiation, and fatty acid metabolism during horn bud development. These results advance our understanding of the molecular mechanisms underlying horn development.