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Background: Lanping black-boned sheep (LPB) represent a distinctive mammalian species characterized by hyperpigmentation, resulting in black bone and muscle features, in contrast to their conventional counterparts exhibiting red muscle and white bone. The genetic basis underlying LPB hyperpigmentation has remained enigmatic. Methods: In this study, we conducted whole-genome sequencing of 100 LPB and 50 Lanping normal sheep (LPN), and integrated this data with 421 sequenced datasets from wild and domestic sheep, shedding light on the genetic backdrop and genomic variations associated with LPB. Furthermore, we performed comparative RNA-Seq analysis using liver sample to pinpoint genes implicated in the pigmentation process. We generated a comprehensive dataset comprising 97,944,357 SNPs from 571 sheep, facilitating an in-depth exploration of genetic factors. Results: Population genetic structure analysis revealed that the LPB breed traces its origin back to LPN, having evolved into a distinct breed. The integration of positively selected genes with differentially expressed genes identified two candidates, ERBB4 and ROR1, potentially linked to LPB hyperpigmentation. Comparative analysis of ERBB4 and ROR1 mRNA relative expression levels in liver, spleen, and kidney tissues of LPB, in comparison to Diqing sheep, revealed significant upregulation, except for ERBB4 in the liver. Gene expression heatmaps further underscored marked allelic frequency disparities in different populations. Conclusion: Our findings establish the evolutionary lineage of the LPB breed from LPN and underscore the involvement of ERBB4 and ROR1 genes in melanin synthesis. These results enhance our comprehension of the molecular basis of hyperpigmentation and contribute to a more comprehensive depiction of sheep diversity. [ABSTRACT FROM AUTHOR]

The economic significance of ruminants in agriculture underscores the need for advanced research methodologies to enhance their traits. This review aims to elucidate the transformative role of pan-omics technologies in ruminant research, focusing on their application in uncovering the genetic mechanisms underlying complex traits such as growth, reproduction, production performance, and rumen function. Pan-omics analysis not only helps in identifying key genes and their regulatory networks associated with important economic traits but also reveals the impact of environmental factors on trait expression. By integrating genomics, epigenomics, transcriptomics, metabolomics, and microbiomics, pan-omics enables a comprehensive analysis of the interplay between genetics and environmental factors, offering a holistic understanding of trait expression. We explore specific examples of economic traits where these technologies have been pivotal, highlighting key genes and regulatory networks identified through pan-omics approaches. Additionally, we trace the historical evolution of each omics field, detailing their progression from foundational discoveries to high-throughput platforms. This review provides a critical synthesis of recent advancements, offering new insights and practical recommendations for the application of pan-omics in the ruminant industry. The broader implications for modern animal husbandry are discussed, emphasizing the potential for these technologies to drive sustainable improvements in ruminant production systems. [ABSTRACT FROM AUTHOR]

Simple Summary: This article first introduces the basic principles and analysis process of genome-wide association studies and metabolome genome-wide association studies, then summarizes the latest research progress regarding their applications in animal genetic breeding, and finally briefly compares and elaborates on the advantages and disadvantages of genome-wide association studies and metabolome genome-wide association studies. Given the current emphasis on the analysis of genome-wide association studies and metabolome genome-wide association studies as a focal point of scientific research, our aim in publishing this review is to provide a resource for fellow scientists to efficiently grasp the advancements within our domain. In recent years, genome-wide association studies (GWAS) and metabolome genome-wide association studies (mGWAS) have emerged as crucial methods for investigating complex traits in animals and plants. These have played pivotal roles in research on livestock and poultry breeding, facilitating a deeper understanding of genetic diversity, the relationship between genes, and genetic bases in livestock and poultry. This article provides a review of the applications of GWAS and mGWAS in animal genetic breeding, aiming to offer reference and inspiration for relevant researchers, promote innovation in animal genetic improvement and breeding methods, and contribute to the sustainable development of animal husbandry. [ABSTRACT FROM AUTHOR]

At present, there are few reports about the proteomics changes provoked by butylated hydroxytoluene (BHT) supplementation on cryopreserved semen in mammals. Thus, we aimed to evaluate the effects of different concentrations of BHT on goat sperm and to investigate the proteomics changes of adding BHT to cryopreserved goat (Capra hircus) sperm. Firstly, semen samples were collected from four goats, and frozen in the basic extenders containing different concentrations of BHT (0.5 mM, 1.0 mM, 2.0 mM) and a control without BHT, respectively. After thawing, the protective effects of dose-dependent replenished BHT to the freezing medium on post-thaw sperm motility, integrities of plasma membrane and acrosome, reactive oxygen species levels were confirmed, with 0.5 mM BHT being the best (B group) as compared to the control (without BHT, C group). Afterwards, TMT-based quantitative proteomic technique was performed to profile proteome of the goat sperm between C group and B group. Parallel reaction monitoring was used to confirm reliability of the data. Overall, 2,476 proteins were identified and quantified via this approach. Comparing the C and B groups directly (C vs. B), there were 17 differentially abundant proteins (DAPs) po-tentially associated with sperm characteristics and functions were identified, wherein three were upregulated and 14 were downregulated, respectively. GO annotation analysis demonstrated the potential involvement of the identified DAPs in metabolic process, multi-organism process, reproduction, reproductive process, and cellular process. KEGG enrichment analysis further indicated their potential roles in renin-angiotensin system and glutathione metabolism pathways. Together, this novel study clearly shows that BHT can effectively improve quality parameters and fertility potential of post-thawed goat sperm at the optimal concentration, and its cryoprotection may be realized through regulation of sperm metabolism and antioxidative capability from the perspective of sperm proteomic modification. [ABSTRACT FROM AUTHOR]

In the intricate tapestry of Yunnan Province's biodiversity, the Lanping black-boned sheep (LPBB) emerges as a captivating enigma, distinguished by its profound melanin pigmentation adorning both its skin and its internal organs. Initially cataloged in the 1950s within the confines of Lanping County, this exceptional mammalian species presents a scarcity and uniqueness that extends beyond its geographic origins. Here, we collected 100 blood samples from Lanping black-boned sheep along with 50 samples each from Lanping normal sheep (LPN) and Huize normal sheep (HZN), all sourced from Yunnan Province. Our investigation focused on the association between the platelet-derived growth factor receptor-like gene (PDGFRL) polymorphism and the distinctive melanin characteristics observed in Lanping black-boned sheep. Utilizing UV–visible spectrophotometry, we assessed the melanin indexes present, such as tyrosinase activity and true melanin in the sheep blood, and the results demonstrated a significant elevation in melanin indexes for Lanping black-boned sheep compared to the control group (P<0.05). We also identified three synonymous mutation sites within a partial 1128 bp exon fragment of the gene-encoding PDGFRL (EX2-G408A, EX5-T184C, and EX5-G222T). Notably, Lanping black-boned sheep, harboring genotypes GG, TT, and GG at these specific sites, showcased a pronounced surge in tyrosinase activity, eumelanin / total melanin ratios, and plasma colorimetric values when contrasted with the control group (P<0.05). The discernment of GG, TT, and GG as the prevailing genotypes at their respective genetic loci in Lanping black-boned sheep heralds a breakthrough in our understanding of the genetic markers associated with black pigmentation. However, all three loci are silent mutations and do not alter the phenotypic changes. Whether they affect changes in melanin content through other metabolic pathways requires further study. In conclusion, the PDGFRL gene was silenced by mutations in our study and affected blood melanin levels. However, the gene did not undergo a missense mutation that altered the phenotypic changes, and the exact channel through which the changes in melanin content were affected needs to be further verified. [ABSTRACT FROM AUTHOR]

The Chungtien schizothoracin (Ptychobarbus chungtienensis), an endangered fish species endemic to the Zhongdian Plateau, remains underexplored in terms of transcriptomic sequencing. This investigation used tissues from five distinct organs (heart, liver, spleen, kidney, and brain) of the Chungtien schizothoracin for PacBio Iso-seq and RNA-seq analyses, yielding a repertoire of 16,598 full-length transcripts spanning lengths from 363 bp to 7,157 bp. Gene family clustering and phylogenetic analysis encompassed a comprehensive set of 13 fish species, all of which were cyprinids, including the zebrafish and the examined species Ptychobarbus chungtienensis. Moreover, the identification of long non-coding RNAs (lncRNAs) and coding sequences was accomplished across all five tissues. Comprehensive analyses of gene expression profiles and differentially expressed genes among the above five tissues were performed. In summary, the obtained full-length transcripts and detailed gene expression profiles of the Chungtien schizothoracin tissues furnish crucial expression data and genetic sequences, laying the groundwork for future investigations and fostering a holistic comprehension of the adaptive mechanisms inherent in the Chungtien schizothoracin under various conditions. [ABSTRACT FROM AUTHOR]

Simple Summary: Panomics refers to the integration of multiple omics technologies to comprehensively examine and interpret biomolecular data at different levels. This approach facilitates the study of sheep genetics and related functions, providing valuable insights into sheep breeding, disease prevention, and treatment strategies. By analyzing the complex interactions between genes, proteins, and metabolites, we can gain a deeper understanding of sheep biology and ultimately improve productivity and reproduction. Panomics, in particular, allows for the prediction, screening, and pinpointing of animal genetic traits, overcoming the limitations of traditional breeding methods like age constraints and issues with accuracy and reliability. This advancement holds immense importance for sheep breeding and agricultural production. Multi-omics-integrated analysis, known as panomics, represents an advanced methodology that harnesses various high-throughput technologies encompassing genomics, epigenomics, transcriptomics, proteomics, and metabolomics. Sheep, playing a pivotal role in agricultural sectors due to their substantial economic importance, have witnessed remarkable advancements in genetic breeding through the amalgamation of multiomics analyses, particularly with the evolution of high-throughput technologies. This integrative approach has established a robust theoretical foundation, enabling a deeper understanding of sheep genetics and fostering improvements in breeding strategies. The comprehensive insights obtained through this approach shed light on diverse facets of sheep development, including growth, reproduction, disease resistance, and the quality of livestock products. This review primarily focuses on the application of principal omics analysis technologies in sheep, emphasizing correlation studies between multiomics data and specific traits such as meat quality, wool characteristics, and reproductive features. Additionally, this paper anticipates forthcoming trends and potential developments in this field. [ABSTRACT FROM AUTHOR]

As an exemplary model for examining molecular mechanisms responsible for extreme phenotypic variations, plumage color has garnered significant interest. The Cygnus genus features two species, Cygnus olor and Cygnus atratus, that exhibit striking disparities in plumage color. However, the molecular foundation for this differentiation has remained elusive. Herein, we present two high-quality genomes for C. olor and C. atratus, procured using the Illumina and Nanopore technologies. The assembled genome of C. olor was 1.12 Gb in size with a contig N50 of 26.82 Mb, while its counterpart was 1.13 Gb in size with a contig N50 of 21.91 Mb. A comparative analysis unveiled three genes (TYR, SLC45A2, and SLC7A11) with structural variants in the melanogenic pathway. Notably, we also identified a novel gene, PWWP domain containing 2A (PWWP2A), that is related to plumage color, for the first time. Using targeted gene modification analysis, we demonstrated the potential genetic effect of the PWWP2A variant on pigment gene expression and melanin production. Finally, our findings offer insight into the intricate pattern of pigmentation and the role of polygenes in birds. Furthermore, these two high-quality genome references provide a comprehensive resource and perspective for comparative functional and genetic studies of evolution within the Cygnus genus. [ABSTRACT FROM AUTHOR]

Among the numerous transmissible spongiform encephalopathies (TSEs), bovine spongiform encephalopathy (BSE) is the most well-known TSEs. It is a potential Creutzfeldt–Jakob (CJD) disease mutation that can be transferred through cattle to humans. In several animals, the prion protein gene (PRNP) is recognized to take active part in TSE vulnerability or tolerance. Previous studies have found indels polymorphism in PRNP gene promoter and intron1 region linked to BSE vulnerability. It's linked with 23 bp indels polymorphism in putative promoter and 12 bp indel in intron 1 of the PRNP gene. The aim of this study was to compare the allele, genotype and haplotype frequencies of PRNP indel polymorphisms in Zhongdian Yak (Bos grunniens) (YK), Zhongdian Yellow cattle (Bos taurus) (YC) and Zhongdian Yakow (Bos primigenius taurus × Bos grunniens) (PK) with worldwide reported healthy or affected BSE cattle, in order to assess their potential resistance to BSE. A comparison of Chinese bovine populations with healthy and BSE-affected German and Swiss cattle from globally was conducted, and result indicating significant difference (p <.001) between healthy and affected cattle. Additionally, as compared to prior studies with Chinese bovine population, the significant results were found. In this study, the allelic frequency D23 finding high deletion in all analyzed Chinese bovine species, and haplotype D12–D23 exhibited a less significant inclination toward susceptibility to BSE. [ABSTRACT FROM AUTHOR]

Simple Summary: Bovine spongiform encephalopathy (BSE), a neurological disorder with a significant effect on cattle health, has been recognized pathologically and medically. It is associated with a 12 bp indel in intron 1 of the PRNP gene and a 23 bp indel polymorphism in the putative promoter. The main focus of this work was to assess the allele, genotype, and haplotype frequencies of PRNP indel polymorphisms in Zhongdian Yak, Zhongdian Yellow cattle, and Zhongdian Yakow, as well as to investigate the effect of PRNP gene expressions of 23 bp and 12 bp indels using PCR. Two variable sites—a 23 bp indel polymorphism holding AP1 binding site and a 12 bp indel polymorphism holding SP1 binding site—were also investigated. Overall, the study results suggest that the PRNP genotype may contribute to the high variation in PRNP expression. Bovine spongiform encephalopathy (BSE) is a fatal disease in cattle caused by misfolded prion proteins and linked to indel polymorphisms in the promoter and intron 1 of the PRNP gene. The aim of this study was to determine the allele, genotype, and haplotype frequencies of PRNP indel polymorphisms and to investigate the effect of PRNP gene expressions of 23 bp and 12 bp indels via polymerase chain reaction (PCR) in Zhongdian Yak (Bos-grunniens) (YK), Zhongdian Yellow cattle (Bos-taurus) (YC), and Zhongdian Yakow (Bos-primigenius taurus × Bos-grunniens) (PK). Resultant high allelic frequencies were found in 23− and 12+, while haplotype frequencies were very low in 23+/12 in YK, YC, and PK. PRNP expression was higher in the +−/−− diplotype of the PK and (mean ± SE) was 3.6578 ± 1.85964. Furthermore, two variable sites were investigated—a 23 bp indel polymorphism holding AP1 binding site and a 12 bp indel polymorphism holding SP1 binding site. Additionally, reporter gene assays revealed a link between two proposed transcription factors and lower expression levels of the +/+ allele compared with the −/− allele. The expression level of PRNP was shown to be dependent on two indel polymorphisms in the bovine PRNP promoter, which includes binding sites for RP58 and SP1 transcription factors. These findings raised the possibility that the PRNP genotype may contribute to the high variation in PRNP expression. [ABSTRACT FROM AUTHOR]

Simple Summary: Due to a lack of understanding of the 5′ regulatory region of the SLC11A1 gene in the yak population, we conducted a comprehensive analysis of the regulatory region of the yak SLC11A1 gene by cloning gene sequences of different lengths. Through transient transfection experiments, we confirmed the promoter activity of four distinct-length sequences within the 5′ regulatory region of the yak SLC11A1 gene in the RAW264.7 cell line. Moreover, our analysis identified six novel SNPs in the 5′ regulatory region sequence of the SLC11A1 gene in yaks. Bioinformatic analysis emphasized the proximity of the −1057 G>T and −127 G>A loci to the transcription factor binding sites NF-1 and NF-1/L. This observation suggests their potential impact on NF-1 and NF-1/L transcription factor binding. In summary, this study serves as a foundational reference for future research on the connection between promoter region polymorphism of the yak SLC11A1 gene and disease resistance. It also lays the foundation for investigating the transcriptional regulation mechanisms of this gene, and opens the door to further exploration in this important field. The solute transport protein family 11 A1 (SLC11A1), also recognized as natural resistance-associated macrophage protein 1 (NRAMP1), represents a transmembrane protein encoded by the SLC11A1 gene. A variety of prior investigations have illuminated its involvement in conferring resistance or susceptibility to bacterial agents, positioning it as a promising candidate gene for breeding disease-resistant animals. Yaks (Bos grunniens), renowned inhabitants of the Qinghai-Tibet Plateau in China, stand as robust ruminants distinguished by their adaptability and formidable disease resistance. Notwithstanding these unique traits, there is scant literature on the SLC11A1 gene in the yak population. Our inquiry commences with the cloning of the 5′ regulatory region sequence of the Zhongdian yak SLC11A1 gene. We employ bioinformatics tools to identify transcription factor binding sites, delineating pivotal elements like enhancers and cis-acting elements. To ascertain the promoter activity of this region, we amplify four distinct promoter fragments within the 5′ regulatory region of the yak SLC11A1 gene. Subsequently, we design a luciferase reporter gene vector containing four site-specific deletion mutations and perform transient transfection experiments. Through these experiments, we measure and compare the activity of disparate gene fragments located within the 5′ regulatory region, revealing regions bearing promoter functionality and discerning key regulatory elements. Our findings validate the promoter functionality of the 5′ regulatory region, offering preliminary insights into the core and principal regulatory segments of this promoter. Notably, we identified single nucleotide polymorphisms (SNPs) that may be associated with important regulatory elements such as NF-1 and NF-1/L. This study provides a theoretical framework for in-depth research on the function and expression regulation mechanism of the yak SLC11A1 gene. [ABSTRACT FROM AUTHOR]

Simple Summary: In the face of the challenge posed by antibiotic prohibition, the identification of sustainable, eco-friendly alternatives to antibiotics is important. Ampelopsis grossedentata flavonoids, a plant-based extract, have high antioxidant and anti-inflammatory activities provide a non-toxic and innocuous option for the extended application of additives. This study examined the viability of Ampelopsis grossedentata flavonoids as a potential substitute for antibiotics. The results showed that supplementation of Ampelopsis grossedentata flavonoids in the diet exhibited the capacity to enhance rumen microbial diversity and immune competence, thereby fostering improved growth performance among weaned kids. Consequently, this study provides an important reference for the future development of Ampelopsis grossedentata flavonoids as a new environmentally friendly additive. This study was conducted to evaluate the influences of supplementing Ampelopsis grossedentata flavonoids (AGF) on the rumen bacterial microbiome, plasma physiology and biochemistry, and growth performance of goats. Twenty-four Nubian kids were randomly allocated to three dietary treatments: the control (CON, basal diet), the 1.0 g/kg AGF treatment (AGF), and the 12.5 mg/kg monensin treatment (MN). This trial consisted of 10 days for adaptation and 90 days for data and sample collection. The results reveal that Bacteroidetes, Firmicutes, and Proteobacteria are the dominant phyla in kids' rumen. Compared with the CON group, the alpha diversity in the MN and AGF groups significantly increased (p < 0.01). Beta-diversity shows that rumen microbial composition is more similar in the MN and AGF groups. LEfSe analysis shows that Prevotella_1 in the AGF group were significantly higher than those in the MN and CON group. The high-density lipoprotein cholesterol and glucose levels in the AGF group were significantly higher than those in the CON group (p < 0.05), whereas the low-density lipoprotein cholesterol, glutamic-pyruvic transaminase, and alkaline phosphatase levels exhibited the opposite trend. The average daily gains in the AGF and MN groups significantly increased, while the feed-to-gain ratios were significantly decreased (p < 0.05). The results suggest that adding AGF to the diet improves microbial composition and has important implications for studying juvenile livestock growth and improving economic benefits. [ABSTRACT FROM AUTHOR]

Polyethylene (PE) and carbon black (CB) were premixed in this study for bitumen modification. The service performance of PE/CB-modified bitumen (PMB) was mainly explored by multiple stress creep recovery (MSCR) and linear amplitude sweep (LAS) tests to reveal the rutting resistance and fatigue life, respectively. Low-temperature properties were evaluated by glass transition temperature (Tg) measured by dynamic mechanical analysis (DMA). X-ray diffraction (XRD) results suggested that the crystalline structure of PE was almost the same regardless of different CB loading additions. It was found that the both rutting resistance and fatigue life of PMBs showed nonmonotonic variation with CB loading. The mechanism for this variation was closely related to the microstructure induced by phase separation, CB nanoparticle aggregation and PE crystallinity. As revealed by optical and atomic force microscopy, two different phase structures, network and droplet-matrix structure, can be formed in PMBs when the CB loading changes. In particular, a double percolated network structure can be formed, consisting of a PE-rich network in the bitumen-matrix and CB nanoparticle network within a PE-rich phase. With the presence of this structure, the rutting resistance and fatigue life of PMB can be significantly improved. [ABSTRACT FROM AUTHOR]

The Y chromosome plays key roles in male fertility and reflects the evolutionary history of paternal lineages. Here, we present a de novo genome assembly of the Hu sheep with the first draft assembly of ovine Y chromosome (oMSY), using nanopore sequencing and Hi-C technologies. The oMSY that we generated spans 10.6 Mb from which 775 Y-SNPs were identified by applying a large panel of whole genome sequences from worldwide sheep and wild Iranian mouflons. Three major paternal lineages (HY1a, HY1b and HY2) were defined across domestic sheep, of which HY2 was newly detected. Surprisingly, HY2 forms a monophyletic clade with the Iranian mouflons and is highly divergent from both HY1a and HY1b. Demographic analysis of Y chromosomes, mitochondrial and nuclear genomes confirmed that HY2 and the maternal counterpart of lineage C represented a distinct wild mouflon population in Iran that diverge from the direct ancestor of domestic sheep, the wild mouflons in Southeastern Anatolia. Our results suggest that wild Iranian mouflons had introgressed into domestic sheep and thereby introduced this Iranian mouflon specific lineage carrying HY2 to both East Asian and Africa sheep populations. [ABSTRACT FROM AUTHOR]

Dogs represent such a rich potential resource to further understand diseases and genetic traits. Comparing the genomes of three species of canine, human, and rat in terms of genome analysis, it is found that dogs are highly conservative with humans and rats. The special population structure of dogs makes it a good model for studying the diversity of morphology and behavior, the genetic basis of mammalian evolution, and diseases. This article gives a brief review of recent advances in domestic dog origin and evolution, genomic structure, genetic variation in dog phenotypic characteristics, and gene mapping. These research results are expected to provide a better theoretical basis for canine genetic breeding research and provide new ideas and methods for the prevention, diagnosis and treatment of human diseases. [ABSTRACT FROM AUTHOR]

Lanping black-boned sheep was first discovered in the 1950s in Lanping county of China and characterized by black pigmentation on skin and internal organs. Due to the novel and unique trait, the genetic background of Lanping black-boned sheep is of great interest. Here, we genotyped genome-wide SNPs (single nucleotide polymorphisms) of Lanping black-boned sheep and Lanping normal sheep using Illumina OvineSNP50 BeadChip to investigate the genetic diversity and genetic origin of Lanping black-boned sheep. We also downloaded a subset SNP dataset of two Tibet-lineage sheep breeds and four other sheep breeds from the International Sheep Genomics Consortium (ISGC) as a reference for interpreting. Lanping black-boned sheep had a lower genetic diversity level when compared to seven other sheep breeds. Principal component analysis (PCA) showed that Lanping black-boned sheep and Lanping normal sheep were clustered into the Asian group, but there was no clear separation between the two breeds. Structure analysis demonstrated a high ancestry coefficient in Lanping black-boned sheep and Lanping normal sheep. However, the two populations were separated into two distinct branches in a neighbor-joining (NJ) tree. We further evaluated the genetic divergence using population FST , which showed that the genetic differentiation that existed between Lanping black-boned sheep and Lanping normal sheep was higher than that between Tibet sheep and Changthangi sheep, which revealed that Lanping black-boned sheep is a different breed from Lanping normal sheep on the genetic level. In addition, structure analysis and NJ tree showed that Lanping black-boned sheep had a relatively close relation with Tibet sheep. The results reported herein are a first step toward understanding the genetic background of Lanping black-boned sheep, and it will provide informative knowledge on the unique genetic resource conservation and mechanism of novel breed formation. [ABSTRACT FROM AUTHOR]

Resistance to fatal disease bovine spongiform encephalopathy (BSE), due to misfolded prion protein in cattle, is associated with a 23-bp indel polymorphism in the putative promoter and a 12-bp indel in intron 1 of the PRNP gene. Gayal (Bos frontalis) is an important semiwild bovid species and of great conservation concern, but till today these indel polymorphisms have not been evaluated in gayals. Therefore, we collected 225 samples of gayals and evaluated the genetic indel polymorphism in the two regions of this PRNP gene. The results revealed high allelic frequencies of insertions at these indel sites: 0.909 and 0.667 for, respectively, the 23 bp and 12 bp indels, both also with significant genotype frequencies (χ2: 9.81; 23 bp and χ2: 43.56; 12 bp). At the same time, the haplotype data showed indel polymorphisms with extremely low deletion (0.01) in both regions of the PRNP gene. We compared these data with those reported for healthy and BSE-affected cattle (Bos taurus) breeds from two European countries, Germany and Switzerland, and significant difference (P<0.001) was observed between BSE-affected as well as the healthy cattle. Further, our data were also extensively compared with previous reports on BSE and highly significant (P<0.001) outcomes were observed. This result suggested negligible genetic susceptibility to BSE in gayals. To the best of our knowledge, this study is the first comprehensive deciphering information about the PRNP indel polymorphisms of 23 bp and 12 bp in gayals, a semiwild species of China. [ABSTRACT FROM AUTHOR]

The species origin of Yunnan gayal has been controversial since many years. However, few recent genetic studies have suggested that it has perhaps originated from the hybridization between male Bos frontalis and female B. taurus or B. indicus. Being an important semi-wild bovid species, this has also been listed under the red list of International Union of Conservation of Nature and Natural Resources. However, there is limited information available about the immunogenicity of this precarious species of Bos. Major histocompatibility complex (MHC) plays a pivotal role in immune response to infectious diseases in vertebrates. In the present study, we have investigated the structural and functional characteristics and possible duplication of the MHC-DQA genes in gayal (B. frontalis). Two full-length cDNA clones of the MHC-DQA genes were amplified and designated as Bofr-DQA1 (DQA*0101) and Bofr-DQA2 (DQA*2001) with GenBank accession numbers KT318732 and KT318733, respectively. A comparison between Bofr-DQA1, Bofr-DQA2 and to other MHC-DQA molecules from different animal species showed that nucleotide and encoded amino acid sequences of these two identified MHC-DQA genes have more similarity to alleles of specific DQA1 and DQA2 molecules from other Ruminantia species than to each other. The phylogenic investigation also demonstrated a large genetic distance between these two genes than to homologous from the other species. The large genetic distance between Bofr-DQA1 and Bofr-DQA2, and the presence of different bovine DQA putative motifs clarify that these sequences are nonallelic type. These results could suggest that duplication of the DQA genes has also occurred in gayal. The findings of the present study have strengthened our understanding to MHC diversity in rare ruminants and mutation of immunological functions, selective and evolutionary forces that affect MHC variation within and between species. [ABSTRACT FROM AUTHOR]

The effects of mutations of the gene for tyrosinase-related protein 1 (TYRP1) on the black muscles and coat color in Nanping black-boned sheep were investigated. Tyrosinase activity and melanin content in plasma were measured and compared in three random groups of sheep: Nanping black-boned (101 heads), Nanping normal (106 heads) and Romney Marsh sheep (82 heads, Ovis aries). Eight exons and their partial flanking regions of the TYRP1 gene were amplified. Six intronic mutations and six exonic polymorphisms including two non-synonymous mutations [c.203C >T (p.A68V) and c.1202T>C (p.V401A)] were identified. Using a bi-directional polymerase chain reaction allele-specific amplification (bi-PASA) of the mutation c.203C>T it was shown that the frequencies of allele C in the Nanping black-boned, Nanping normal and Romney Marsh sheep were respectively 0.955, 0.967 and 0.744. For the mutation c.1202T>C, the frequencies of allele T in the three populations of sheep were respectively 0.777, 0.745 and 0.793 as measured using the single-strand conformation polymorphism. When the data from sheep of all three populations with the CC genotype of SNP c.203C>T were pooled, it was found that there was significantly higher (P <0.05) tyrosinase activity, content of alkali-soluble melanin and ratio of eumelanin : total melanin than in the plasma of sheep with the CT and TT genotypes. This was not so within each of the three groups of sheep. No significant effect of the TRYP1 genotype on coat color was found. Further studies will be necessary to determine the cause of the black traits in Nanping black-boned sheep. [ABSTRACT FROM AUTHOR]

The major histocompatibility class (MHC) DQ molecules are dimeric glycoproteins revealing antigen presentation to CD T cells. In the present study, the exon 2 of the MHC class II DQB gene from 32 yaks ( Bos grunniens) was cloned, sequenced and compared with previously reported patterns for other bovidae. It was revealed by sequence analyses that there are 25 DQB exon 2 alleles among 32 yaks, all alleles are found to belong to DQB1 loci. These alleles exhibited a high degree of nucleotide and amino acid polymorphisms with most amino acid variations occurring at positions forming the peptide-binding sites. The DQB loci were analyzed for patterns of synonymous ( d) and non-synonymous ( d) substitution. The yak was observed to be under strong positive selection in the DQB exon 2 peptide-binding sites ( d = 0.15, P < 0.001). It appears that this variability among yaks confers the ability to mount immune responses to a wide variety of peptides or pathogens. [ABSTRACT FROM AUTHOR]

Packer slips prone to fracture under tremendous pressure during drilling, it will affect the sealing performance of the packer directly, and affect the process of mining and safety in production wells. The slip was analysised using the finite element analysis software. When the applied load is 140 kN, the slip's maximum stress is 230.11 MPa, which exceeding the maximum compressive strength of this material. The slip packer test mode was undergo a fracturing test, slip fractured when the test pressure is 186.33 kN, the compressive strength is measured 233 MPa. Slip structure was designed, the spacing sizes of slip tooth were 15 mm, 25 mm and 30 mm. According to the results of finite element analysis, when the spacing size of slip tooth is 30 mm, the distribution of the slip's stress and strain tends to uniform. When 240 kN load is applied, the maximum stress exceeds the maximum compressive strength of slip's material, and the slip's maximum stress is 230.66 MPa, the maximum deformation is 0.058 mm, and provides the slip structure size is reasonable. [ABSTRACT FROM AUTHOR]

The melanocortin 1 receptor gene ( MC1R) plays a crucial role in determining coat colour of mammals. To investigate the relationship of polymorphism of the MC1R with coat colour in gayal, the coding sequence (CDS), and the 5′- and 3′-untranslated regions (UTR) of the MC1R were sequenced from 63 samples from the gayal and compared with the sequences of the MC1R from other ruminant species. A sequence of 1,136 bp including the whole CDS (954 bp) and parts of the 5′- and 3′-UTR (164 and 18 bp, respectively) of the gayal MC1R was obtained. A total of nine single nucleotide polymorphisms (SNPs) including four SNPs (c.−129T>C, c.−127A>C, c.−106C>T, c.−1G>A) in the 5′-UTR and five SNPs (c.201C>T, c.583C>T, c.663T>C, c.871A>G and c.876T>C) in the CDS were detected, revealing high genetic diversity. Three novel coding SNPs including c.201C>T, c.583C>T and c.876T>C, which have not been reported previously in bovid species, were retrieved. Within five coding SNPs, c.201C>T, c.663T>C and c.876T>C were silent mutations, while c.583C>T and c.871A>G were mis-sense mutations, resulting in changes in the amino acids located in the fifth (p.L195F) and seventh (p.T291A) transmembrane regions, respectively. The alignment of amino acid sequences was found to be very similar to those for other bovid species. It was demonstrated, using the functional effect prediction, that the p.T291A amino acid replacement could have an effect on MC1R protein function but not for the p.L195F substitution. Using phylogenetic analyses it was revealed that the gayal has a close genetic relationship with the yak. However, three classical bovine MC1R loci the E, E and e were not retrieved in the gayal, indicating other genes or factors could affect coat colour in this species. [ABSTRACT FROM AUTHOR]

The gayal ( Bos frontalis) is a rare semi-wild bovid species in which bovine spongiform encephalopathy (BSE) has not been reported. Polymorphisms of the prion protein gene ( PRNP) have been correlated significantly with resistance to BSE. In this study, the coding region of PRNP was cloned and characterized in samples from 125 gayal. A total of ten single nucleotide polymorphisms (SNPs), including six silent mutations (C60T, G75A, A108T, G126A, C357T and C678T) and four mis-sense mutations (C8A, G145A, G461A and C756G), corresponding to amino acids T3K, G49S9, N154S and I252M were identified, revealing high genetic diversity. Three novel SNPs including C60T, G145A and C756G, which have not been reported previously in bovid species, were retrieved. There also was one insertion-deletion (187Del24) at the N-terminal octapeptide repeat region. Alignment of nucleotide and amino acid sequences showed a high degree of similarity with other bovid species. Using phylogenetic analyses it was revealed that gayal has a close genetic relationship with Zebu cattle. In short, preliminary information is provided about genotypes of the PRNP in gayal. This could assist with the study of the pathogenesis of transmissible spongiform encephalopathies and cross species transmission as well as a molecular breeding project for gayal in China. [ABSTRACT FROM AUTHOR]

The complete coding sequences of three of sheep genes SLC25A4, SLC25A5 and SLC25A6 were firstly amplified using the reverse transcriptase polymerase chain reaction (RT-PCR) according to the conserved sequence information of the cattle or other mammals and known highly homologous sheep ESTs. Sheep SLC25A4, SLC25A5 and SLC25A6 genes encode three corresponding proteins of 298 amino acids which contain the identically conserved putative mitochondrial carrier protein domain. Sheep SLC25A4 protein has high homology with the SLC25A4 proteins of six species—cattle (99%), human (95%), rat (95%), mouse (94%), dog (94%) and chicken (89%). Sheep SLC25A5 protein has high identity with the SLC25A5 proteins of five species—cattle (100%), dog (99%), mouse (98%), rat (98%) and human (98%). Sheep SLC25A6 protein also has high homology with the SLC25A6 proteins of four species—cattle (99%), human (97%), pig (97%) and chicken (93%). The phylogenetic tree analysis demonstrated that sheep SLC25A4, SLC25A5 and SLC25A6 proteins share a common ancestor. Moreover, SLC25A4, SLC25A5 and SLC25A6 proteins present stronger interaction each other. The tissue expression analysis indicated that sheep SLC25A4, SLC25A5 and SLC25A6 genes were expressed in a range of tissues including leg muscle, kidney, skin, longissimus dorsi muscle, spleen, heart and liver. Our experiment is the first to provide the primary foundation for further insight into these three sheep genes. [ABSTRACT FROM AUTHOR]

Background: Black bone sheep was first discovered in Yunnan province of China in 1970, with unique black pigmentation on the body and internal organs. Endothelin 3 (EDN3) has been known as a key gene causing hyperpigmentation in black bone chicken, the Silky fowl. Methods: In this study, EDN3 was employed as a candidate gene for regulating black color pigmentation. First, EDN3 was cloned from sheep to obtain the full-length cDNA by using the rapid amplification of cDNA ends (RACE). Genomic EDN3 was screened and a total of thirty predicted single nucleotide polymorphisms (SNPs) were genotyped for allele and genotype frequency analysis in a case-control study involving two black bone sheep populations. Genomic copy number analysis of EDN3 in sheep was conducted to measure the variation in copy number. EDN3 expression levels were observed among the groups in adult liver, lymph node, and kidney tissues, as well as embryo kidney samples. Also, among the tissues of black bone and non-black bone sheep. Results: The size of the full-length cDNA was 1,578 bp, which included 426 bp of 5′-untranslated region (5′-UTR), an open reading frame (ORF) of 639 bp encoding a protein of 212 amino acids, and a 3′-UTR of 513 bp. Genotype and allele frequencies of all the discovered SNPs were found insignificantly different in black bone and non-black bone sheep (P > 0.05). Genomic copy number analysis of EDN3 in sheep revealed no significant difference between the two sheep groups. No significant variations were found in the adult liver and kidney embryo samples. However, the expression in lymph node and kidney tissue was significantly higher in black bone sheep than that in non-black bone sheep (P < 0.05). Significant variations in the EDN3 expression levels were observed among the tissues of non-black bone sheep. Conclusions: The findings of the present study indicate that unlike in Silky chickens, EDN3 is not responsible for hyperpigmentation but may play a key functional role in immune and excretory systems of black bone sheep. [ABSTRACT FROM AUTHOR]