Analysis of the Selection Signal of the Tibetan Black Chicken Genome Based on Whole-Genome Sequencing.

BACKGROUND: The Tibetan chicken has adapted well to high altitudes genetically after its long-term habitation in the plateau. In this study, we analyzed the selection signal of Tibetan black chickens (TBCs) and discovered genes associated with the characteristics of germplasm. METHODS: Whole-genome sequencing (WGS) was used to identify the single-nucleotide polymorphism (SNP) markers and genetic structures in the genome of Tibetan black chickens. Further, we performed a comparative population genomics analysis between the genomic data obtained in this present study and the genomic data for five wild red jungle fowls (RJFs) accessed from the NCBI database (GenBank accession number PRJNA241474). Thereafter, the Fst and Pi selections were used to identify genes under positive selection in the Tibetan black chicken genome. RESULTS: A total of 9,490,690 SNPs were identified in the Tibetan black chickens. In addition, the results from the gene ontology (GO) analysis showed that 732 genes of TBCs were enriched in a total of 210 GO terms with specific molecular functions such as regulation of cellular catabolic process, the MAPK signaling pathway, regulation of ion transport, growth, morphogenesis and lung alveolus development which may provide a better mechanism to facilitate oxygen transport and utilization in TBCs. Moreover, the results from the KEGG analysis showed that 732 genes of the TBCs were significantly enriched in the calcium signaling pathway, circadian entrainment (ADCY1, GNG7 and PER3), oxytocin signaling pathway and pathways of multiple neurodegeneration diseases. In addition, the CD86 antigen (CD86) was identified as a gene associated with the immune response in chickens. It was also revealed that genes such as TRIT1, HPCAL4, NT5C1A and HEYL were discovered under selection in Tibetan black chickens on chromosome 23. These genes may be related to the local adaptive characteristics of Tibetan black chickens, for instance, NT5C1A and HEYL may be involved in the high-altitude adaption of oxygen delivery in Tibetan black chickens. CONCLUSIONS: In summary, we found that selection mainly affects the disease resistance and cold acclimatization of Tibetan black chickens. Hence, these results may provide important genetic information for the evolution and breeding of Tibetan black chickens.

Metagenomic Profiles of Yak and Cattle Manure Resistomes in Different Feeding Patterns before and after Composting.

Antibiotic resistance is a global threat to public health, with antibiotic resistance genes (ARGs) being one of the emerging contaminants; furthermore, animal manure is an important reservoir of biocide resistance genes (BRGs) and metal resistance genes (MRGs). However, few studies have reported differences in the abundance and diversity of BRGs and MRGs between different types of animal manure and the changes in BRGs and MRGs before and after composting. This study employed a metagenomics-based approach to investigate ARGs, BRGs, MRGs, and mobile genetic elements (MGEs) of yak and cattle manure before and after composting under grazing and intensive feeding patterns. The total abundances of ARGs, clinical ARGs, BRGs, MRGs, and MGEs were lower in the manure of grazing livestock than in the manure of the intensively fed group. After composting, the total abundances of ARGs, clinical ARGs, and MGEs in intensively fed livestock manure decreased, whereas those of ARGs, clinical ARGs, MRGs, and MGEs increased in grazing livestock manure. The synergy between MGEs mediated horizontal gene transfer and vertical gene transmission via host bacteria proliferation, which was the main driver that altered the abundance and diversity of ARGs, BRGs, and MRGs in livestock manure and compost. Additionally, tetQ, IS91, mdtF, and fabK were potential indicators for estimating the total abundance of clinical ARGs, BRGs, MRGs, and MGEs in livestock manure and compost. These findings suggest that grazing livestock manure can be directly discharged into the fields, whereas intensively fed livestock manure should be composted before returning to the field. IMPORTANCE The recent increase in the prevalence of antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), and metal resistance genes (MRGs) in livestock manure poses risks to human health. Composting is known to be a promising technology for reducing the abundance of resistance genes. This study investigated the differences and changes in the abundances of ARGs, BRGs, and MRGs between yak and cattle manure under grazing and intensive feeding patterns before and after composting. The results indicate that the feeding pattern significantly affected the abundances of resistance genes in livestock manure. Manure in intensive farming should be composted before being discharged into the field, while grazing livestock manure is not suitable for composting due to an increased number of resistance genes.

Exogenous fibrolytic enzymes promoted energy and nitrogen utilization and decreased CH4 emission per unit dry matter intake of tan sheep grazed a typical steppe by enhancing nutrient digestibility on China loess plateau.

Exogenous fibrolytic enzyme (EFE) products in ruminant nutrition may be an important alternative to meet the increased demands for animal products in the future with reduced environmental impacts. This study aimed to evaluate the dose-response of EFE supplementation on the nutrient digestibility, nitrogen and energy utilization, and methane (CH4) emissions of Tan sheep grazed in summer and winter. A total of 20 Tan wether sheep with an initial body weight of 23.17 ±â€…0.24 kg were used in a randomized complete block design and categorized into two groups. Animals fed orally with 1 g of EFE (10,000 U/g) mixed with 30 mL of water using a drencher constituted the EFE group. For experimental accuracy, the control (CON) group was orally administered with 30 mL of normal saline daily before grazing. The following results were obtained: EFE in the diet increased dry matter intake (DMI) (P < 0.05), average daily gain (ADG) (P < 0.05), and digestibility (P < 0.05) compared with CON in summer and winter. DMI increased but ADG and digestibility decreased in winter compared with those in summer. Sheep fed with the EFE diet increased the concentrations of rumen ammonia nitrogen (P < 0.05) and total volatile fatty acids (P > 0.05), but reduced pH (P > 0.05), compared with CON in summer and winter. EFE increased nitrogen (N) intake, digestible N, retained N, and retained N/digestible N (P < 0.05) but reduced fecal N/N intake, urinary N/N intake, and excretion N/N intake in summer and winter (P < 0.05), compared with CON. Retained N/N intake was reduced and excretion N/N intake increased in winter relative to those in summer. In winter, gross energy (GE), manure E/GE, CH4 emissions, CH4/DMI, and CH4/GE increased but digestion energy and metabolic energy decreased compared with those in summer. Sheep fed with the EFE diet had a greater GE intake than those fed with the CON diet (P < 0.05) but had lesser CH4/DMI and CH4E/GE (P < 0.05) than those fed with the CON diet in both summer and winter. In conclusion, EFE supplementation increased DMI, apparent digestibility, and N deposition rate. These effects were beneficial for animal production. The CH4 emission per unit DMI of grazing Tan sheep was lesser and conducive for augmenting the environmental benefits.

Globally, the supply­demand relationship between grassland and livestock is mainly mediated by the optimization of pasture management. The interaction between grassland and livestock is one of the fundamental drivers of grassland occurrence and development. Natural grassland yields and quality are affected by precipitation, heat, and grazing, and their dynamics vary seasonally with distinct peaks and troughs. The use of exogenous fibrolytic enzymes during troughs can improve the growth performance, digestion, and metabolism of grazing sheep. The exogenous fibrolytic enzyme supplement used in this research may aid in improving the health and overall productivity of grazing sheep.

Combined Analysis of RRBS DNA Methylome and Transcriptome Reveal Novel Candidate Genes Related to Porcine Clostridium perfringens Type C-Induced Diarrhea.

Clostridium perfringens type C (Cp) is one of the principal microorganisms responsible for bacterial diarrhea in neonatal and pre-weaning piglets. To better understand the molecular effects of Cp infection, we performed a genome-wide comparison of the changes in DNA methylation and gene expression in Cp infected resistant and susceptible piglets. We characterized the pattern of changes in methylation and found 6485, 5968, and 6472 differentially methylated regions (DMRs) of piglets infected with Cp in IR vs. IC, IS vs. IC, and IS vs. IR groups, respectively. These methylation changes for genes mainly involved in immune and inflammatory responses, cell adhesion, and activation of transcription factors. Gene ontology and KEGG pathway analyses showed that the differentially methylated genes (DMGs) were associated with negative regulation of transcription, apoptotic processes, protein binding, and kinase activity. In addition, they were enriched in immunity-related pathways, such as MAPK signaling pathway, Toll-like receptor signaling pathway, and NF-kappa B signaling pathway. Integrative analysis identified 168, 198, and 7 mRNAs showing inverse correlations between methylation and expression with Cp infection. Altered DNA methylation and expression of various genes suggested their roles and potential functional interactions upon Cp infection, 14 immune-associated mRNAs with differential methylation and transcriptional repression were identified in IS vs. IR, commonly revealing that the differentially expressed genes (DEGs) LBP, TBX21, and LCN2 were likely involved in the piglets against Cp infection. The present results provide further insight into the DNA methylation epigenetic alterations of C. perfringens type C infected piglet ileum tissues, and may advance the identification of biomarkers and drug targets for predicting susceptibility to and controlling C. perfringens type C-induced piglet diarrhea.

Effect of Clostridium perfringens type C on TLR4/MyD88/NF-κB signaling pathway in piglet small intestines.

Clostridium perfringens (C. perfringens), a Gram-positive bacterium, is one of the main causing piglet diarrhea, which leads serious economic loss in the world swine industries. Generally, the innate immune response plays a critical role in host defense against pathogen invasion. TLR4, a member of the TLR (Toll-like receptor) family, has been considered to implicate in the host immune responses and induce secretion of inflammatory cytokines during bacterial infection. However, little is clear about the effects of TLR4 and key signaling genes in the process of piglet inflammatory and immune responses after C. perfringens infection. This study aims to explore the effect of C. perfringens type C infection on the key mRNAs of TLR4/MyD88/NF-κB signaling pathways during the process of piglet diarrhea. In this study, the expressions of TLR4 and other key mRNAs in the TLR4/MyD88/NF-κB signaling pathways were quantified in piglet ileum and jejunum tissues among IR (intestinal resistance), IS (intestinal susceptibility) and IC (intestinal control) groups by qPCR and Western blot methods, the concentrations of pro-inflammatory cytokines in intestinal tissues and serum immunoglobulins were also tested by ELISA kits. Results showed that compared to IC group, expressions of ileum TLR4 and TNF-α was significantly increased in the IS and IR groups, specially TBK1 gene; the expressions of ileum TLR2, TRAF6, MyD88 and IL-8 mRNAs was significantly up-regulated in the IS group, the expressions of TLR9, NF-κB, IL-6, IFN-γ and MAPK1 genes were not significant differences among the IR, IS and IC groups. Meanwhile, the protein levels of TLR4, HMGB1 and NF-κB were higher in the IS and IR groups. The levels of jejunum IFN-γ and IL-6, ileum IL-6 and IL-12 were risen in the IR group. Serum immunoglobulin IgA and IgG in the IR and IS groups reached a peak on the 72 h and 48 h post infection, respectively. These findings suggest that C. perfringens type C infection induces host immune responses involving in the TLR4/MyD88/NF-κB signaling pathways in ileum than in jejunum, which may provide valuable information for innate immune mechanisms involved in regulation of piglet diarrhea caused by C. perfringens type C infection.

Integrative Analyses of Long Non-coding RNA and mRNA Involved in Piglet Ileum Immune Response to Clostridium perfringens Type C Infection.

Long non-coding RNAs (lncRNAs) have been shown to play important roles in regulating host immune and inflammatory responses to bacterial infection. Infection with Clostridium perfringens (C. perfringens), a food-borne zoonotic pathogen, can lead to a series of inflammatory diseases in human and piglet, greatly challenging the healthy development of global pig industry. However, the roles of lncRNAs involved in piglet immune response against C. perfringens type C infection remain unknown. In this study, the regulatory functions of ileum lncRNAs and mRNAs were investigated in piglet immune response to C. perfringens type C infection among resistance (IR), susceptibility (IS) and sham-inoculation (control, IC) groups. A total of 480 lncRNAs and 3,669 mRNAs were significantly differentially expressed, the differentially expressed lncRNAs and mRNAs in the IR and IS groups were enriched in various pathways of ABC transporters, olfactory transduction, PPAR signaling pathway, chemokine signaling pathway and Toll-like receptor signaling pathway, involving in regulating piglet immune responses and resistance during infection. There were 212 lncRNAs and 505 target mRNAs found to have important association with C. perfringens infectious diseases, furthermore, 25 dysregulated lncRNAs corresponding to 13 immune-related target mRNAs were identified to play potential roles in defense against bacterial infection. In conclusion, the results improve our understanding on the characteristics of lncRNAs and mRNAs on regulating host immune response against C. perfringens type C infection, which will provide a reference for future research into exploring C. perfringens-related diseases in human.

Analyses of long non-coding RNA and mRNA profiling in the spleen of diarrheic piglets caused by Clostridium perfringens type C.

BACKGROUND: Clostridium perfringens (C. perfringens) type C is the most common bacteria causing piglet diarrheal disease and it greatly affects the economy of the global pig industry. The spleen is an important immune organ in mammals; it plays an irreplaceable role in resisting and eradicating pathogenic microorganisms. Based on different immune capacity in piglets, individuals display the resistance and susceptibility to diarrhea caused by C. perfringens type C. Recently, long non-coding RNA (lncRNA) and mRNA have been found to be involved in host immune and inflammatory responses to pathogenic infections. However, little is known about spleen transcriptome information in piglet diarrhea caused by C. perfringens type C. METHODS: Hence, we infected 7-day-old piglets with C. perfringens type C to lead to diarrhea. Then, we investigated lncRNA and mRNA expression profiles in spleens of piglets, including control (SC), susceptible (SS), and resistant (SR) groups. RESULTS: As a result, 2,056 novel lncRNAs and 2,417 differentially expressed genes were found. These lncRNAs shared the same characteristics of fewer exons and shorter length. Bioinformatics analysis identified that two lncRNAs (ALDBSSCT0000006918 and ALDBSSCT0000007366) may be involved in five immune/inflammation-related pathways (such as Toll-like receptor signaling pathway, MAPK signaling pathway, and Jak-STAT signaling pathway), which were associated with resistance and susceptibility to C. perfringens type C infection. This study contributes to the understanding of potential mechanisms involved in the immune response of piglets infected with C. perfringens type C.