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Chacón RD, Sánchez-Llatas CJ, L Pajuelo S, Diaz Forero AJ, Jimenez-Vasquez V, Médico JA, Soto-Ugaldi LF, Astolfi-Ferreira CS, Piantino Ferreira AJ. Molecular characterization of the meq oncogene of Marek's disease virus in vaccinated Brazilian poultry farms reveals selective pressure on prevalent strains. Vet Q 2024; 44:1-13. [PMID: 38465827 DOI: 10.1080/01652176.2024.2318198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 02/05/2024] [Indexed: 03/12/2024] Open
Abstract
Marek's disease virus (MDV) has become an increasingly virulent pathogen in the poultry industry despite vaccination efforts to control it. Brazil has experienced a significant rise of Marek's disease (MD) outbreaks in recent years. Our study aimed to analyze the complete meq gene sequences to understand the molecular epidemiological basis of MD outbreaks in Brazilian vaccinated layer farms. We detected a high incidence rate of visceral MD (67.74%) and multiple circulating MDV strains. The most prevalent and geographically widespread genotype presented several clinical and molecular characteristics of a highly virulent strain and evolving under positive selective pressure. Phylogenetic and phylogeographic analysis revealed a closer relationship with strains from the USA and Japan. This study sheds light on the circulation of MDV strains capable of infecting vaccinated birds. We emphasize the urgency of adopting preventive measures to manage MDV outbreaks threatening the poultry farming industry.
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Affiliation(s)
- Ruy D Chacón
- Department of Pathology, School of Veterinary Medicine, University of São Paulo, São Paulo, Brazil
| | - Christian J Sánchez-Llatas
- Department of Genetics, Physiology, and Microbiology, Faculty of Biology, Complutense University of Madrid, Madrid, Spain
| | | | - Andrea J Diaz Forero
- Department of Pathology, School of Veterinary Medicine, University of São Paulo, São Paulo, Brazil
| | | | - Jack A Médico
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | - Luis F Soto-Ugaldi
- Tri-Institutional Program in Computational Biology and Medicine, New York, NY, USA
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2
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Chen L, Cheng Y, Zhang G, Zhou Y, Zhang Z, Chen Q, Feng Y. WGBS of embryonic gonads revealed that long non-coding RNAs in the MHM region might be involved in cell autonomous sex identity and female gonadal development in chickens. Epigenetics 2024; 19:2283657. [PMID: 38037805 PMCID: PMC10761181 DOI: 10.1080/15592294.2023.2283657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 10/01/2023] [Indexed: 12/02/2023] Open
Abstract
DNA methylation plays a key role in sex determination and differentiation in vertebrates. However, there are few studies on DNA methylation involved in chicken gonad development, and most focused on male hypermethylated regions (MHM). It is unclear whether there are specific differentially methylated regions (DMRs) in chicken embryonic gonads regulating sex determination and differentiation. Here, the DNA methylation maps showed that the difference of DNA methylation level between sexes was much higher at embryonic day 10 (E10) than that at embryonic day 6 (E6), and the significant differentially methylated regions at both stages were mainly distributed on the Z chromosome, including MHM1 and MHM2. The results of bisulphite sequencing PCR (BSP) and qRT-PCR showed hypomethylation of female MHM and upregulation of long non-coding RNAs (lncRNAs) whose promoter in the MHM region was consistent with the sequencing results, and similar results were in brain and muscle. In female sex-reversed gonads, the methylation pattern of MHM remained unchanged, and the expression levels of the three candidate lncRNAs were significantly decreased compared with those in females, but were significantly increased compared to males. The fluorescence in situ hybridization (FISH) results also showed that these lncRNAs were highly expressed in female embryonic gonads. The results of methyltransferase inhibitor and dual-luciferase reporter assay suggest that lncRNA expression may be regulated by DNA methylation within their promoters. Therefore, we speculated that MHM may be involved in cell-autonomous sex identity in chickens, and that lncRNAs regulated by MHM may be involved in female sexual differentiation.
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Affiliation(s)
- Ligen Chen
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Yu Cheng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Guixin Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Zhen Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Qianhong Chen
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Yanping Feng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
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3
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Seo YJ, Lim C, Lim B, Kim JM. Microbial-transcriptome integrative analysis of heat stress effects on amino acid metabolism and lipid peroxidation in poultry jejunum. Anim Biotechnol 2024; 35:2331179. [PMID: 38519440 DOI: 10.1080/10495398.2024.2331179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2024]
Abstract
Despite the significant threat of heat stress to livestock animals, only a few studies have considered the potential relationship between broiler chickens and their microbiota. Therefore, this study examined microbial modifications, transcriptional changes and host-microbiome interactions using a predicted metabolome data-based approach to understand the impact of heat stress on poultry. After the analysis, the host functional enrichment analysis revealed that pathways related to lipid and protein metabolism were elevated under heat stress conditions. In contrast, pathways related to the cell cycle were suppressed under normal environmental temperatures. In line with the transcriptome analysis, the microbial analysis results indicate that taxonomic changes affect lipid degradation. Heat stress engendered statistically significant difference in the abundance of 11 microorganisms, including Bacteroides and Peptostreptococcacea. Together, integrative approach analysis suggests that microbiota-induced metabolites affect host fatty acid peroxidation metabolism, which is correlated with the gene families of Acyl-CoA dehydrogenase long chain (ACADL), Acyl-CoA Oxidase (ACOX) and Acetyl-CoA Acyltransferase (ACAA). This integrated approach provides novel insights into heat stress problems and identifies potential biomarkers associated with heat stress.
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Affiliation(s)
- Young-Jun Seo
- Department of Animal Science and Technology, Chung-Ang University, Anseong, Republic of Korea
| | - Chiwoong Lim
- Department of Animal Science and Technology, Chung-Ang University, Anseong, Republic of Korea
| | - Byeonghwi Lim
- Department of Animal Science and Technology, Chung-Ang University, Anseong, Republic of Korea
| | - Jun-Mo Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong, Republic of Korea
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4
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Chigede N, Chikwambi Z, Mpofu IDT, Madzimure J. Isolation and characterization of biosurfactant-producing microbes isolated from the gastrointestinal system of broiler birds fed a commercial diet. Anim Biotechnol 2024; 35:2263771. [PMID: 37814822 DOI: 10.1080/10495398.2023.2263771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
Antimicrobial drug resistance (AMR) from improper use of antibiotics in various livestock products is a growing hazard for humans worldwide, with current death rate in excess of 700,000 per annum linked to the problem. Microorganisms are a rich source of structurally distinct bioactive compounds designed to protect the microbes and can offset AMR challenge. A study was conducted at Chinhoyi University of Technology to isolate, identify and characterize biosurfactant secreting microbes from broiler bird's gastrointestinal tract. Analysis of variance was performed in Genstat software. 16S rRNA technique was used to identify the DNA of isolates, annotated by similarity using BLASTn analysis against the NCBI nucleotide database. Phylogenetic analysis was performed on the BLASTn outcome to have an appreciation of the evolutionary genetic relationships. Small intestine-derived samples had a wider hemolytic activity of 5.6 mm, with a 39% emulsification index. At 98.29% sequence similarity, the bacterium producing biosurfactants was identified as an Escherichia coli strain similar to the 7.1994/NIST 0056 strain. The biosurfactant substance is a derivative of decane with beta lactams, tetracyclines and sulfa drugs properties which were responsible for the observed antibacterial activity. We recommend endogenous biosurfactant production optimization experiments and in-vivo trials to evaluate the potential impacts of a biosurfactant based feed additive in broilers.
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Affiliation(s)
- Ngavaite Chigede
- School of Agricultural Sciences and Technology, Department of Animal Production and Technology, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
- Gary Magadzire School of Agriculture and Engineering, Department of Livestock, Wildlife and Fisheries, Great Zimbabwe University, Masvingo, Zimbabwe
| | - Zedias Chikwambi
- School of Agricultural Sciences and Technology, Department of Animal Production and Technology, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | - Irvin D T Mpofu
- School of Agricultural Sciences and Technology, Department of Animal Production and Technology, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | - James Madzimure
- School of Agricultural Sciences and Technology, Department of Animal Production and Technology, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
- College of Health, Agriculture and Natural Sciences, Department of Agricultural Sciences, Africa University, Mutare, Zimbabwe
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Huang Z, Xie L, Feng H, Lan M, Xu T, Chen D, Pu L, Lu Y. DAZL regulate germline, pluripotency, and proliferation related genes in chicken PGCs and cooperate with DDX4. Theriogenology 2024; 222:22-30. [PMID: 38615433 DOI: 10.1016/j.theriogenology.2024.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 03/15/2024] [Accepted: 03/15/2024] [Indexed: 04/16/2024]
Abstract
Primordial germ cells (PGCs) are the precursors of germ cells and play a crucial role in germline transmission. In chickens, PGCs can be cultured in vitro while maintaining their germline stem cell characteristics. The Deleted in Azoospermia-Like (DAZL) gene, which is highly expressed in PGCs, is essential for germ cell development. Here, through gene knockout experiments, we discovered that the loss of DAZL expression in chicken PGCs led to decreased proliferation and survival. By next employed techniques such as RIP-seq (RNA Binding Protein Immunoprecipitation) and Co-IP-MS/MS (Co-immunoprecipitation Mass Spectrometry), we identified genes directly regulated by DAZL or cooperating with DAZL at the transcriptomic and proteomic levels. DAZL was found to control genes related to germline development, pluripotency, and cell proliferation in PGCs. Additionally, we observed a significant overlap between RNAs and proteins that interact with both DAZL and DDX4, indicating their cooperation in the gene regulation network in chicken PGCs. Our research provides valuable insights into the function of the DAZL gene in germline cells.
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Affiliation(s)
- Zhenwen Huang
- From the Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530004, China
| | - Long Xie
- From the Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530004, China
| | - Hu Feng
- From the Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Meiyu Lan
- From the Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530004, China
| | - Tianpeng Xu
- From the Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530004, China
| | - Dongyang Chen
- From the Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530004, China
| | - Liping Pu
- From the Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530004, China
| | - Yangqing Lu
- From the Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530004, China.
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6
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Kaliappan A, Ramakrishnan S, Thomas P, Verma SK, Panwar K, Singh M, Dey S, Mohan Chellappa M. Polymorphism in the leucine-rich repeats of TLR7 in different breeds of chicken and in silico analysis of its effect on TLR7 structure and function. Gene 2024; 912:148373. [PMID: 38490513 DOI: 10.1016/j.gene.2024.148373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 03/02/2024] [Accepted: 03/12/2024] [Indexed: 03/17/2024]
Abstract
Chicken toll-like receptor 7 (chTLR7) is a viral sensing pattern recognition receptor and detects ssRNA. The ligand binding site comprises leucine-rich repeats (LRRs) located in the ectodomain of chTLR7. Hence, any polymorphism in the binding site would modify its functional interaction with the ligand, resulting in varied strength of immune response. This study first aimed to compare the single nucleotide polymorphisms (SNPs) associated with the ligand binding site of TLR7 in three indigenous chicken breeds namely Aseel, Kadaknath, Nicobari along with an exotic breed White Leghorn. Four synonymous SNPs (P123P, I171I, N339N and L421L) and four non-synonymous SNPs (I121V, S135T, F356S and S447G) were identified among various breeds. We employed in silico tools to screen the pathogenic nsSNPs and one nsSNP was identified as having potential impact on chTLR7 protein. Moreover, sequence and structure-based methods were used to determine the effect of nsSNPs on protein stability. It revealed I121V, F356S, and S447G as decreasing the stability while S135T increasing the stability of chTLR7. Additionally, docking analysis confirmed that I121V and F356S reduced the binding affinity of ligands (R-848 and polyU) to chTLR7 protein. The results suggest that the nsSNPs found in this study could alter the ligand binding of chTLR7 and modify the immune response between different breeds further contributing to disease susceptibility or resistance. Further, in vitro and in vivo studies are needed to analyze the effect of these SNPs on susceptibility or resistance against various viral diseases in poultry.
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Affiliation(s)
- Abinaya Kaliappan
- Immunology Section, ICAR - Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243 122, India
| | - Saravanan Ramakrishnan
- Immunology Section, ICAR - Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243 122, India.
| | - Prasad Thomas
- Division of Bacteriology and Mycology, ICAR - Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243 122, India
| | - Surya Kant Verma
- Immunology Section, ICAR - Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243 122, India
| | - Khushboo Panwar
- Immunology Section, ICAR - Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243 122, India
| | - Mithilesh Singh
- Immunology Section, ICAR - Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243 122, India
| | - Sohini Dey
- Recombinant DNA Laboratory, Division of Veterinary Biotechnology, ICAR - Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243 122, India
| | - Madhan Mohan Chellappa
- Recombinant DNA Laboratory, Division of Veterinary Biotechnology, ICAR - Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243 122, India
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7
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Song W, Zhao L, Liu S, Jia Y, Ma L, Liao M, Dai M. Analysis of H5N8 influenza virus infection in chicken with mApple reporter genes in vivo and in vitro. Vet Microbiol 2024; 292:110052. [PMID: 38492531 DOI: 10.1016/j.vetmic.2024.110052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/04/2024] [Accepted: 03/09/2024] [Indexed: 03/18/2024]
Abstract
H5N8 highly pathogenic avian influenza virus (HPAIV) has caused huge losses to the global poultry industry and critically threatens public health. Chickens are the important host for the transmission. However, the distribution of H5N8 avian influenza virus (AIV) in chicken and the infected cell types are limitedly studied. Therefore, in this study, we detected viral replication and infection by generating recombinant H5N8 AIV expressing an easily tracked mApple fluorescent reporter. The results showed that recombinant viruses passaged four times in chicken embryos successfully expressed mApple proteins detected by fluorescence microscopy and WB, which verified that the constructed recombinant viruses were stable. Compared to parental virus, although recombinant virus attenuated for replication in MDCK cells, it can still replicate effectively, and form visible plaques. Importantly, the experiments on infection of chicken PBMCs in vitro showed a strong correlation between mApple positivity rate and NP positivity rate (r = 0.7594, P =0.0176), demonstrating that mApple reporter could be used as an indicator to accurately reflect AIV infection. Then we infected monocytes/macrophages in PBMCs in vitro and detected the mApple positive percentage was 55.1%-80.4%, which confirmed the chicken primary monocytic/macrophages are important target cells for avian influenza virus infection. In chicken, compared with parental virus, the recombinant virus-infected chickens had lower viral titers in oropharyngeal cloacal and organs, but it can cause significant pathogenicity in chicken and the mortality rate was approximately 66%. In addition, the results of bioluminescent imaging showed that the fluorescence in the lungs was strongest at 5 days post-infection (DPI). Finally, we discovered the mApple positive expression in chicken lung immune cells (CD45+ cells), especially some T cells (CD4 and CD8 T cells) also carrying mApple, which indicates that the H5N8 AIV showed a tropism for immune cells including chicken T cells causing potentially aggressive against cellular immunity. We have provided a simple visualization for further exploration of H5N8 AIV infected chicken immune cells, which contributes to further understanding pathogenic mechanism of H5N8 AIV infection in chicken.
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Affiliation(s)
- Wei Song
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; UK-China Centre of Exellence for Research on Avain Diseases, Guangzhou 510642, China
| | - Li Zhao
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; UK-China Centre of Exellence for Research on Avain Diseases, Guangzhou 510642, China
| | - Sairu Liu
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; UK-China Centre of Exellence for Research on Avain Diseases, Guangzhou 510642, China
| | - Yusheng Jia
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; UK-China Centre of Exellence for Research on Avain Diseases, Guangzhou 510642, China
| | - Lulu Ma
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; UK-China Centre of Exellence for Research on Avain Diseases, Guangzhou 510642, China
| | - Ming Liao
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; UK-China Centre of Exellence for Research on Avain Diseases, Guangzhou 510642, China.
| | - Manman Dai
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; UK-China Centre of Exellence for Research on Avain Diseases, Guangzhou 510642, China.
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8
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Li W, Lin Y, Wang X, Yang H, Ding Y, Chen Z, He Z, Zhang J, Zhao L, Jiao P. Chicken UFL1 Restricts Avian Influenza Virus Replication by Disrupting the Viral Polymerase Complex and Facilitating Type I IFN Production. J Immunol 2024; 212:1479-1492. [PMID: 38477617 DOI: 10.4049/jimmunol.2300613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 02/12/2024] [Indexed: 03/14/2024]
Abstract
During avian influenza virus (AIV) infection, host defensive proteins promote antiviral innate immunity or antagonize viral components to limit viral replication. UFM1-specific ligase 1 (UFL1) is involved in regulating innate immunity and DNA virus replication in mammals, but the molecular mechanism by which chicken (ch)UFL1 regulates AIV replication is unclear. In this study, we first identified chUFL1 as a negative regulator of AIV replication by enhancing innate immunity and disrupting the assembly of the viral polymerase complex. Mechanistically, chUFL1 interacted with chicken stimulator of IFN genes (chSTING) and contributed to chSTING dimerization and the formation of the STING-TBK1-IRF7 complex. We further demonstrated that chUFL1 promoted K63-linked polyubiquitination of chSTING at K308 to facilitate chSTING-mediated type I IFN production independent of UFMylation. Additionally, chUFL1 expression was upregulated in response to AIV infection. Importantly, chUFL1 also interacted with the AIV PA protein to inhibit viral polymerase activity. Furthermore, chUFL1 impeded the nuclear import of the AIV PA protein and the assembly of the viral polymerase complex to suppress AIV replication. Collectively, these findings demonstrate that chUFL1 restricts AIV replication by disrupting the viral polymerase complex and facilitating type I IFN production, which provides new insights into the regulation of AIV replication in chickens.
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Affiliation(s)
- Weiqiang Li
- College of Veterinary Medicine, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China; and
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, Guangzhou, China
| | - Yu Lin
- College of Veterinary Medicine, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China; and
| | - Xiyi Wang
- College of Veterinary Medicine, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China; and
| | - Huixing Yang
- College of Veterinary Medicine, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China; and
| | - Yangbao Ding
- College of Veterinary Medicine, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China; and
| | - Zuxian Chen
- College of Veterinary Medicine, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China; and
| | - Zhuoliang He
- College of Veterinary Medicine, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China; and
| | - Junsheng Zhang
- College of Veterinary Medicine, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China; and
| | - Luxiang Zhao
- College of Veterinary Medicine, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China; and
| | - Peirong Jiao
- College of Veterinary Medicine, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China; and
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, Guangzhou, China
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9
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Videla Rodriguez EA, Mitchell JBO, Smith VA. Robust identification of interactions between heat-stress responsive genes in the chicken brain using Bayesian networks and augmented expression data. Sci Rep 2024; 14:9019. [PMID: 38641606 PMCID: PMC11031576 DOI: 10.1038/s41598-024-58679-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 04/02/2024] [Indexed: 04/21/2024] Open
Abstract
Bayesian networks represent a useful tool to explore interactions within biological systems. The aims of this study were to identify a reduced number of genes associated with a stress condition in chickens (Gallus gallus) and to unravel their interactions by implementing a Bayesian network approach. Initially, one publicly available dataset (3 control vs. 3 heat-stressed chickens) was used to identify the stress signal, represented by 25 differentially expressed genes (DEGs). The dataset was augmented by looking for the 25 DEGs in other four publicly available databases. Bayesian network algorithms were used to discover the informative relationships between the DEGs. Only ten out of the 25 DEGs displayed interactions. Four of them were Heat Shock Proteins that could be playing a key role, especially under stress conditions, where maintaining the correct functioning of the cell machinery might be crucial. One of the DEGs is an open reading frame whose function is yet unknown, highlighting the power of Bayesian networks in knowledge discovery. Identifying an initial stress signal, augmenting it by combining other databases, and finally learning the structure of Bayesian networks allowed us to find genes closely related to stress, with the possibility of further exploring the system in future studies.
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Affiliation(s)
| | - John B O Mitchell
- EaStCHEM School of Chemistry and BSRC, University of St Andrews, St Andrews, Fife, KY16 9ST, UK
| | - V Anne Smith
- School of Biology, University of St Andrews, St Andrews, Fife, KY16 9TH, UK.
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10
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Vanderhout RJ, Abdalla EA, Leishman EM, Barbut S, Wood BJ, Baes CF. Genetic architecture of white striping in turkeys (Meleagris gallopavo). Sci Rep 2024; 14:9007. [PMID: 38637585 PMCID: PMC11026500 DOI: 10.1038/s41598-024-59309-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 04/09/2024] [Indexed: 04/20/2024] Open
Abstract
White striping (WS) is a myopathy of growing concern to the turkey industry. It is rising in prevalence and has negative consequences for consumer acceptance and the functional properties of turkey meat. The objective of this study was to conduct a genome-wide association study (GWAS) and functional analysis on WS severity. Phenotypic data consisted of white striping scored on turkey breast fillets (N = 8422) by trained observers on a 0-3 scale (none to severe). Of the phenotyped birds, 4667 genotypic records were available using a proprietary 65 K single nucleotide polymorphism (SNP) chip. The SNP effects were estimated using a linear mixed model with a 30-SNP sliding window approach used to express the percentage genetic variance explained. Positional candidate genes were those located within 50 kb of the top 1% of SNP windows explaining the most genetic variance. Of the 95 positional candidate genes, seven were further classified as functional candidate genes because of their association with both a significant gene ontology and molecular function term. The results of the GWAS emphasize the polygenic nature of the trait with no specific genomic region contributing a large portion to the overall genetic variance. Significant pathways relating to growth, muscle development, collagen formation, circulatory system development, cell response to stimulus, and cytokine production were identified. These results help to support published biological associations between WS and hypoxia and oxidative stress and provide information that may be useful for future-omics studies in understanding the biological associations with WS development in turkeys.
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Affiliation(s)
- Ryley J Vanderhout
- Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
- Hybrid Turkeys, 650 Riverbend Drive Suite C, Kitchener, ON, N2K 3S2, Canada
| | - Emhimad A Abdalla
- Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
- Vereinigte Informationssysteme Tierhaltung W.V. (Vit), Heinrich-Schröder-Weg 1, 27283, Verden, Germany
| | - Emily M Leishman
- Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Shai Barbut
- Department of Food Science, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Benjamin J Wood
- Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
- Hybrid Turkeys, 650 Riverbend Drive Suite C, Kitchener, ON, N2K 3S2, Canada
- School of Veterinary Science, University of Queensland, Gatton, QLD, 4343, Australia
| | - Christine F Baes
- Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada.
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.
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11
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Zeinali S, Sutton K, Zefreh MG, Mabbott N, Vervelde L. Discrimination of distinct chicken M cell subsets based on CSF1R expression. Sci Rep 2024; 14:8795. [PMID: 38627516 PMCID: PMC11021470 DOI: 10.1038/s41598-024-59368-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 04/09/2024] [Indexed: 04/19/2024] Open
Abstract
In mammals, a subset of follicle-associated epithelial (FAE) cells, known as M cells, conduct the transcytosis of antigens across the epithelium into the underlying lymphoid tissues. We previously revealed that M cells in the FAE of the chicken lung, bursa of Fabricius (bursa), and caecum based on the expression of CSF1R. Here, we applied RNA-seq analysis on highly enriched CSF1R-expressing bursal M cells to investigate their transcriptome and identify novel chicken M cell-associated genes. Our data show that, like mammalian M cells, those in the FAE of the chicken bursa also express SOX8, MARCKSL1, TNFAIP2 and PRNP. Immunohistochemical analysis also confirmed the expression of SOX8 in CSF1R-expressing cells in the lung, bursa, and caecum. However, we found that many other mammalian M cell-associated genes such as SPIB and GP2 were not expressed by chicken M cells or represented in the chicken genome. Instead, we show bursal M cells express high levels of related genes such as SPI1. Whereas our data show that bursal M cells expressed CSF1R-highly, the M cells in the small intestine lacked CSF1R and both expressed SOX8. This study offers insights into the transcriptome of chicken M cells, revealing the expression of CSF1R in M cells is tissue-specific.
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Affiliation(s)
- Safieh Zeinali
- Division of Immunology, The Roslin Institute & Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Kate Sutton
- Division of Immunology, The Roslin Institute & Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9RG, UK.
| | - Masoud Ghaderi Zefreh
- Division of Genetics and Genomics, The Roslin Institute & Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Neil Mabbott
- Division of Immunology, The Roslin Institute & Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Lonneke Vervelde
- Division of Immunology, The Roslin Institute & Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9RG, UK.
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12
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Cui Y, Ru M, Wang Y, Weng L, Haji RA, Liang H, Zeng Q, Wei Q, Xie X, Yin C, Huang J. Epigenetic regulation of H3K27me3 in laying hens with fatty liver hemorrhagic syndrome induced by high-energy and low-protein diets. BMC Genomics 2024; 25:374. [PMID: 38627644 PMCID: PMC11022457 DOI: 10.1186/s12864-024-10270-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 03/29/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Fatty liver hemorrhagic syndrome (FLHS) in the modern poultry industry is primarily caused by nutrition. Despite encouraging progress on FLHS, the mechanism through which nutrition influences susceptibility to FLHS is still lacking in terms of epigenetics. RESULTS In this study, we analyzed the genome-wide patterns of trimethylated lysine residue 27 of histone H3 (H3K27me3) enrichment by chromatin immunoprecipitation-sequencing (ChIP-seq), and examined its association with transcriptomes in healthy and FLHS hens. The study results indicated that H3K27me3 levels were increased in the FLHS hens on a genome-wide scale. Additionally, H3K27me3 was found to occupy the entire gene and the distant intergenic region, which may function as silencer-like regulatory elements. The analysis of transcription factor (TF) motifs in hypermethylated peaks has demonstrated that 23 TFs are involved in the regulation of liver metabolism and development. Transcriptomic analysis indicated that differentially expressed genes (DEGs) were enriched in fatty acid metabolism, amino acid, and carbohydrate metabolism. The hub gene identified from PPI network is fatty acid synthase (FASN). Combined ChIP-seq and transcriptome analysis revealed that the increased H3K27me3 and down-regulated genes have significant enrichment in the ECM-receptor interaction, tight junction, cell adhesion molecules, adherens junction, and TGF-beta signaling pathways. CONCLUSIONS Overall, the trimethylation modification of H3K27 has been shown to have significant regulatory function in FLHS, mediating the expression of crucial genes associated with the ECM-receptor interaction pathway. This highlights the epigenetic mechanisms of H3K27me3 and provides insights into exploring core regulatory targets and nutritional regulation strategies in FLHS.
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Affiliation(s)
- Yong Cui
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Meng Ru
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Yujie Wang
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Linjian Weng
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Ramlat Ali Haji
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Haiping Liang
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Qingjie Zeng
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Qing Wei
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xianhua Xie
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Chao Yin
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jianzhen Huang
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
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13
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Dementieva NV, Shcherbakov YS, Stanishevskaya OI, Vakhrameev AB, Larkina TA, Dysin AP, Nikolaeva OA, Ryabova AE, Azovtseva AI, Mitrofanova OV, Peglivanyan GK, Reinbach NR, Griffin DK, Romanov MN. Large-scale genome-wide SNP analysis reveals the rugged (and ragged) landscape of global ancestry, phylogeny, and demographic history in chicken breeds. J Zhejiang Univ Sci B 2024; 25:324-340. [PMID: 38584094 PMCID: PMC11009443 DOI: 10.1631/jzus.b2300443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/10/2023] [Indexed: 04/09/2024]
Abstract
The worldwide chicken gene pool encompasses a remarkable, but shrinking, number of divergently selected breeds of diverse origin. This study was a large-scale genome-wide analysis of the landscape of the complex molecular architecture, genetic variability, and detailed structure among 49 populations. These populations represent a significant sample of the world's chicken breeds from Europe (Russia, Czech Republic, France, Spain, UK, etc.), Asia (China), North America (USA), and Oceania (Australia). Based on the results of breed genotyping using the Illumina 60K single nucleotide polymorphism (SNP) chip, a bioinformatic analysis was carried out. This included the calculation of heterozygosity/homozygosity statistics, inbreeding coefficients, and effective population size. It also included assessment of linkage disequilibrium and construction of phylogenetic trees. Using multidimensional scaling, principal component analysis, and ADMIXTURE-assisted global ancestry analysis, we explored the genetic structure of populations and subpopulations in each breed. An overall 49-population phylogeny analysis was also performed, and a refined evolutionary model of chicken breed formation was proposed, which included egg, meat, dual-purpose types, and ambiguous breeds. Such a large-scale survey of genetic resources in poultry farming using modern genomic methods is of great interest both from the viewpoint of a general understanding of the genetics of the domestic chicken and for the further development of genomic technologies and approaches in poultry breeding. In general, whole genome SNP genotyping of promising chicken breeds from the worldwide gene pool will promote the further development of modern genomic science as applied to poultry.
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Affiliation(s)
- Natalia V Dementieva
- Russian Research Institute of Farm Animal Genetics and Breeding ‒ Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, St. Petersburg, 196601, Russia.
| | - Yuri S Shcherbakov
- Russian Research Institute of Farm Animal Genetics and Breeding ‒ Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, St. Petersburg, 196601, Russia
| | - Olga I Stanishevskaya
- Russian Research Institute of Farm Animal Genetics and Breeding ‒ Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, St. Petersburg, 196601, Russia
| | - Anatoly B Vakhrameev
- Russian Research Institute of Farm Animal Genetics and Breeding ‒ Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, St. Petersburg, 196601, Russia
| | - Tatiana A Larkina
- Russian Research Institute of Farm Animal Genetics and Breeding ‒ Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, St. Petersburg, 196601, Russia
| | - Artem P Dysin
- Russian Research Institute of Farm Animal Genetics and Breeding ‒ Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, St. Petersburg, 196601, Russia
| | - Olga A Nikolaeva
- Russian Research Institute of Farm Animal Genetics and Breeding ‒ Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, St. Petersburg, 196601, Russia
| | - Anna E Ryabova
- Russian Research Institute of Farm Animal Genetics and Breeding ‒ Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, St. Petersburg, 196601, Russia
| | - Anastasiia I Azovtseva
- Russian Research Institute of Farm Animal Genetics and Breeding ‒ Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, St. Petersburg, 196601, Russia
| | - Olga V Mitrofanova
- Russian Research Institute of Farm Animal Genetics and Breeding ‒ Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, St. Petersburg, 196601, Russia
| | - Grigoriy K Peglivanyan
- Russian Research Institute of Farm Animal Genetics and Breeding ‒ Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, St. Petersburg, 196601, Russia
| | - Natalia R Reinbach
- Russian Research Institute of Farm Animal Genetics and Breeding ‒ Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, St. Petersburg, 196601, Russia
| | - Darren K Griffin
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK. ,
| | - Michael N Romanov
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK. ,
- L K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Oblast, 142132, Russia. ,
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14
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Wei Y, Shen X, Zhao X, He H, Zhang Y, Zhu Q, Yin H. Circular RNA circRPS19 promotes chicken granulosa cell proliferation and steroid hormone synthesis by interrupting the miR-218-5p/INHBB axis. Theriogenology 2024; 219:103-115. [PMID: 38422566 DOI: 10.1016/j.theriogenology.2024.02.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 02/22/2024] [Accepted: 02/22/2024] [Indexed: 03/02/2024]
Abstract
Ovarian follicle development is an important physiological activity for females and makes great significance in maintaining female health and reproduction performance. The development of ovarian follicle is mainly affected by the granulosa cells (GCs), whose growth is regulated by a variety of factors. Here, we identified a novel circular RNA (circRNA) derived from the Ribosomal protein S19 (RPS19) gene, named circRPS19, which is differentially expressed during chicken ovarian follicle development. Further explorations identified that circRPS19 promotes GCs proliferation and steroid hormone synthesis. Furthermore, circRPS19 was found to target and regulate miR-218-5p through a competitive manner with endogenous RNA (ceRNA). Functionals investigation revealed that miR-218-5p attenuates GCs proliferation and steroidogenesis, which is opposite to that of circRPS19. In addition, we also confirmed that circRPS19 upregulates the expression of Inhibin beta B subunit (INHBB) by binding with miR-218-5p to facilitate GCs proliferation and steroidogenesis. Overall, this study revealed that circRPS19 regulates GCs development by releasing the repression of miR-218-5p on INHBB, which suggests a novel mechanism in respect to circRNA and miRNA regulation in ovarian follicle development.
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Affiliation(s)
- Yuanhang Wei
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiaoxu Shen
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiyu Zhao
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Haorong He
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yao Zhang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Qing Zhu
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| | - Huadong Yin
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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15
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Kövesi B, Worlanyo AP, Kulcsár S, Ancsin Z, Erdélyi M, Zándoki E, Mézes M, Balogh K. Curcumin mitigates ochratoxin A-induced oxidative stress and alters gene expression in broiler chicken liver and kidney. Acta Vet Hung 2024; 72:41-50. [PMID: 38536404 DOI: 10.1556/004.2024.01016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/28/2024] [Indexed: 04/13/2024]
Abstract
The study aimed to evaluate the effect of curcumin (CURC) supplementation on broiler chickens exposed to ochratoxin A (OTA), by examining biochemical parameters and the expression of glutathione redox system genes and their regulation. OTA reduced glutathione content in the liver while increasing glutathione peroxidase activity. CURC showed no significant effects. Kidney parameters remained mostly unaffected. Gene expression analysis revealed OTA-induced upregulation of KEAP1, NRF2, AHR, GPx4 and GSR genes in the liver. CURC supplementation led to the upregulation of GPx4 and AHR genes with OTA+CURC treatment, resulting in the downregulation of GPx4, KEAP1, NRF2 and AHR genes compared to OTA treatment alone. In the kidney, GPx4 was downregulated, and NRF2 and AHR were upregulated as an effect of OTA, while CURC upregulated the NRF2 gene only. OTA+CURC treatment led to the downregulation of GPx4, GSS and AHR genes compared to the control and downregulation of NRF2 and AHR genes compared to OTA. The results suggested that CURC is partly effective against OTA-induced oxidative stress and that the effect of OTA and CURC on the antioxidant response is regulated through the KEAP1-NRF2-ARE and AHR pathways.
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Affiliation(s)
- Benjámin Kövesi
- 1Department of Feed Safety, Institute of Physiology and Nutrition, Hungarian University of Agriculture and Life Sciences, Szent István Campus, H-2100 Gödöllő, Hungary
| | - Adanu Paul Worlanyo
- 1Department of Feed Safety, Institute of Physiology and Nutrition, Hungarian University of Agriculture and Life Sciences, Szent István Campus, H-2100 Gödöllő, Hungary
| | - Szabina Kulcsár
- 2HUN-REN-MATE Mycotoxins in the Food Chain Research Group, Hungarian University of Agriculture and Life Sciences, H-7400 Kaposvár, Hungary
| | - Zsolt Ancsin
- 1Department of Feed Safety, Institute of Physiology and Nutrition, Hungarian University of Agriculture and Life Sciences, Szent István Campus, H-2100 Gödöllő, Hungary
| | - Márta Erdélyi
- 1Department of Feed Safety, Institute of Physiology and Nutrition, Hungarian University of Agriculture and Life Sciences, Szent István Campus, H-2100 Gödöllő, Hungary
| | - Erika Zándoki
- 2HUN-REN-MATE Mycotoxins in the Food Chain Research Group, Hungarian University of Agriculture and Life Sciences, H-7400 Kaposvár, Hungary
| | - Miklós Mézes
- 1Department of Feed Safety, Institute of Physiology and Nutrition, Hungarian University of Agriculture and Life Sciences, Szent István Campus, H-2100 Gödöllő, Hungary
- 2HUN-REN-MATE Mycotoxins in the Food Chain Research Group, Hungarian University of Agriculture and Life Sciences, H-7400 Kaposvár, Hungary
| | - Krisztián Balogh
- 1Department of Feed Safety, Institute of Physiology and Nutrition, Hungarian University of Agriculture and Life Sciences, Szent István Campus, H-2100 Gödöllő, Hungary
- 2HUN-REN-MATE Mycotoxins in the Food Chain Research Group, Hungarian University of Agriculture and Life Sciences, H-7400 Kaposvár, Hungary
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16
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Chen G, Yu D, Yang Y, Li X, Wang X, Sun D, Lu Y, Ke R, Zhang G, Cui J, Feng S. Adaptive expansion of ERVK solo-LTRs is associated with Passeriformes speciation events. Nat Commun 2024; 15:3151. [PMID: 38605055 PMCID: PMC11009239 DOI: 10.1038/s41467-024-47501-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 04/02/2024] [Indexed: 04/13/2024] Open
Abstract
Endogenous retroviruses (ERVs) are ancient retroviral remnants integrated in host genomes, and commonly deleted through unequal homologous recombination, leaving solitary long terminal repeats (solo-LTRs). This study, analysing the genomes of 362 bird species and their reptilian and mammalian outgroups, reveals an unusually higher level of solo-LTRs formation in birds, indicating evolutionary forces might have purged ERVs during evolution. Strikingly in the order Passeriformes, and especially the parvorder Passerida, endogenous retrovirus K (ERVK) solo-LTRs showed bursts of formation and recurrent accumulations coinciding with speciation events over past 22 million years. Moreover, our results indicate that the ongoing expansion of ERVK solo-LTRs in these bird species, marked by high transcriptional activity of ERVK retroviral genes in reproductive organs, caused variation of solo-LTRs between individual zebra finches. We experimentally demonstrated that cis-regulatory activity of recently evolved ERVK solo-LTRs may significantly increase the expression level of ITGA2 in the brain of zebra finches compared to chickens. These findings suggest that ERVK solo-LTRs expansion may introduce novel genomic sequences acting as cis-regulatory elements and contribute to adaptive evolution. Overall, our results underscore that the residual sequences of ancient retroviruses could influence the adaptive diversification of species by regulating host gene expression.
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Affiliation(s)
- Guangji Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- BGI Research, Wuhan, China
| | - Dan Yu
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Center for Genomic Research, International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Yu Yang
- School of Medicine, Huaqiao University, Xiamen, Fujian, 361021, China
| | - Xiang Li
- CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Xiaojing Wang
- CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Danyang Sun
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Center for Genomic Research, International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Yanlin Lu
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Center for Genomic Research, International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Rongqin Ke
- School of Medicine, Huaqiao University, Xiamen, Fujian, 361021, China
| | - Guojie Zhang
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, China
| | - Jie Cui
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Huashan Hospital, Institute of Infection and Health Research, Fudan University, Shanghai, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China.
- Shanghai Sci-Tech Inno Center for Infection & Immunity, Shanghai, 200052, China.
- Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China.
| | - Shaohong Feng
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China.
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, China.
- Department of General Surgery of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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Tan Y, Huang Y, Xu C, Huang X, Li S, Yin Z. Long noncoding RNAs and mRNAs profiling in ovary during laying and broodiness in Taihe Black-Bone Silky Fowls (Gallus gallus Domesticus Brisson). BMC Genomics 2024; 25:357. [PMID: 38600449 PMCID: PMC11005167 DOI: 10.1186/s12864-024-10281-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 04/02/2024] [Indexed: 04/12/2024] Open
Abstract
BACKGROUND Broodiness significantly impacts poultry egg production, particularly notable in specific breeds such as the black-boned Silky, characterized by pronounced broodiness. An understanding of the alterations in ovarian signaling is essential for elucidating the mechanisms that influence broodiness. However, comparative research on the characteristics of long non-coding RNAs (lncRNAs) in the ovaries of broody chickens (BC) and high egg-laying chickens (GC) remains scant. In this investigation, we employed RNA sequencing to assess the ovarian transcriptomes, which include both lncRNAs and mRNAs, in eight Taihe Black-Bone Silky Fowls (TBsf), categorized into broody and high egg-laying groups. This study aims to provide a clearer understanding of the genetic underpinnings associated with broodiness and egg production. RESULTS We have identified a total of 16,444 mRNAs and 18,756 lncRNAs, of which 349 mRNAs and 651 lncRNAs exhibited significantly different expression (DE) between the BC and GC groups. Furthermore, we have identified the cis-regulated and trans-regulated target genes of differentially abundant lncRNA transcripts and have constructed an lncRNA-mRNA trans-regulated interaction network linked to ovarian follicle development. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation analyses have revealed that DE mRNAs and the target genes of DE lncRNAs are associated with pathways including neuroactive ligand-receptor interaction, CCR6 chemokine receptor binding, G-protein coupled receptor binding, cytokine-cytokine receptor interaction, and ECM-receptor interaction. CONCLUSION Our research presents a comprehensive compilation of lncRNAs and mRNAs linked to ovarian development. Additionally, it establishes a predictive interaction network involving differentially abundant lncRNAs and differentially expressed genes (DEGs) within TBsf. This significantly contributes to our understanding of the intricate interactions between lncRNAs and genes governing brooding behavior.
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Affiliation(s)
- Yuting Tan
- Zijingang Campus, Animal Science College, Zhejiang University, Hangzhou, 310058, China
| | - Yunyan Huang
- Zijingang Campus, Animal Science College, Zhejiang University, Hangzhou, 310058, China
| | - Chunhui Xu
- Zijingang Campus, Animal Science College, Zhejiang University, Hangzhou, 310058, China
| | - Xuan Huang
- Zijingang Campus, Animal Science College, Zhejiang University, Hangzhou, 310058, China
| | - Shibao Li
- Zijingang Campus, Animal Science College, Zhejiang University, Hangzhou, 310058, China
| | - Zhaozheng Yin
- Zijingang Campus, Animal Science College, Zhejiang University, Hangzhou, 310058, China.
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18
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Wang X, Zhang T, Li W, Wang H, Yan L, Zhang X, Zhao L, Wang N, Zhang B. Arginine alleviates Clostridium perfringens α toxin-induced intestinal injury in vivo and in vitro via the SLC38A9/mTORC1 pathway. Front Immunol 2024; 15:1357072. [PMID: 38638435 PMCID: PMC11024335 DOI: 10.3389/fimmu.2024.1357072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 03/26/2024] [Indexed: 04/20/2024] Open
Abstract
Introduction Clostridium perfringens α toxin is a main virulence factor responsible for gut damage in animals. Arginine is a functional amino acid exhibiting significant immunoregulatory activities. However, the effects and immunoregulatory mechanisms of arginine supplementation on α toxin-induced intestinal injury remain unclear. Methods In vivo, 256 male Arbor Acres chickens were randomly assigned to a 2×2 factorial arrangement, involving diet treatments (with or without 0.3% arginine supplementation) and immunological stress (with or without α toxin challenge). In vitro, IEC-6 cells were treated with or without arginine in the presence or absence of α toxin. Moreover, IEC-6 cells were transfected with siRNA targeting mTOR and SLC38A9 to explore the underlying mechanisms. Results and discussion The results showed that in vivo, arginine supplementation significantly alleviated the α toxin-induced growth performance impairment, decreases in serum immunoglobulin (Ig)A and IgG levels, and intestinal morphology damage. Arginine supplementation also significantly reduced the α toxin-induced increase in jejunal proinflammatory cytokines interleukin (IL)-1β, IL-6 and IL-17 mRNA expression. Clostridium perfringens α toxin significantly decreased jejunal mechanistic target of rapamycin (mTOR) and solute carrier family 38 member 9 (SLC38A9) mRNA expression, while arginine supplementation significantly increased mTOR and SLC38A9 mRNA expression. In vitro, arginine pretreatment mitigated the α toxin-induced decrease in cell viability and the increase in cytotoxicity and apoptosis. Arginine pretreatment also alleviated the α toxin-induced upregulation of mRNA expression of inflammation-related cytokines IL-6, C-X-C motif chemokine ligand (CXCL)10, CXCL11 and transforming growth factor-β (TGF-β), as well as apoptosis-related genes B-cell lymphoma-2 associated X protein (Bax), B-cell lymphoma-2 (Bcl-2), B-cell lymphoma-extra large (Bcl-XL) and cysteinyl aspartate specific proteinase 3 (Caspase-3) and the ratio of Bax to Bcl-2. Arginine pretreatment significantly increased the α toxin-induced decrease in mTOR, SLC38A9, eukaryotic translation initiation factor 4E (eIF4E)-binding protein 1 (4EBP1) and ribosomal protein S6 kinase (S6K) mRNA expression. Knockdown SLC38A9 and mTOR largely abrogated the positive effects of arginine pretreatment on α toxin-induced intracellular changes. Furthermore, SLC38A9 silencing abolished the increased mTOR mRNA expression caused by arginine pretreatment. In conclusion, arginine administration attenuated α toxin-induced intestinal injury in vivo and in vitro, which could be associated with the downregulation of inflammation via regulating SLC38A9/mTORC1 pathway.
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Affiliation(s)
- Xiaohui Wang
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Tong Zhang
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Wenli Li
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Heliang Wang
- Qingdao Sino-science Gene Technology Co., Ltd, Qingdao, China
| | - Lei Yan
- Shandong New Hope Liuhe Group, Qingdao, China
| | - Xiaowen Zhang
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Lianwen Zhao
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Nianxue Wang
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Beibei Zhang
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
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19
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Peters C, Richter KK, Wilkin S, Stark S, Mir-Makhamad B, Fernandes R, Maksudov F, Mirzaakhmedov S, Rahmonov H, Schirmer S, Ashastina K, Begmatov A, Frachetti M, Kurbanov S, Shenkar M, Hermes T, Kidd F, Omelchenko A, Huber B, Boivin N, Wang S, Lurje P, von Baeyer M, Dal Martello R, Spengler RN. Archaeological and molecular evidence for ancient chickens in Central Asia. Nat Commun 2024; 15:2697. [PMID: 38565545 PMCID: PMC10987595 DOI: 10.1038/s41467-024-46093-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 02/14/2024] [Indexed: 04/04/2024] Open
Abstract
The origins and dispersal of the chicken across the ancient world remains one of the most enigmatic questions regarding Eurasian domesticated animals. The lack of agreement concerning timing and centers of origin is due to issues with morphological identifications, a lack of direct dating, and poor preservation of thin, brittle bird bones. Here we show that chickens were widely raised across southern Central Asia from the fourth century BC through medieval periods, likely dispersing along the ancient Silk Road. We present archaeological and molecular evidence for the raising of chickens for egg production, based on material from 12 different archaeological sites spanning a millennium and a half. These eggshells were recovered in high abundance at all of these sites, suggesting that chickens may have been an important part of the overall diet and that chickens may have lost seasonal egg-laying.
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Affiliation(s)
- Carli Peters
- Department of Archaeology, Max Planck Institute of Geoanthropology, 07745, Jena, Germany
| | - Kristine K Richter
- Department of Anthropology, Harvard University, Cambridge, MA, 02138, USA
| | - Shevan Wilkin
- Department of Archaeology, Max Planck Institute of Geoanthropology, 07745, Jena, Germany
- Institute of Evolutionary Medicine, Medical Faculty, University of Zurich, 8057, Zurich, Switzerland
| | - Sören Stark
- Institute for the Study of the Ancient World, New York University, New York City, NY, 10028, USA
| | - Basira Mir-Makhamad
- Department of Archaeology, Max Planck Institute of Geoanthropology, 07745, Jena, Germany
- Domestication and Anthropogenic Evolution Research Group, Max Planck Institute of Geoanthropology, 07745, Jena, Germany
| | - Ricardo Fernandes
- Department of Archaeology, Max Planck Institute of Geoanthropology, 07745, Jena, Germany
- Faculty of Arts, Masaryk University, Nováka 1, 602 00, Brno-střed, Czech Republic
- Department of Bioarchaeology, Faculty of Archaeology, University of Warsaw, ul. Krakowskie Przedmieście 26/28, Warszawa, 00-927, Poland
- Climate Change and History Research Initiative, Princeton University, Princeton, USA
| | - Farhod Maksudov
- National Center of Archaeology, Uzbekistan Academy of Sciences, Tashkent, 100000, Uzbekistan
| | - Sirojidin Mirzaakhmedov
- Samarkand Institute of Archaeology, Agency for Cultural Heritage, 1000060, Samarkand, Uzbekistan
| | - Husniddin Rahmonov
- Samarkand Institute of Archaeology, Agency for Cultural Heritage, 1000060, Samarkand, Uzbekistan
| | - Stefanie Schirmer
- Department of Archaeology, Max Planck Institute of Geoanthropology, 07745, Jena, Germany
- Domestication and Anthropogenic Evolution Research Group, Max Planck Institute of Geoanthropology, 07745, Jena, Germany
| | - Kseniia Ashastina
- Department of Archaeology, Max Planck Institute of Geoanthropology, 07745, Jena, Germany
- Domestication and Anthropogenic Evolution Research Group, Max Planck Institute of Geoanthropology, 07745, Jena, Germany
| | - Alisher Begmatov
- Berlin-Brandenburg Academy of Sciences and Humanities, 10117, Berlin, Germany
- Department of Linguistics, University of Vienna, Wien, 1090, Austria
- Department of Archaeology, Samarkand State University, Samarkand City, 140104, Uzbekistan
| | - Michael Frachetti
- Department of Anthropology, Washington University in St Louis, St Louis, MO, 63130, USA
- School of Cultural Heritage, Northwest University, Xi'an, 710069, China
| | - Sharof Kurbanov
- Institute of History, Archaeology and Ethnography named after Ahmad Donish of the Academy of Sciences of Tajikistan, Dushanbe, Tajikistan
| | - Michael Shenkar
- Department of Islamic and Middle Eastern Studies, The Hebrew University of Jerusalem, Mt Scopus, 91905, Jerusalem, Israel
- New Uzbekistan University, 54 Mustaqillik Ave, Tashkent, 100007, Uzbekistan
| | - Taylor Hermes
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
- Department of Anthropology, University of Arkansas, AR, 72701, Fayetteville, USA
| | - Fiona Kidd
- New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | | | - Barbara Huber
- Department of Archaeology, Max Planck Institute of Geoanthropology, 07745, Jena, Germany
- Centre de Recherche et d'Enseignement des Géosciences de l'Environnement, Aix-Marseille Université, CNRS, IRD, INRAE, 13545, Aix-en-Provence, France
- Institute of Archaeological Science, University of Tübingen, 72070, Tübingen, Germany
| | - Nicole Boivin
- Department of Archaeology, Max Planck Institute of Geoanthropology, 07745, Jena, Germany
- Griffith Sciences, Griffith University, Nathan, QLD, 4111, Australia
- School of Social Science, The University of Queensland, Brisbane, QLD, 4071, Australia
| | - Shujing Wang
- School of Archaeology and Museology, Peking University, Beijing, 100871, China
| | - Pavel Lurje
- State Hermitage Museum, St Petersburg, 190000, Russia
| | - Madelynn von Baeyer
- Department of Archaeology, Max Planck Institute of Geoanthropology, 07745, Jena, Germany
- Domestication and Anthropogenic Evolution Research Group, Max Planck Institute of Geoanthropology, 07745, Jena, Germany
| | - Rita Dal Martello
- Department of Archaeology, Max Planck Institute of Geoanthropology, 07745, Jena, Germany
- Domestication and Anthropogenic Evolution Research Group, Max Planck Institute of Geoanthropology, 07745, Jena, Germany
| | - Robert N Spengler
- Department of Archaeology, Max Planck Institute of Geoanthropology, 07745, Jena, Germany.
- Domestication and Anthropogenic Evolution Research Group, Max Planck Institute of Geoanthropology, 07745, Jena, Germany.
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20
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Zhu H, Bendall AJ. Measuring transcription factor function with cell type-specific somatic transgenesis in chicken embryos. Dev Biol 2024; 508:1-7. [PMID: 38218394 DOI: 10.1016/j.ydbio.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 01/03/2024] [Accepted: 01/10/2024] [Indexed: 01/15/2024]
Abstract
Retroviral-mediated misexpression in chicken embryos has been a powerful research tool for developmental biologists in the last two decades. In the RCASBP retroviral vectors that are widely used for in vivo somatic transgenesis, a coding sequence of interest is under the transcriptional control of a strong viral promoter in the long terminal repeat. While this has proven to be effective for studying secreted signalling proteins, interpretation of the mechanisms of action of nuclear factors is more difficult using this system since it is not clear whether phenotypic effects are cell-autonomous or not, and therefore whether they represent a function of the endogenous protein. Here, we report the consequences of retroviral expression using the RCANBP backbone, in which the transcription factor Dlx5 is expressed under the control of chondrocyte-specific regulatory sequences from the Col2a1 gene. To our knowledge, this is the first demonstration of a tissue-specific phenotype in the chicken embryo.
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Affiliation(s)
- Hui Zhu
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Andrew J Bendall
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.
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21
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Ding J, Liu J, Chen J, Cheng X, Cao H, Guo X, Hu G, Zhuang Y. Sodium butyrate alleviates free fatty acid-induced steatosis in primary chicken hepatocytes via the AMPK/PPARα pathway. Poult Sci 2024; 103:103482. [PMID: 38387286 PMCID: PMC10899032 DOI: 10.1016/j.psj.2024.103482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 02/24/2024] Open
Abstract
Fatty liver hemorrhagic syndrome (FLHS) is a prevalent metabolic disorder observed in egg-laying hens, characterized by fatty deposits and cellular steatosis in the liver. Our preliminary investigations have revealed a marked decrease in the concentration of butyric acid in the FLHS strain of laying hens. It has been established that sodium butyrate (NaB) protects against metabolic disorders. However, the underlying mechanism by which butyrate modulates hepato-lipid metabolism to a great extent remains unexplored. In this study, we constructed an isolated in vitro model of chicken primary hepatocytes to induce hepatic steatosis by free fatty acids (FFA). Our results demonstrate that treatment with NaB effectively mitigated FFA-induced hepatic steatosis in chicken hepatocytes by inhibiting lipid accumulation, downregulating the mRNA expression of lipo-synthesis-related genes (sterol regulatory element binding transcription factor 1 (SREBF1), acetyl-CoA carboxylase 1(ACC1), fatty acid synthase (FASN), stearoyl-CoA desaturase 1 (SCD1), liver X receptor α (LXRα), 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR)) (P < 0.05), and upregulating the mRNA and protein expression of AMP-activated protein kinase α1 (AMPKα1), peroxisome proliferator-activated receptor α (PPARα), and carnitine palmitoyl-transferase 1A (CPT1A) (P < 0.05). Moreover, AMPK and PPARα inhibitors (Compound C (Comp C) and GW6471, respectively) reversed the protective effects of NaB against FFA-induced hepatic steatosis by blocking the AMPK/PPARα pathway, leading to lipid droplet accumulation and triglyceride (TG) contents in chicken primary hepatocytes. With these findings, NaB can alleviate hepatocyte lipoatrophy injury by activating the AMPK/PPARα pathway, promoting fatty acid oxidation, and reducing lipid synthesis in chicken hepatocytes, potentially being able to provide new ideas for the treatment of FLHS.
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Affiliation(s)
- Jiayi Ding
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, PR China
| | - Jiuyue Liu
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, PR China
| | - Jinyan Chen
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, PR China
| | - Xinyi Cheng
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, PR China
| | - Huabin Cao
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, PR China
| | - Xiaoquan Guo
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, PR China
| | - Guoliang Hu
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, PR China
| | - Yu Zhuang
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, PR China.
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22
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Chen X, Li X, Zhong C, Jiang X, Wu G, Li G, Yan Y, Yang N, Sun C. Genetic patterns and genome-wide association analysis of eggshell quality traits of egg-type chicken across an extended laying period. Poult Sci 2024; 103:103458. [PMID: 38350384 PMCID: PMC10875610 DOI: 10.1016/j.psj.2024.103458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 12/24/2023] [Accepted: 01/08/2024] [Indexed: 02/15/2024] Open
Abstract
The industry of egg-type chicken has shown a trend of extending the rearing period, with the goal of breeding chicken breeds capable of producing 500 qualified eggs by 700 d of age. However, the rapid decline in eggshell quality during the late laying period is one of the major challenges. In this study, a total of 3,261 Rhode Island Red chickens were used to measure eggshell quality traits including eggshell strength (ESS), eggshell thickness (EST), eggshell color (ESC) and eggshell gloss (ESG) at seven age points ranging from 36 to 90 wk of age. Phenotypic variations increased with the aging process, especially during the late laying period (> 55 wk), and the heritability during this period decreased by 22.7 to 81.4% compared to the initial and peak laying periods. Then we performed genome-wide association study (GWAS) to identify the genomic variants that associated with eggshell quality, with a custom Illumina 50K BeadChip, named PhenoixChip-I. The results indicated that 2 genomic regions on GGA1(23.24-25.15Mb; 175.95-176.05 Mb) were significantly (P < 4.48E-06) or suggestively (P < 8.97E-05) associated with ESS, which can explain 9.59% and 0.48% of the phenotypic variations of ESS46 and ESS36, respectively. Three genes, FRY, PCNX2, and ENSGALG00000052468, were considered to be the candidate genes for ESS. For other traits, the genome-wide suggestive SNPs were identified at each age point, exhibiting a certain trend with aging process. Additionally, SNP enrichment analysis and functional annotation of cross-tissue regulatory elements to ESS36 revealed a high concentration of enhancer elements specific to shell gland and kidney tissues. This study, deepened our knowledge of eggshells and laying a valued scientific foundation for chicken molecular breeding.
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Affiliation(s)
- Xiaoman Chen
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, China
| | - Xiaochang Li
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, China
| | - Conghao Zhong
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, China
| | - Xinwei Jiang
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, China
| | - Guiqin Wu
- Beijing Engineering Research Center of Layer, Beijing, 101206, China
| | - Guangqi Li
- Beijing Engineering Research Center of Layer, Beijing, 101206, China
| | - Yiyuan Yan
- Beijing Engineering Research Center of Layer, Beijing, 101206, China
| | - Ning Yang
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, China
| | - Congjiao Sun
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, China.
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23
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Phu DH, Wongtawan T, Wintachai P, Nhung NT, Yen NTP, Carrique-Mas J, Turni C, Omaleki L, Blackall PJ, Thomrongsuwannakij T. Molecular characterization of Campylobacter spp. isolates obtained from commercial broilers and native chickens in Southern Thailand using whole genome sequencing. Poult Sci 2024; 103:103485. [PMID: 38335668 PMCID: PMC10869288 DOI: 10.1016/j.psj.2024.103485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 01/12/2024] [Accepted: 01/17/2024] [Indexed: 02/12/2024] Open
Abstract
Chickens are the primary reservoirs of Campylobacter spp., mainly C. jejuni and C. coli, that cause human bacterial gastrointestinal infections. However, genomic characteristics and antimicrobial resistance of Campylobacter spp. in low- to middle-income countries need more comprehensive exploration. This study aimed to characterize 21 C. jejuni and 5 C. coli isolates from commercial broilers and native chickens using whole genome sequencing and compare them to 28 reference Campylobacter sequences. Among the 26 isolates, 13 sequence types (ST) were identified in C. jejuni and 5 ST in C. coli. The prominent ST was ST 2274 (5 isolates, 19.2%), followed by ST 51, 460, 2409, and 6455 (2 isolates in each ST, 7.7%), while all remaining ST (464, 536, 595, 2083, 6736, 6964, 8096, 10437, 828, 872, 900, 8237, and 13540) had 1 isolate per ST (3.8%). Six types of antimicrobial resistance genes (ant(6)-Ia, aph(3')-III, blaOXA, cat, erm(B), and tet(O)) and one point mutations in the gyrA gene (Threonine-86-Isoleucine) and another in the rpsL gene (Lysine-43-Arginine) were detected. The blaOXA resistance gene was present in all isolates, the gyrA mutations was in 95.2% of C. jejuni and 80.0% of C. coli, and the tet(O) resistance gene in 76.2% of C. jejuni and 80.0% of C. coli. Additionally, 203 virulence-associated genes linked to 16 virulence factors were identified. In terms of phenotypic resistance, the C. jejuni isolates were all resistant to ciprofloxacin, enrofloxacin, and nalidixic acid, with lower levels of resistance to tetracycline (76.2%), tylosin (52.3%), erythromycin (23.8%), azithromycin (22.2%), and gentamicin (11.1%). Most C. coli isolates were resistant to all tested antimicrobials, while 1 C. coli was pan-susceptible except for tylosin. Single-nucleotide polymorphisms concordance varied widely, with differences of up to 13,375 single-nucleotide polymorphisms compared to the reference Campylobacter isolates, highlighting genetic divergence among comparative genomes. This study contributes to a deeper understanding of the molecular epidemiology of Campylobacter spp. in Thai chicken production systems.
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Affiliation(s)
- Doan Hoang Phu
- Akkhraratchakumari Veterinary College, Walailak University, Nakhon Si Thammarat 80160, Thailand; Doctoral Program in Health Sciences, College of Graduate Studies, Walailak University, Nakhon Si Thammarat 80160, Thailand; Faculty of Animal Science and Veterinary Medicine, Nong Lam University, Ho Chi Minh City 70000, Vietnam
| | - Tuempong Wongtawan
- Akkhraratchakumari Veterinary College, Walailak University, Nakhon Si Thammarat 80160, Thailand; Centre for One Health, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | | | - Nguyen Thi Nhung
- Oxford University Clinical Research Unit, Ho Chi Minh City 70000, Vietnam
| | | | - Juan Carrique-Mas
- Food and Agriculture Organization of the United Nations, Ha Noi 10000, Vietnam
| | - Conny Turni
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Lida Omaleki
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Patrick J Blackall
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Thotsapol Thomrongsuwannakij
- Akkhraratchakumari Veterinary College, Walailak University, Nakhon Si Thammarat 80160, Thailand; Centre for One Health, Walailak University, Nakhon Si Thammarat 80160, Thailand.
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24
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Dzungwe JT, Tozo K, Chrysostome CAAM, Tankouano RA, Oke OE, Tona K. Effect of crossbreeding on egg quality, incubation, and hatching activities of the pure and reciprocal cross between the Sasso and Wassache chickens. Poult Sci 2024; 103:103406. [PMID: 38335664 PMCID: PMC10869303 DOI: 10.1016/j.psj.2023.103406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 12/17/2023] [Accepted: 12/22/2023] [Indexed: 02/12/2024] Open
Abstract
Understanding the effect of crossbreeding on egg quality and incubation is essential for the selection of superior genetic combinations in breeding programs. This study evaluated the effect of crossbreeding on egg quality and incubation activities of the Sasso and Wassache chickens in a pure (Sasso X Sasso [SS]; Wassache X Wassache [WW]) and reciprocal cross (Wassache X Sasso [WS]; Sasso X Wassache [SW]) design. A total of 1431 eggs were incubated while 400 eggs were selected for egg quality. Fertility, hatchability, and hatching activities were expressed in percentage, while egg quality traits were determined. The crosses with Sasso hens laid similar (P > 0.05) but heavier (P < 0.05) eggs with higher (P < 0.05) egg components compared to the crosses with Wassache hens. The SS, SW, and WW genotypes recorded similar (P > 0.05) early embryonic mortality (EEM) and were lower (P < 0.05) compared to the WS genotype. Late embryonic mortality (LEM) between the reciprocal crosses and SS was similar (P > 0.05) and lower (P < 0.05) compared to the WW. The hatchability and hatchability of fertile eggs between the purebreds and the SW cross were comparable (P > 0.05), while those of the WS genotype was lower compared to the SS cross. Hatch duration in the crossbreds was shorter (P < 0.05) compared to the pure Sasso. Mortality between the SW and WW was similar (P > 0.05) while the WS cross recorded a higher (P < 0.05) mortality compared to the purebreds. Crossbreeding improved egg quality, reduced LEM, and accelerated crossbred hatching events. The SW cross is recommended for better performance.
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Affiliation(s)
- Joshua T Dzungwe
- Centre d'Excellence Régionale sur les Science Aviares (CERSA), Université de Lomé, Lomé, Togo; Department of Animal Breeding and Physiology, Joseph Sarwuan Tarka University, Makurdi, Nigeria.
| | - Koffi Tozo
- Centre d'Excellence Régionale sur les Science Aviares (CERSA), Université de Lomé, Lomé, Togo
| | | | - Rachida A Tankouano
- Centre d'Excellence Régionale sur les Science Aviares (CERSA), Université de Lomé, Lomé, Togo
| | - Oyegunle E Oke
- Centre d'Excellence Régionale sur les Science Aviares (CERSA), Université de Lomé, Lomé, Togo; Department of Animal Physiology, Federal University of Agriculture, Abeokuta, Nigeria
| | - Kokou Tona
- Centre d'Excellence Régionale sur les Science Aviares (CERSA), Université de Lomé, Lomé, Togo
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25
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Ma J, Song Y, Mabrouk I, Zhou Y, Liu Q, Yu J, Li X, Xue G, Wang J, Yu Z, Sun Y. miR-140-y targets TCF4 to regulate the Wnt signaling pathway and promote embryonic feather follicle development in Hungarian white goose. Poult Sci 2024; 103:103508. [PMID: 38350393 PMCID: PMC10874752 DOI: 10.1016/j.psj.2024.103508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 01/24/2024] [Accepted: 01/24/2024] [Indexed: 02/15/2024] Open
Abstract
Goose down feather has become one of the most important economical products in the goose breeding industry and it provides several essential physiological roles in birds. Therefore, understanding and regulating the development of skin and feather follicles during embryogenesis is critical for avian biology and the poultry industry. MicroRNAs are known to play an important role in controlling gene expression during skin and feather follicle development. In this study, bioinformatics analysis was conducted to select miR-140-y as a potential miRNA involved in skin and feather follicle development and to predict TCF4 as its target gene. This gene was expressed at significant levels during embryonic feather follicle development, as identified by qPCR and Western blot. The targeting relationship was confirmed by a dual-luciferase assay in 293T cells. Then, the miR-140-y/TCF4 function in dermal fibroblast cells was explored. The results showed that miR-140-y could suppress the proliferation of goose embryonic dermal fibroblast cells (GEDFs) by suppressing the activity of some Wingless-types (Wnt) pathway related genes and proliferation marker genes, while miR-140-y inhibition led to the opposite effect. Similarly, the inhibition of the TCF4 gene results in blocking the proliferation of GEDFs by reducing the activity of some Wnt pathway-related genes. Finally, the co-transfection of miR-140-y inhibitor and siRNA-TCF4 results in a rescue of the TCF4 function and an increase of the Wnt signaling pathway and GEDFs proliferation. In conclusion, these results demonstrated that the miR-140-y-TCF4 axis influences the activity of the Wnt signaling pathway and works as a dynamic regulator during skin and feather follicle development.
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Affiliation(s)
- Jingyun Ma
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Yupu Song
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Ichraf Mabrouk
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Yuxuan Zhou
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Qiuyuan Liu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Jin Yu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Xinyue Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Guizhen Xue
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Jingbo Wang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Zhiye Yu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Yongfeng Sun
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China; Key Laboratory of Animal Production, Product Quality and Security, Jilin Agricultural University, Ministry of Education, Changchun, 130118, China; Joint Laboratory of Modern Agricultural Technology International Cooperation, Ministry of Education, Jilin Agricultural University, Changchun, 130118, China.
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26
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Siegel PB, Honaker CF, Andersson L. Research Note: Phenotypic trends for the multigenerational advanced intercross of the Virginia body weight lines of chickens. Poult Sci 2024; 103:103480. [PMID: 38330887 PMCID: PMC10864792 DOI: 10.1016/j.psj.2024.103480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/05/2024] [Accepted: 01/15/2024] [Indexed: 02/10/2024] Open
Abstract
Random samples from generation S41 of the Virginia high and low 8-week body weight lines formed the base population for producing a multigenerational reciprocal intercross population. Although genetic mapping from this intercross has been reported, lacking are phenotypic trends across multiple generations. Here, we provide phenotypic information for the parental base population, the F1 reciprocal cross, and subsequent segregating recombinant generations F2 to F17. Heterosis for the selected trait in the F1 was negative for both reciprocal crosses. Phenotypic correlations for the selected trait in the recombinant generations were essentially nil for both males and females as was percent sexual dimorphism and coefficients of variation.
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Affiliation(s)
- P B Siegel
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 USA.
| | - C F Honaker
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 USA
| | - L Andersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, S-75123 Uppsala, Sweden; Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
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27
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Shiina K, Kobayashi E. Genetic mapping of the novel congenital loco locus on chromosome Z in Silkie Fowl chickens. Br Poult Sci 2024; 65:111-118. [PMID: 38230423 DOI: 10.1080/00071668.2023.2297806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 11/24/2023] [Indexed: 01/18/2024]
Abstract
1. 'Congenital loco' is a disorder in birds expressed at hatching, and the primary symptom is dorsal backward bending of the neck. It is a recessive disease caused by a mutation in a specific genetic locus. The following study identified a novel locus associated with congenital loco in Silkie Fowl chickens.2. Normal and congenital loco-affected Silkie Fowl chicks exhibited no differences in the frequencies of markers on chromosome 12 adjacent to the congenital loco locus reported in a previous study in Rhode Island Red chickens. Sex determination of congenital loco-affected chicks revealed that they were female only.3. Bulked segregant analyses using next-generation sequencing narrowed the causative region of congenital loco to approximately 3.3 Mb between bases 9,569,012 and 12,863,792 on chromosome Z.
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Affiliation(s)
- K Shiina
- Tokyo Metropolitan Agriculture and Forestry Research Center, Ome, Japan
| | - E Kobayashi
- Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
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28
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Li X, Wang Z, Yang B. Identification of the hub genes linked to zearalenone-induced hepatotoxicity in broiler chickens. Environ Res 2024; 246:118094. [PMID: 38176630 DOI: 10.1016/j.envres.2023.118094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/14/2023] [Accepted: 12/31/2023] [Indexed: 01/06/2024]
Abstract
Zearalenone (ZEN) is a mycotoxin found in food and feed that impairs the function of multiple organs, especially the liver. However, the specific mechanisms through which ZEN induces liver damage in broiler chickens are not well understood. Therefore, this study aimed to identify the key genes linked to the hepatotoxicity induced by ZEN exposure in broiler chickens. Gene expression data from ZEN-treated and control chicken embryo primary hepatocytes (CEPHs) were used to implement differential expression analysis. Totally, 436 differentially expressed genes (DEGs) were detected, in which 223 and 213 genes were up- and down-regulated in ZEN-treated CEPHs, respectively. Gene ontology analysis suggested that these DEGs were involved in various biological processes, including chromosome segregation, mitotic cytokinesis, mitotic cell cycle, cell division, and mitotic spindle organization. Pathway analysis showed that the DEGs were associated with p53, FoxO, ubiquitin-mediated proteolysis, cell cycle, and mismatch repair signaling pathways. Furthermore, the hub genes, including BRCA1, CDC45, CDCA3, CDKN3, CENPE, CENPF, CENPI, CENPM, CENPU, and CEP55, potentially contributed to ZEN-induced hepatotoxicity. In conclusion, our study provides the valuable insight into the mechanism underlying ZEN-induced hepatotoxicity in broiler chickens.
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Affiliation(s)
- Xiaofeng Li
- College of Animal Science, Anhui Science and Technology University, Fengyang, 233100, China
| | - Zhongyuan Wang
- College of Animal Science, Anhui Science and Technology University, Fengyang, 233100, China
| | - Bing Yang
- College of Animal Science, Anhui Science and Technology University, Fengyang, 233100, China.
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29
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Zhang G, Liu P, Liang R, Ying F, Liu D, Su M, Chen L, Zhang Q, Liu Y, Liu S, Zhao G, Li Q. Transcriptome analysis reveals the genes involved in spermatogenesis in white feather broilers. Poult Sci 2024; 103:103468. [PMID: 38359768 PMCID: PMC10875292 DOI: 10.1016/j.psj.2024.103468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/23/2023] [Accepted: 01/10/2024] [Indexed: 02/17/2024] Open
Abstract
Semen volume is an important economic trait of broilers and one of the important indices for continuous breeding. The objective of this study was to identify genes related to semen volume through transcriptome analysis of the testis tissue of white feather broilers. The testis samples with the highest semen volume (H group, n = 5) and lowest semen volume (L group, n = 5) were selected from 400-day-old roosters for transcriptome analysis by RNA sequencing. During the screening of differentially expressed genes (DEGs) between the H and L groups, a total of 386 DEGs were identified, among which 348 were upregulated and 38 were downregulated. Gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the immune response, leukocyte differentiation, cell adhesion molecules and collagen binding played vital roles in spermatogenesis. The results showed that 4 genes related to spermatogenesis, namely, COL1A1, CD74, ARPC1B and APOA1, were significantly expressed in Group H, which was consistent with the phenotype results. Our findings may provide a basis for further research on the genetic mechanism of semen volume in white feather broilers.
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Affiliation(s)
- Gaomeng Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Peihao Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Ruiping Liang
- Beijing Changping District Center for Animal Disease Prevention and Control, Beijing, P. R. China
| | - Fan Ying
- MiLe Xinguang Agricultural and Animal Industrials Corporation, Mile, P. R. China
| | - Dawei Liu
- MiLe Xinguang Agricultural and Animal Industrials Corporation, Mile, P. R. China
| | - Meng Su
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Li Chen
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, P.R. China
| | - Qi Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Yuhong Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Sha Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Guiping Zhao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Qinghe Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P. R. China.
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30
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Zheng X, Chen J, Nie R, Miao H, Chen Z, He J, Xie Y, Zhang H. Differential expression of ASIP transcripts reveals genetic mechanism underpinning black-tail independence from body plumage in yellow-bodied chickens. Anim Genet 2024; 55:249-256. [PMID: 38194424 DOI: 10.1111/age.13395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 11/30/2023] [Accepted: 12/27/2023] [Indexed: 01/11/2024]
Abstract
The genetic foundation of chicken body plumage color has been extensively studied. However, little attention has been paid to the inheritance patterns and molecular mechanisms underlying the formation of distal feather colors (tail and wingtip). Differences in these colors are common; for example, the Chinese Huiyang Beard chicken has black tail feathers, but yellow body plumage. Here, the hybrid offspring of Huiyang Beard and White Leghorn chickens were used to study the inheritance patterns of tail-feather color. The expression levels of pigment genes in differently colored feather follicles were analyzed using quantitative real-time PCR. The results showed that genetic regulation of tail-feather color was independent of body-plumage color. The Dominant White locus inhibited eumelanin synthesis in tail feathers without affecting the formation of yellow body plumage, whereas the Silver locus had the opposite effect. The expression of agouti signaling protein (ASIP) gene class 1 transcripts was significantly lower in black tail-feather follicles than in yellow body follicles, whereas tyrosinase-related protein 1 (TYRP1) gene expression was significantly higher in black tail feathers. These differentially expressed genes were confirmed to exert an effect on eumelanin and pheomelanin formation in feathers, thus influencing the regulation of chicken tail-feather color. In conclusion, this study lays the foundation for further research on the genetic mechanisms of regional differences in feather color, contributing to a better understanding of plumage pigmentation in chickens.
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Affiliation(s)
- Xiaotong Zheng
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Jianfei Chen
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Ruixue Nie
- State Key Laboratory of Farm Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Huanhuan Miao
- State Key Laboratory of Farm Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ziwei Chen
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Jiaheng He
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Yinku Xie
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Hao Zhang
- State Key Laboratory of Farm Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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31
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Jiang Y, Lu Y, Xu H, Hu Z, Du R, Zhou Y, Deng Q, Wang X, Liu Y, Wang Y. miR-206a-3p suppresses the proliferation and differentiation of chicken chondrocytes in tibial dyschondroplasia by targeting BMP6. Poult Sci 2024; 103:103534. [PMID: 38401226 PMCID: PMC10906518 DOI: 10.1016/j.psj.2024.103534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 01/16/2024] [Accepted: 02/03/2024] [Indexed: 02/26/2024] Open
Abstract
The poultry skeletal system serves multiple functions, not only providing structural integrity but also maintaining the balance of essential minerals such as calcium and phosphorus. However, in recent years, the consideration of skeletal traits has been overlooked in the selective breeding of broilers, resulting in an inadequate adaptation of the skeletal system to cope with the rapid increase in body weight. Consequently, this leads to lameness and bone diseases such as tibial dyschondroplasia (TD), which significantly impact the production performance of broilers. Accumulating evidence has shown that microRNAs (miRNA) play a crucial role in the differentiation, formation, and disease of cartilage. However, the miRNA-mediated molecular mechanism underlying chicken TD formation is still poorly understood. The objective of this study was to investigate the biological function and regulatory mechanism of miRNA in chicken TD formation. Based on transcriptome sequencing of tibial cartilage in the healthy group and TD group, miR-206a-3p was found to be highly expressed in TD cartilage. The function of miR-206a-3p was explored through the transfection test of miR-206a-3p mimics and miR-206a-3p inhibitor. In this study, we utilized qRT-PCR, CCK-8, EdU, western blot, and flow cytometry to detect the proliferation, differentiation, and apoptosis of chondrocytes. The results revealed that miR-206a-3p suppressed the proliferation and differentiation of TD chondrocytes while promoting their programmed cell death. Furthermore, through biosynthesis and dual luciferase assays, it was determined that BMP6 was the direct target gene of miR-206a-3p. This finding was further supported by rescue experiments which confirmed the involvement of BMP6 in the regulatory pathway governed by miR-206a-3p. Our results suggest that miR-206a-3p can inhibits the proliferation and differentiation promote apoptosis through the target gene BMP-6 and suppressing the Smad2/3 signaling pathway in chicken TD chondrocytes.
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Affiliation(s)
- Yuru Jiang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; State Key Laboratory of Swine and Poultry Breeding Industry, Sichuan Agricultural University, Chengdu 611130, China
| | - Yuxiang Lu
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; State Key Laboratory of Swine and Poultry Breeding Industry, Sichuan Agricultural University, Chengdu 611130, China
| | - Hengyong Xu
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; State Key Laboratory of Swine and Poultry Breeding Industry, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhi Hu
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; State Key Laboratory of Swine and Poultry Breeding Industry, Sichuan Agricultural University, Chengdu 611130, China
| | - Ranran Du
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; State Key Laboratory of Swine and Poultry Breeding Industry, Sichuan Agricultural University, Chengdu 611130, China
| | - Yuxin Zhou
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; State Key Laboratory of Swine and Poultry Breeding Industry, Sichuan Agricultural University, Chengdu 611130, China
| | - Qingqing Deng
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; State Key Laboratory of Swine and Poultry Breeding Industry, Sichuan Agricultural University, Chengdu 611130, China
| | - Xi Wang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; State Key Laboratory of Swine and Poultry Breeding Industry, Sichuan Agricultural University, Chengdu 611130, China
| | - Yiping Liu
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; State Key Laboratory of Swine and Poultry Breeding Industry, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Wang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; State Key Laboratory of Swine and Poultry Breeding Industry, Sichuan Agricultural University, Chengdu 611130, China.
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32
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Fu H, Zhao M, Chen S, Huang Y, Wan C. Simultaneous detection and differentiation of DuCV-1 and DuCV-2 by high-resolution melting analysis. Poult Sci 2024; 103:103566. [PMID: 38417341 PMCID: PMC10907865 DOI: 10.1016/j.psj.2024.103566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 02/05/2024] [Accepted: 02/12/2024] [Indexed: 03/01/2024] Open
Abstract
Birds infected with duck circovirus (DuCV) can potentially cause immunosuppression by damaging lymphoid tissues, causing great losses in the duck breeding industry. Duck circovirus can be divided into two genotypes (DuCV-1 and DuCV-2), but simultaneous detection and differentiation of DuCV-1 and DuCV-2 by high-resolution melting (HRM) analysis is still lacking. Here, we designed specific primers according to the sequence characteristics of the newly identified ORF3 gene and then established a PCR-HRM method for the simultaneous detection and differentiation of DuCV-1 and DuCV-2 via high-resolution melting analysis. Our data showed that the established PCR-HRM assay had the advantages of specificity, with the lowest detection limits of 61.9 copies/μL (for DuCV-1) and 60.6 copies/μL (for DuCV-2). The melting curve of the PCR-HRM results indicated that the amplification product was specific, with no cross-reaction with common waterfowl origin pathogens and a low coefficient of variation less than 1.50% in both intra-batch and inter-batch repetitions, indicating the advantages of repeatability. We found that the percentage of DuCV-2-positive ducks was higher than that of DuCV-1-positive ducks, with 8.62% rate of DuCV-1 and DuCV-2 coinfection. In addition, we found DuCV-2-positive in geese firstly. In conclusion, this study provides a candidate PCR-HRM assay for the detection and accurate differentiation of DuCV-1 and DuCV-2 infection, which will help us for further epidemiological surveillance of DuCVs.
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Affiliation(s)
- Huanru Fu
- Institute of Animal Husbandry and Veterinary Medicine/Fujian Key Laboratory for Avian Diseases Control and Prevention/Fujian Animal Diseases Control Technology Development Centre, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China; School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Min Zhao
- Institute of Animal Husbandry and Veterinary Medicine/Fujian Key Laboratory for Avian Diseases Control and Prevention/Fujian Animal Diseases Control Technology Development Centre, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China; School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shuyu Chen
- Institute of Animal Husbandry and Veterinary Medicine/Fujian Key Laboratory for Avian Diseases Control and Prevention/Fujian Animal Diseases Control Technology Development Centre, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China; School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yu Huang
- Institute of Animal Husbandry and Veterinary Medicine/Fujian Key Laboratory for Avian Diseases Control and Prevention/Fujian Animal Diseases Control Technology Development Centre, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Chunhe Wan
- Institute of Animal Husbandry and Veterinary Medicine/Fujian Key Laboratory for Avian Diseases Control and Prevention/Fujian Animal Diseases Control Technology Development Centre, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China.
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Budi T, Singchat W, Tanglertpaibul N, Thong T, Panthum T, Noito K, Wattanadilokchatkun P, Jehangir M, Chaiyes A, Wongloet W, Vangnai K, Yokthongwattana C, Sinthuvanich C, Ahmad SF, Muangmai N, Han K, Nunome M, Supnithi T, Koga A, Duengkae P, Matsuda Y, Srikulnath K. Research Note: Possible influence of thermal selection on patterns of HSP70 and HSP90 gene polymorphisms in Thai indigenous and local chicken breeds and red junglefowls. Poult Sci 2024; 103:103503. [PMID: 38330888 PMCID: PMC10864794 DOI: 10.1016/j.psj.2024.103503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/06/2024] [Accepted: 01/22/2024] [Indexed: 02/10/2024] Open
Abstract
The thermal stress caused by global climate change adversely affects the welfare, productivity, and reproductive performance of farm animals, including chickens, and causes substantial economic losses. However, the understanding of the genetic basis of the indigenous chicken adaptation to high ambient temperatures is limited. Hence, to reveal the genetic basis of thermal stress adaptation in chickens, this study investigated polymorphisms in the heat shock protein 70 (HSP70) and HSP90 genes, known mechanisms of cellular defense against thermal stress in indigenous and local chicken breeds and red junglefowls in Thailand. The result revealed seven alleles of the HSP70 gene. One allele exhibited a missense mutation, where an amino acid changed from Asn to His in the substrate-binding and peptide-binding domains, which is exclusive to the Lao Pa Koi chicken breed. Twenty new alleles with silent mutations in the HSP90 gene highlighted its greater complexity. Despite this diversity, distinct population structures were not found for either HSP70 or HSP90, which suggests incomplete impact on the domestication process and selection. The low genetic diversity, shown by the sharing of alleles between red junglefowls and Thai indigenous and local chicken breeds, aligns with the hypothesis that these alleles have undergone selection in tropical regions, such as Thailand. Selection signature analysis suggests the purifying selection of HSP70 for thermotolerance. This study provides valuable insights for enhancing the conservation of genetic resources with thermotolerant traits, which are essential for developing breeding programs to increase poultry production in the context of global climate change.
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Affiliation(s)
- Trifan Budi
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand; Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Nivit Tanglertpaibul
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand; Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Thanyapat Thong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand; Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Kantika Noito
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Pish Wattanadilokchatkun
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Maryam Jehangir
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Aingorn Chaiyes
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand; School of Agriculture and Cooperatives, Sukhothai Thammathirat Open University, Nonthaburi 11120, Thailand
| | - Wongsathit Wongloet
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Kanithaporn Vangnai
- Department of Food Science and Technology, Faculty of Agro-Industry, Kasetsart University, Bangkok, 10900, Thailand
| | - Chotika Yokthongwattana
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Chomdao Sinthuvanich
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand; Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand; Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Narongrit Muangmai
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand; Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand
| | - Kyudong Han
- Department of Microbiology, Dankook University, Cheonan 31116, Republic of Korea; Bio-Medical Engineering Core Facility Research Center, Dankook University, Cheonan 31116, Republic of Korea; Smart Animal Bio institute, Dankook University, Cheonan 31116, Republic of Korea
| | - Mitsuo Nunome
- Department of Zoology, Faculty of Science, Okayama University of Science, Kita-ku, Okayama 700-0005, Japan
| | - Thepchai Supnithi
- National Electronics and Computer Technology Center (NECTEC), Khlong Luang, Pathum Thani 12120, Thailand
| | - Akihiko Koga
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Yoichi Matsuda
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand; Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok 10900, Thailand; Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University (CASTNAR, NRU-KU), Kasetsart University, Bangkok 10900, Thailand.
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Tai Y, Han D, Yang X, Cai G, Li H, Zhang Y, Li J, Deng X. In vitro culture and tissue-derived specific expression of melanocytes from ovary of adult Silky Fowl. Poult Sci 2024; 103:103379. [PMID: 38306917 PMCID: PMC10847685 DOI: 10.1016/j.psj.2023.103379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/10/2023] [Accepted: 12/12/2023] [Indexed: 02/04/2024] Open
Abstract
The presence of a significant number of melanocytes in the ovary and follicular membrane of Silky Fowl suggests their potential involvement in follicle development. Currently, there is a lack of available data regarding to the isolation of primary melanocytes from adult chickens. To date, primary melanocytes and their in vitro culture system have been successfully conducted in the peritoneum of chicken embryos. Herein, melanocytes from silky fowl ovaries were isolated and identified. Silky Fowl ovaries were obtained by mixed digestion of 0.1% collagenase II and 0.25% trypsin-EDTA. Melanocytes could be further purified and cultured up to 5 generations in vitro. RNA-seq analysis was used to investigate whether there were differences in the functional status of melanocytes in different tissues and developmental stages. Consequently, differential gene expressions between peritoneal and ovarian melanocytes were compared. These findings demonstrated that the Silky Fowl ovary had higher expression levels of genes involved in the production of sexual hormones and melanogenesis, while those of melanocytes derived from the peritoneum were involved in amino acid metabolism, lipid synthesis, and overall metabolic rates. This suggests that the role of melanocytes is dependent on the origin tissue and developmental stage, and is tightly connected to the function of the specific source tissue from which the cells were derived. This study provides a method for isolating adult melanocytes and serve as a basis for further investigate the effect of SFOM on germ cells.
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Affiliation(s)
- Yurong Tai
- Hainan Sanya Research Institute, Seed Laboratory & Sanya Research Institute, Hainan, China; State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of the Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China
| | - Deping Han
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong 261325, China
| | - Xue Yang
- State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of the Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China
| | - Ganxian Cai
- State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of the Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China
| | - HuaiYu Li
- State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of the Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China
| | - Yuanyuan Zhang
- State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of the Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China
| | - Junying Li
- State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of the Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China
| | - Xuemei Deng
- Hainan Sanya Research Institute, Seed Laboratory & Sanya Research Institute, Hainan, China; State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of the Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China.
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35
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Yu B, Cai Z, Liu J, Zhang T, Feng X, Wang C, Li J, Gu Y, Zhang J. Identification of key differentially methylated genes in regulating muscle development and intramuscular fat deposition in chickens. Int J Biol Macromol 2024; 264:130737. [PMID: 38460642 DOI: 10.1016/j.ijbiomac.2024.130737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/26/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024]
Abstract
Muscle development and intramuscular fat (IMF) deposition are intricate physiological processes characterized by multiple gene expressions and interactions. In this research, the phenotypic variations in the breast muscle of Jingyuan chickens were examined at three different time points: 42, 126, and 180 days old. Differential expression analysis and weighted gene co-expression network analysis (WGCNA) were performed to identify differentially methylated genes (DMGs) responsible for regulating muscle development and IMF deposition. The findings indicate a significant increase in breast muscle weight (BMW), myofiber diameter, and cross-sectional area, as well as IMF content, in correlation with the progressive number of growing days in Jingyuan chickens. The findings also revealed that 380 hypo-methylated and 253 hyper-methylated DMGs were identified between the three groups of breast muscle. Module gene and DMG association analysis identified m6A methylation-mediated multiple DMGs associated with muscle development and fat metabolism. In vitro cell modeling analysis reveals stage-specific differences in the expression of CUBN, MEGF10, BOP1, and BMPR2 during the differentiation of myoblasts and intramuscular preadipocytes. Cycloleucine treatment significantly inhibited the expression levels of CUBN, BOP1, and BMPR2, and promoted the expression of MEGF10. These results suggest that m6A methylation-mediated CUBN, MEGF10, BOP1, and BMPR2 can serve as potential candidate genes for regulating muscle development and IMF deposition, and provide an important theoretical basis for further investigation of the functional mechanism of m6A modification involved in adipogenesis.
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Affiliation(s)
- Baojun Yu
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Zhengyun Cai
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Jiamin Liu
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Tong Zhang
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Xiaofang Feng
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Chuanchuan Wang
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Jiwei Li
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Yaling Gu
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Juan Zhang
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China.
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Gao L, Wang Y, Gao Q, Chen Y, Zhang Z. Transcriptional control of CCAAT/enhancer binding protein zeta gene in chicken adipose tissue. Poult Sci 2024; 103:103540. [PMID: 38417330 PMCID: PMC10907851 DOI: 10.1016/j.psj.2024.103540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/25/2024] [Accepted: 02/05/2024] [Indexed: 03/01/2024] Open
Abstract
CCAAT/enhancer binding protein zeta (C/EBPZ) was differentially expressed in abdominal adipose tissues of fat and lean broilers and regulated adipogenesis in chicken. The objective of this study was to elucidate the transcriptional regulation of C/EBPZ gene in chicken adipose tissue. A 2,031-base pair (bp) chicken C/EBPZ sequence (2,025 nucleotides upstream to 6 nucleotides downstream from the initiator codon, -2,025/+6) was studied. The sequence exhibited a significant promoter activity (P < 0.05) and had some cis-acting elements, notably, a core promoter was identified in nucleotides -94 to +6. Additionally, DNA pull-down assay showed that proteins interacted with chicken C/EBPZ promoter (-173/+6) in preadipocytes were implicated in transcription, post-transcriptional regulation and translation. In addition, KLF2 facilitated the activities of chicken C/EBPZ promoter (-2,025/+6, -1,409/+6, -793/+6, -485/+6, -173/+6, and -94/+6) in preadipocytes (P < 0.05). The expression levels of KLF2 and C/EBPZ in chicken abdominal adipose tissue were substantially associated (r = 0.5978278, P < 0.0001), and KLF2 increased C/EBPZ expression in vitro (P < 0.05). Additionally, chromatin immunoprecipitation (ChIP)-PCR analysis revealed that KLF2 has the ability to interact with the chicken C/EBPZ promoter regions at least at the positions -1,245/-1,048 and -571/-397. Mutation analysis showed that the CGCAGCGCCCG motif located in the chicken C/EBPZ promoter at positions -45 to -35 is involved in regulating transcription and facilitates trans activation by KLF2. These results provided some information of transcription control of C/EBPZ in chicken adipose tissue.
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Affiliation(s)
- Lingyu Gao
- Department of Histology and Embryology, Shihezi University School of Medicine, Shihezi, Xinjiang, 832000, PR China; Key Medical Laboratory of Stem Cell Transformation and Application, The First People's Hospital of Zhengzhou, Zhengzhou, Henan, 450000, PR China
| | - Yingjun Wang
- Department of Histology and Embryology, Shihezi University School of Medicine, Shihezi, Xinjiang, 832000, PR China
| | - Qin Gao
- Department of Histology and Embryology, Shihezi University School of Medicine, Shihezi, Xinjiang, 832000, PR China
| | - Yuechan Chen
- Department of Reproductive Medicine, The First Affiliated Hospital of Shihezi University, Shihezi, Xinjiang, 832000, PR China
| | - Zhiwei Zhang
- Department of Histology and Embryology, Shihezi University School of Medicine, Shihezi, Xinjiang, 832000, PR China.
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Yue Q, Huang C, Zhou R, Zhang Y, Wang D, Zhang Z, Chen H. Integrated transcriptomic and metabolomic analyses reveal potential regulatory pathways regulating bone metabolism pre- and postsexual maturity in hens. Poult Sci 2024; 103:103555. [PMID: 38417334 PMCID: PMC10907858 DOI: 10.1016/j.psj.2024.103555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 02/01/2024] [Accepted: 02/09/2024] [Indexed: 03/01/2024] Open
Abstract
At the onset of sexual maturity, the increasing circulating estrogen stimulates the formation of medullary bone, which provides available calcium for eggshell formation. The bone loss of laying hens is caused by the continuous dynamic changes of structure bone leading to bone fragility and susceptibility. The degree of medullary bone mineralization in sexual maturity is positively correlated with bone quality in the late laying stage. This study aimed to explore the molecular regulation mechanism of bone metabolism pre- and postsexual maturity in hens based on the joint analysis of transcriptome and metabolome. A total of 50 Hy-line Sonia pullets with comparable body weight at 13 wk were selected. Eight pullets were killed at 15 wk (juvenile hens, JH) and 19 wk (laying hens, LH), and LHs were killed within 3 h after oviposition. Differentially expressed genes and metabolites in tibia were analyzed based on transcriptome and metabolome, and then combined to construct the relevant metabolisms and hub genes. In the LH hens, plasma levels of estrogen and tartrate-resistant acid phosphatase were significantly elevated by 1.7 and 1.3 times. In addition, the midpoint diameter, bone mineral density and bone mineral content of the tibia and femur were higher at 19 wk of age. A total of 580 differentially expressed genes were found between the JH and LH group in the tibia, including 280 up-regulated, and 300 down-regulated genes in the LH group. Gene set enrichment analysis (GSEA) showed that the intracellular biosynthesis and secretion of matrix vesicles were significantly enrichment in the LH hens. A total of 21 differential metabolites were identified between JH and LH group. Estradiol valerate positively correlated with L-theanine, tryptophan betaine, dopamine, and perindopril. Joint analysis showed that the top 20 hub genes were enriched in cholesterol biosynthesis and phospholipid metabolism, which played a key regulatory role in bone metabolism during pre- and postsexual maturity. These results provide a theoretical foundation for maintaining efficient egg production and reducing bone health problems in laying hens.
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Affiliation(s)
- Qiaoxian Yue
- College of Animal Science and Technology, Hebei Agricultural University, Baoding 071000, China
| | - Chenxuan Huang
- College of Animal Science and Technology, Hebei Agricultural University, Baoding 071000, China
| | - Rongyan Zhou
- College of Animal Science and Technology, Hebei Agricultural University, Baoding 071000, China.
| | - Yinlang Zhang
- College of Animal Science and Technology, Hebei Agricultural University, Baoding 071000, China
| | - Dehe Wang
- College of Animal Science and Technology, Hebei Agricultural University, Baoding 071000, China
| | - Zhenhong Zhang
- College of Animal Science and Technology, Hebei Agricultural University, Baoding 071000, China
| | - Hui Chen
- College of Animal Science and Technology, Hebei Agricultural University, Baoding 071000, China
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Lu Y, Wei B, Yang Q, Han X, He X, Tao Q, Jiang S, Xu M, Bai Y, Zhang T, Bai L, Hu J, Liu H, Li L. Identification of candidate genes affecting the tibia quality in Nonghua duck. Poult Sci 2024; 103:103515. [PMID: 38350390 PMCID: PMC10875613 DOI: 10.1016/j.psj.2024.103515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/15/2024] Open
Abstract
The skeleton is a vital organ providing structural support in poultry. Weakness in bone structure can lead to deformities, osteoporosis, cage fatigue, and fractures, resulting in economic losses. Research has substantiated that genetic factors play a significant role in influencing bone quality. The discovery of genetic markers associated with bone quality holds paramount importance for enhancing genetic traits related to the skeletal system in poultry. This study analyzed nine phenotypic indicators of tibia quality in 120-day-old ducks. The phenotypic correlation revealed a high correlation among diameter, Perimeter, and weight (0.69-0.78), and a strong correlation was observed between toughness and breaking strength (0.62). Then, we conducted a genome-wide association analysis of the phenotypic indicators to elucidate the genetic basis of tibial quality in Nonghua ducks. Among the 11 candidate genes that were annotated, TAPT1, BST1, and STIM2 were related to the diameter indicator, ZNF652, IGF2BP1, CASK, and GREB1L were associated with the weight and toughness indicators. RFX8, GLP1R, and DNAAF5 were identified for ash, calcium, and phosphorus content, respectively. Finally, KEGG and GO analysis for annotated genes were performed. STIM2 and BST1 were enriched into the Calcium signalling pathway and Niacin and nicotinamide metabolic pathway, which may be key candidate genes affecting bone quality phenotypes. Gene expression analysis of the candidate genes, such as STIM2, BST1, TAPT1, and CASK showed higher expression levels in bones compared to other tissues. The obtained results can contribute to new insights into tibial quality and provide new genetic biomarkers that can be employed in duck breeding.
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Affiliation(s)
- Yinjuan Lu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 613000, China
| | - Bin Wei
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 613000, China
| | - Qinglan Yang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 613000, China
| | - Xu Han
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 613000, China
| | - Xinxin He
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 613000, China
| | - Qiuyu Tao
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 613000, China
| | - Shuaixue Jiang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 613000, China
| | - Mengru Xu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 613000, China
| | - Yuan Bai
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 613000, China
| | - Tao Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 613000, China
| | - Lili Bai
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 613000, China
| | - Jiwei Hu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 613000, China
| | - Hehe Liu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 613000, China
| | - Liang Li
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 613000, China.
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Ma D, Yu M, Zhang M, Feng J. Research Note: The effect of photoperiod on the NLRP3 inflammasome and gut microbiota in broiler chickens. Poult Sci 2024; 103:103507. [PMID: 38387288 PMCID: PMC10900794 DOI: 10.1016/j.psj.2024.103507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/24/2024] Open
Abstract
The present study aimed to investigate the effect of photoperiod on the intestinal inflammation and gut microbiota. A total of 96 broiler chickens were divided into 2 groups and fed separately under 2 different photoperiods (12L:12D group and 23L:1D group) for 21 d. The results showed that the photoperiod of 23L:1D damaged duodenal tissue structure (intestinal villus erosion, mucosal epithelial cell detachment, and inflammatory cell infiltration), significantly increased the concentration of inflammatory cytokines (IL-1β, IL-18, IL-6, and TNF-α) and significantly increased the mRNA expression levels and protein expression levels of NOD-, LRR-, pyrin domain-containing protein 3 (NLRP3) and caspase1 (P <0.05) compared with 12L:12D, which indicating that extended photoperiod induced intestinal injury and activated NLRP3 inflammasome. 16S rRNA sequencing analysis revealed that Bacteroides was significantly decreased, Ruminococcus_torques_group, norank_f_Desulfovibrionaceae, GCA-900066575, Defluviitaleaceae_UCG-011, Lachnospiraceae_FCS020_group, norank_f_UCG-010 and norank_f_norank_o_Clostridia_vadinBB60_group and were significantly increased in the 23L:1D group, compared with the 12L:12D group (P < 0.05). The correlation analysis between differential microbial communities and intestinal inflammation showed that the relative abundance of Bacteroides was negatively correlated with the mRNA expression level of NLRP3 (P < 0.05) and the relative abundance of Ruminococcus_torques_group was positively correlated with the mRNA expression level of NLRP3 (P < 0.05). linear discriminant analysis (LDA) effect size (LEfSe) results (LDA > 4) showed that the relative abundance of Bacteroides was dramatically higher (P < 0.05) in the 12L:12D group, whereas the relative abundance of Ruminococcus_torques_group was noticeably higher (P < 0.05) in the 23L:1D group. By the comprehensive analysis of the gut microbiota, the interaction of gut microbiota (Bacteroides and Ruminococcus_torques_group) and NLRP3 inflammasome may contribute to the intestinal injury under the condition of extended photoperiod.
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Affiliation(s)
- Dandan Ma
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Miao Yu
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Minhong Zhang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Jinghai Feng
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Wang SZ, Wang MD, Wang JY, Yuan M, Li YD, Luo PT, Xiao F, Li H. Genome-wide association study of growth curve parameters reveals novel genomic regions and candidate genes associated with metatarsal bone traits in chickens. Animal 2024; 18:101129. [PMID: 38574453 DOI: 10.1016/j.animal.2024.101129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 03/02/2024] [Accepted: 03/05/2024] [Indexed: 04/06/2024] Open
Abstract
The growth and development of chicken bones have an enormous impact on the health and production performance of chickens. However, the development pattern and genetic regulation of the chicken skeleton are poorly understood. This study aimed to evaluate metatarsal bone growth and development patterns in chickens via non-linear models, and to identify the genetic determinants of metatarsal bone traits using a genome-wide association study (GWAS) based on growth curve parameters. Data on metatarsal length (MeL) and metatarsal circumference (MeC) were obtained from 471 F2 chickens (generated by crossing broiler sires, derived from a line selected for high abdominal fat, with Baier layer dams) at 4, 6, 8, 10, and 12 weeks of age. Four non-linear models (Gompertz, Logistic, von Bertalanffy, and Brody) were used to fit the MeL and MeC growth curves. Subsequently, the estimated growth curve parameters of the mature MeL or MeC (A), time-scale parameter (b), and maturity rate (K) from the non-linear models were utilized as substitutes for the original bone data in GWAS. The Logistic and Brody models displayed the best goodness-of-fit for MeL and MeC, respectively. Single-trait and multi-trait GWASs based on the growth curve parameters of the Logistic and Brody models revealed 4 618 significant single nucleotide polymorphisms (SNPs), annotated to 332 genes, associated with metatarsal bone traits. The majority of these significant SNPs were located on Gallus gallus chromosome (GGA) 1 (167.433-176.318 Mb), GGA2 (96.791-103.543 Mb), GGA4 (65.003-83.104 Mb) and GGA6 (64.685-95.285 Mb). Notably, we identified 12 novel GWAS loci associated with chicken metatarsal bone traits, encompassing 35 candidate genes. In summary, the combination of single-trait and multi-trait GWASs based on growth curve parameters uncovered numerous genomic regions and candidate genes associated with chicken bone traits. The findings benefit an in-depth understanding of the genetic architecture underlying metatarsal growth and development in chickens.
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Affiliation(s)
- S Z Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, PR China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, PR China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China
| | - M D Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, PR China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, PR China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China
| | - J Y Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, PR China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, PR China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China
| | - M Yuan
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, PR China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, PR China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China
| | - Y D Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, PR China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, PR China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China
| | - P T Luo
- Fujian Sunnzer Biotechnology Development Co. Ltd, Guangze, Fujian Province 354100, PR China
| | - F Xiao
- Fujian Sunnzer Biotechnology Development Co. Ltd, Guangze, Fujian Province 354100, PR China
| | - H Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, PR China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, PR China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China.
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Wang L, Xue Z, Tian Y, Zeng W, Zhang T, Lu H. A single-cell transcriptome atlas of Lueyang black-bone chicken skin. Poult Sci 2024; 103:103513. [PMID: 38350389 PMCID: PMC10875617 DOI: 10.1016/j.psj.2024.103513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/15/2024] Open
Abstract
As the largest organ of the body, the skin participates in various physiological activities, such as barrier function, sensory function, and temperature regulation, thereby maintaining the balance between the body and the natural environment. To date, compositional and transcriptional profiles in chicken skin cells have not been reported. Here, we report detailed transcriptome analyses of cell populations present in the skin of a black-feather chicken and a white-feather chicken using single-cell RNA sequencing (scRNA-seq). By analyzing cluster-specific gene expression profiles, we identified 12 cell clusters, and their corresponding cell types were also characterized. Subsequently, we characterized the subpopulations of keratinocytes, myocytes, mesenchymal cells, fibroblasts, and melanocytes. It is worth noting that we have identified a subpopulation of keratinocytes involved in pigment granule capture and a subpopulation of melanocytes involved in pigment granule deposition, both of which have a higher cell abundance in black-feather chicken compared to white-feather chicken. Meanwhile, we also compared the cellular heterogeneity features of Lueyang black-bone chicken skin with different feather colors. In addition, we also screened out 12 genes those could be potential markers of melanocytes. Finally, we validated the specific expression of SGK1, WNT5A, CTSC, TYR, and LAPTM5 in black-feather chicken, which may be the key candidate genes determining the feather color differentiation of Lueyang black-bone chicken. In summary, this study first revealed the transcriptome characteristics of chicken skin cells via scRNA-seq technology. These datasets provide valuable information for the study of avian skin characteristics and have important implications for future poultry breeding.
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Affiliation(s)
- Ling Wang
- School of Biological Science and Engineering, Shaanxi University of Technology, 723001 Hanzhong, China
- Qinba State Key Laboratory of Biological Resources and Ecological Environment, 723001 Hanzhong, China
- Engineering Research Center of Quality Improvement and Safety Control of Qinba Special Meat Products, Universities of Shaanxi Province, 723001 Hanzhong, China
- QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C., Shaanxi University of Technology, 723001 Hanzhong, China
| | - Zhen Xue
- School of Biological Science and Engineering, Shaanxi University of Technology, 723001 Hanzhong, China
| | - Yingmin Tian
- School of Mathematics and Computer Science, Shaanxi University of Technology, 723001 Hanzhong, China
| | - Wenxian Zeng
- School of Biological Science and Engineering, Shaanxi University of Technology, 723001 Hanzhong, China
- Qinba State Key Laboratory of Biological Resources and Ecological Environment, 723001 Hanzhong, China
- Engineering Research Center of Quality Improvement and Safety Control of Qinba Special Meat Products, Universities of Shaanxi Province, 723001 Hanzhong, China
| | - Tao Zhang
- School of Biological Science and Engineering, Shaanxi University of Technology, 723001 Hanzhong, China
- Qinba State Key Laboratory of Biological Resources and Ecological Environment, 723001 Hanzhong, China
- Engineering Research Center of Quality Improvement and Safety Control of Qinba Special Meat Products, Universities of Shaanxi Province, 723001 Hanzhong, China
- QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C., Shaanxi University of Technology, 723001 Hanzhong, China
| | - Hongzhao Lu
- School of Biological Science and Engineering, Shaanxi University of Technology, 723001 Hanzhong, China
- Qinba State Key Laboratory of Biological Resources and Ecological Environment, 723001 Hanzhong, China
- Engineering Research Center of Quality Improvement and Safety Control of Qinba Special Meat Products, Universities of Shaanxi Province, 723001 Hanzhong, China
- QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C., Shaanxi University of Technology, 723001 Hanzhong, China
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Li R, Li D, Xu S, Zhang P, Zhang Z, He F, Li W, Sun G, Jiang R, Li Z, Tian Y, Liu X, Kang X. Whole-transcriptome sequencing reveals a melanin-related ceRNA regulatory network in the breast muscle of Xichuan black-bone chicken. Poult Sci 2024; 103:103539. [PMID: 38382189 PMCID: PMC10900940 DOI: 10.1016/j.psj.2024.103539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/23/2024] Open
Abstract
The economic losses incurred due to reduced muscle pigmentation highlight the crucial role of melanin-based coloration in the meat of black-bone chickens. Melanogenesis in the breast muscle of black-bone chickens is currently poorly understood in terms of molecular mechanisms. This study employed whole-transcriptome sequencing to analyze black and white breast muscle samples from black-bone chickens, leading to the identification of 367 differentially expressed (DE) mRNAs, 48 DElncRNAs, 104 DEcircRNAs, and 112 DEmiRNAs involved in melanin deposition. Based on these findings, a competitive endogenous RNA (ceRNA) network was developed to better understand the complex mechanisms of melanin deposition. Furthermore, our analysis revealed key DEmRNAs (TYR, DCT, EDNRB, MLPH and OCA2) regulated by DEmiRNAs (gga-miR-140-5p, gga-miR-1682, gga-miR-3529, gga-miR-499-3p, novel-m0012-3p, gga-miR-200b-5p, gga-miR-203a, gga-miR-6651-5p, gga-miR-7455-3p, gga-miR-31-5p, miR-140-x, miR-455-x, novel-m0065-3p, gga-miR-29b-1-5p, miR-455-y, novel-m0085-3p, and gga-miR-196-1-3p). These DEmiRNAs competitively interacted with DElncRNAs including MSTRG.2609.2, MSTRG.4185.1, LOC112530666, LOC112533366, LOC771030, LOC107054724, LOC121107411, LOC100859072, LOC101750037, LOC121108550, LOC121109224, LOC121110876, and LOC101749016, as well as DEcircRNAs, such as novel_circ_000158, novel_circ_000623, novel_001518, and novel_circ_003596. The findings from this study provide insight into the mechanisms that regulate lncRNA, circRNA, miRNA, and mRNA expression in chicken melanin deposition.
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Affiliation(s)
- Ruiting Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China
| | - DongHua Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China.
| | - Shuohui Xu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China
| | - Pengwei Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China
| | - Zhiyuan Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China
| | - Fumin He
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China
| | - Wenting Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China; The Shennong Laboratory, Zhengzhou, 450046, China
| | - Guirong Sun
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China; The Shennong Laboratory, Zhengzhou, 450046, China
| | - Ruirui Jiang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China
| | - Zhuanjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China
| | - Yadong Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China
| | - Xiaojun Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China; The Shennong Laboratory, Zhengzhou, 450046, China
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Qi S, Xu X, Liu L, Wang G, Bao Q, Zhang Y, Zhang Y, Zhang Y, Xu Q, Zhao W, Chen G. The development rule of feathers and application of hair root tissue in sex identification of Yangzhou geese. Poult Sci 2024; 103:103529. [PMID: 38350388 PMCID: PMC10875616 DOI: 10.1016/j.psj.2024.103529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/06/2024] [Accepted: 01/28/2024] [Indexed: 02/15/2024] Open
Abstract
Accurate gender identification is crucial for the study of bird reproduction and evolution. The current study aimed to explore and evaluate the effectiveness of a noninvasive method for gender identification in Yangzhou geese. In this experiment, 600 goose eggs were collected. Hair root tissues were used for PCR amplification, molecular sequencing, and anal inversion for early sex recognition in goslings. According to the DNA amplification results for the feather pulp tissue of 2-wk-old geese, bands appeared at 436 bp (CHD1-Z) and 330 bp (CHD1-W) upon gel electrophoresis. This method considered the base of goose feathers to accelerate the process of gender recognition. By examining the sex of anatomized poultry for verification, the accuracy rate of PCR gel electrophoresis and molecular sequencing sex identification was 100%, whereas the average accuracy rate of anal inversion was 97.41%. In the comparison of feather growth trends at 0 to 18 wk of age, the feather root weight (FRW), feather root length (FRL), feather branch length (FBL), and feather shaft diameter (FSD) of Yangzhou goose of the same age were not significantly different between males and females (P > 0.05). At 6 wk of age, the FRW, FRL, and FSD in males and FRL in females increased rapidly; their growth increased by 84.43, 67.58, 45.10, and 69.42%, respectively. At 10 wk of age, the male FRL, male FBL, and female FBL increased by 37.31, 34.81, and 21.72, respectively. The Boltzmann model was found to be the best-fitting model for the feathers of male Yangzhou geese. Early sex identification based on feather growth trends between the sexes is not feasible. This study provides a convenient and reliable technical means for early sex identification of waterfowl and serves as an ecological strategy for protecting the reproduction of poultry populations.
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Affiliation(s)
- Shangzong Qi
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province 225009, P. R. China
| | - Xinlei Xu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province 225009, P. R. China
| | - Linyu Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province 225009, P. R. China
| | - Guoyao Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province 225009, P. R. China
| | - Qiang Bao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province 225009, P. R. China
| | - Yong Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Jiangsu Yangzhou 225009, China
| | - Yu Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province 225009, P. R. China
| | - Yang Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province 225009, P. R. China
| | - Qi Xu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province 225009, P. R. China
| | - Wenming Zhao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province 225009, P. R. China.
| | - Guohong Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province 225009, P. R. China; Key Laboratory for Evaluation and Utilization of Livestock and Poultry Resources (Poultry), Ministry of Agriculture and Rural Affairs, P.R. China
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Ding Y, Zhang C, Zuo Q, Jin K, Li B. lncCPSET1 acts as a scaffold for MLL2/COMPASS to regulate Bmp4 and promote the formation of chicken primordial germ cells. Mol Genet Genomics 2024; 299:41. [PMID: 38551742 DOI: 10.1007/s00438-024-02127-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 02/15/2024] [Indexed: 04/02/2024]
Abstract
Primordial germ cells (PGCs) are the ancestors of female and male germ cells. Recent studies have shown that long non-coding RNA (lncRNA) and histone methylation are key epigenetic factors affecting PGC formation; however, their joint regulatory mechanisms have rarely been studied. Here, we explored the mechanism by which lncCPSET1 and H3K4me2 synergistically regulate the formation of chicken PGCs for the first time. Combined with chromatin immunoprecipitation (CHIP) sequencing and RNA-seq of PGCs transfected with the lncCPSET1 overexpression vector, GO annotation and KEGG enrichment analysis revealed that Wnt and TGF-β signaling pathways were significantly enriched, and Fzd2, Id1, Id4, and Bmp4 were identified as candidate genes. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) showed that ASH2L, DPY30, WDR5, and RBBP5 overexpression significantly increased the expression of Bmp4, which was up-regulated after lncCPSET1 overexpression as well. It indicated that Bmp4 is a target gene co-regulated by lncCPSET1 and MLL2/COMPASS. Interestingly, co-immunoprecipitation results showed that ASH2L, DPY30 and WDR5 combined and RBBP5 weakly combined with DPY30 and WDR5. lncCPSET1 overexpression significantly increased Dpy30 expression and co-immunoprecipitation showed that interference/overexpression of lncCPSET1 did not affect the binding between the proteins in the complexes, but interference with lncCPSET1 inhibited DPY30 expression, which was confirmed by RNA immunoprecipitation that lncCPSET1 binds to DPY30. Additionally, CHIP-qPCR results showed that DPY30 enriched in the Bmp4 promoter region promoted its transcription, thus promoting the formation of PGCs. This study demonstrated that lncCPSET1 and H3K4me2 synergistically promote PGC formation, providing a reference for the study of the regulatory mechanisms between lncRNA and histone methylation, as well as a molecular basis for elucidating the formation mechanism of PGCs in chickens.
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Affiliation(s)
- Ying Ding
- Key Laboratory of Animal Genetics, Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, 88 South University Ave, Yangzhou, Jiangsu, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Chen Zhang
- Key Laboratory of Animal Genetics, Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, 88 South University Ave, Yangzhou, Jiangsu, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, China
- RNA Medicine Center, International Institutes of Medicine, Zhejiang University, Hangzhou, China
| | - Qisheng Zuo
- Key Laboratory of Animal Genetics, Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, 88 South University Ave, Yangzhou, Jiangsu, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Kai Jin
- Key Laboratory of Animal Genetics, Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, 88 South University Ave, Yangzhou, Jiangsu, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, China
- Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou University, Yangzhou, 225009, China
| | - Bichun Li
- Key Laboratory of Animal Genetics, Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, 88 South University Ave, Yangzhou, Jiangsu, 225009, China.
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, China.
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Bouba I, A. Videla Rodriguez E, Smith VA, van den Brand H, Rodenburg TB, Visser B. A two-step Bayesian network approach to identify key SNPs associated to multiple phenotypic traits in four purebred laying hen lines. PLoS One 2024; 19:e0297533. [PMID: 38547081 PMCID: PMC10977676 DOI: 10.1371/journal.pone.0297533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/08/2024] [Indexed: 04/02/2024] Open
Abstract
When purebred laying hen chicks hatch, they remain at a rearing farm until approximately 17 weeks of age, after which they are transferred to a laying farm. Chicks or pullets are removed from the flocks during these 17 weeks if they display any rearing abnormality. The aim of this study was to investigate associations between single nucleotide polymorphisms (SNPs) and rearing success of 4 purebred White Leghorns layer lines by implementing a Bayesian network approach. Phenotypic traits and SNPs of four purebred genetic White Leghorn layer lines were available for 23,000 rearing batches obtained between 2010 and 2020. Associations between incubation traits (clutch size, embryo mortality), rearing traits (genetic line, first week mortality, rearing abnormalities, natural death, rearing success, pullet flock age, and season) and SNPs were analyzed, using a two-step Bayesian Network (BN) approach. Furthermore, the SNPs were connected to their corresponding genes, which were further explored in bioinformatics databases. BN analysis revealed a total of 28 SNPs associated with some of the traits: ten SNPs were associated with clutch size, another 10 with rearing abnormalities, a single SNP with natural death, and seven SNPs with first week mortality. Exploration via bioinformatics databases showed that one of the SNPs (ENAH) had a protein predicted network composed of 11 other proteins. The major hub of this SNP was CDC42 protein, which has a role in egg production and reproduction. The results highlight the power of BNs in knowledge discovery and how their application in complex biological systems can help getting a deeper understanding of functionality underlying genetic variation of rearing success in laying hens. Improved welfare and production might result from the identified SNPs. Selecting for these SNPs through breeding could reduce stress and increase livability during rearing.
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Affiliation(s)
- Ismalia Bouba
- Hendrix Genetics Research Technology & Services B.v, Hendrix Genetics, Boxmeer, North Brabant, The Netherlands
- Animals in Science and Society, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | | | - V. Anne Smith
- School of Biology, University of St Andrews, St Andrews, Scotland, United Kingdom
| | - Henry van den Brand
- Adaptation Physiology Group, Department of Animal Sciences, Wageningen University & Research, Wageningen, Gelderland, The Netherlands
| | - T. Bas Rodenburg
- Animals in Science and Society, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- Adaptation Physiology Group, Department of Animal Sciences, Wageningen University & Research, Wageningen, Gelderland, The Netherlands
| | - Bram Visser
- Hendrix Genetics Research Technology & Services B.v, Hendrix Genetics, Boxmeer, North Brabant, The Netherlands
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Wang J, Liu J, Lei Q, Liu Z, Han H, Zhang S, Qi C, Liu W, Li D, Li F, Cao D, Zhou Y. Elucidation of the genetic determination of body weight and size in Chinese local chicken breeds by large-scale genomic analyses. BMC Genomics 2024; 25:296. [PMID: 38509464 PMCID: PMC10956266 DOI: 10.1186/s12864-024-10185-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 03/04/2024] [Indexed: 03/22/2024] Open
Abstract
BACKGROUND Body weight and size are important economic traits in chickens. While many growth-related quantitative trait loci (QTLs) and candidate genes have been identified, further research is needed to confirm and characterize these findings. In this study, we investigate genetic and genomic markers associated with chicken body weight and size. This study provides new insights into potential markers for genomic selection and breeding strategies to improve meat production in chickens. METHODS We performed whole-genome resequencing of and Wenshang Barred (WB) chickens (n = 596) and three additional breeds with varying body sizes (Recessive White (RW), WB, and Luxi Mini (LM) chickens; (n = 50)). We then used selective sweeps of mutations coupled with genome-wide association study (GWAS) to identify genomic markers associated with body weight and size. RESULTS We identified over 9.4 million high-quality single nucleotide polymorphisms (SNPs) among three chicken breeds/lines. Among these breeds, 287 protein-coding genes exhibited positive selection in the RW and WB populations, while 241 protein-coding genes showed positive selection in the LM and WB populations. Genomic heritability estimates were calculated for 26 body weight and size traits, including body weight, chest breadth, chest depth, thoracic horn, body oblique length, keel length, pelvic width, shank length, and shank circumference in the WB breed. The estimates ranged from 0.04 to 0.67. Our analysis also identified a total of 2,522 genome-wide significant SNPs, with 2,474 SNPs clustered around two genomic regions. The first region, located on chromosome 4 (7.41-7.64 Mb), was linked to body weight after ten weeks and body size traits. LCORL, LDB2, and PPARGC1A were identified as candidate genes in this region. The other region, located on chromosome 1 (170.46-171.53 Mb), was associated with body weight from four to eighteen weeks and body size traits. This region contained CAB39L and WDFY2 as candidate genes. Notably, LCORL, LDB2, and PPARGC1A showed highly selective signatures among the three breeds of chicken with varying body sizes. CONCLUSION Overall this study provides a comprehensive map of genomic variants associated with body weight and size in chickens. We propose two genomic regions, one on chromosome 1 and the other on chromosome 4, that could helpful for developing genome selection breeding strategies to enhance meat yield in chickens.
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Affiliation(s)
- Jie Wang
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250023, China
- Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, Jinan, Shandong, 250023, China
| | - Jie Liu
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250023, China
- Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, Jinan, Shandong, 250023, China
| | - Qiuxia Lei
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250023, China
- Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, Jinan, Shandong, 250023, China
| | - Zhihe Liu
- Sichuan agricultural university college of animal science and technology, Chengdu, 611130, China
| | - Haixia Han
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250023, China
- Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, Jinan, Shandong, 250023, China
| | - Shuer Zhang
- Shandong Animal Husbandry General Station, Jinan, 250023, China
| | - Chao Qi
- Shandong Animal Husbandry General Station, Jinan, 250023, China
| | - Wei Liu
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250023, China
- Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, Jinan, Shandong, 250023, China
| | - Dapeng Li
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250023, China
- Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, Jinan, Shandong, 250023, China
| | - Fuwei Li
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250023, China
- Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, Jinan, Shandong, 250023, China
| | - Dingguo Cao
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250023, China
- Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, Jinan, Shandong, 250023, China
| | - Yan Zhou
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250023, China.
- Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, Jinan, Shandong, 250023, China.
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Degalez F, Charles M, Foissac S, Zhou H, Guan D, Fang L, Klopp C, Allain C, Lagoutte L, Lecerf F, Acloque H, Giuffra E, Pitel F, Lagarrigue S. Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues. Sci Rep 2024; 14:6588. [PMID: 38504112 PMCID: PMC10951430 DOI: 10.1038/s41598-024-56705-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 03/09/2024] [Indexed: 03/21/2024] Open
Abstract
Gene atlases for livestock are steadily improving thanks to new genome assemblies and new expression data improving the gene annotation. However, gene content varies across databases due to differences in RNA sequencing data and bioinformatics pipelines, especially for long non-coding RNAs (lncRNAs) which have higher tissue and developmental specificity and are harder to consistently identify compared to protein coding genes (PCGs). As done previously in 2020 for chicken assemblies galgal5 and GRCg6a, we provide a new gene atlas, lncRNA-enriched, for the latest GRCg7b chicken assembly, integrating "NCBI RefSeq", "EMBL-EBI Ensembl/GENCODE" reference annotations and other resources such as FAANG and NONCODE. As a result, the number of PCGs increases from 18,022 (RefSeq) and 17,007 (Ensembl) to 24,102, and that of lncRNAs from 5789 (RefSeq) and 11,944 (Ensembl) to 44,428. Using 1400 public RNA-seq transcriptome representing 47 tissues, we provided expression evidence for 35,257 (79%) lncRNAs and 22,468 (93%) PCGs, supporting the relevance of this atlas. Further characterization including tissue-specificity, sex-differential expression and gene configurations are provided. We also identified conserved miRNA-hosting genes with human counterparts, suggesting common function. The annotated atlas is available at gega.sigenae.org.
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Affiliation(s)
- Fabien Degalez
- PEGASE, INRAE, Institut Agro, 35590, Saint Gilles, France
| | - Mathieu Charles
- INRAE, BioinfOmics, GenoToul Bioinformatics facility, Sigenae, Université Fédérale de Toulouse, 31326, Castanet-Tolosan, France
- INRAE, AgroParisTech, GABI, Paris-Saclay University, 78350, Jouy-en-Josas, France
| | - Sylvain Foissac
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | | | - Dailu Guan
- University of California Davis, Davis, USA
| | | | - Christophe Klopp
- INRAE, BioinfOmics, GenoToul Bioinformatics facility, Sigenae, Université Fédérale de Toulouse, 31326, Castanet-Tolosan, France
| | - Coralie Allain
- PEGASE, INRAE, Institut Agro, 35590, Saint Gilles, France
| | | | | | - Hervé Acloque
- INRAE, AgroParisTech, GABI, Paris-Saclay University, 78350, Jouy-en-Josas, France
| | - Elisabetta Giuffra
- INRAE, AgroParisTech, GABI, Paris-Saclay University, 78350, Jouy-en-Josas, France
| | - Frédérique Pitel
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
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48
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Hosseinzadeh S, Hasanpur K. Whole genome discovery of regulatory genes responsible for the response of chicken to heat stress. Sci Rep 2024; 14:6544. [PMID: 38503864 PMCID: PMC10951342 DOI: 10.1038/s41598-024-56757-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 03/11/2024] [Indexed: 03/21/2024] Open
Abstract
Long noncoding RNAs (lncRNAs) are functional bridges connecting the genome with phenotypes by interacting with DNA, mRNA, and proteins. Using publically available acute heat stress (AHS)-related RNA-seq data, we discovered novel lncRNAs and tested their association with AHS along with ~ 8800 known lncRNAs and ~ 28,000 mRNA transcripts. Our pipeline discovered a total of 145 potentially novel-lncRNAs. One of them (Fishcomb_p-value = 0.06) along with another novel transcript (annotated as protein-coding; Fishcomb_p-value = 0.03) were identified as significantly associated with AHS. We found five known-lncRNAs and 134 mRNAs transcripts that were significantly associated with AHS. Four novel lncRNAs interact cis-regulated with 12 mRNA transcripts and are targeted by 11 miRNAs. Also six meta-lncRNAs associate with 134 meta-mRNAs through trans-acting co-expression, each targeted by 15 and 216 miRNAs, respectively. Three of the known-lncRNAs significantly co-expressed with almost 97 of the significant mRNAs (Pearson correlation p-value < 0.05). We report the mentioned three known-lncRNAs (ENSGALT00000099876, ENSGALT00000107573, and ENSGALT00000106323) as the most, significantly regulatory elements of AHS in chicken. It can be concluded that in order to alleviate the adverse effects of AHS on chicken, the manipulation of the three regulatory lncRNAs could lead to a more desirable result than the manipulation of the most significant mRNAs.
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Affiliation(s)
- Sevda Hosseinzadeh
- Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Karim Hasanpur
- Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran.
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Berghof TVL, Bedere N, Peeters K, Poppe M, Visscher J, Mulder HA. The genetics of resilience and its relationships with egg production traits and antibody traits in chickens. Genet Sel Evol 2024; 56:20. [PMID: 38504219 PMCID: PMC10953135 DOI: 10.1186/s12711-024-00888-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 03/06/2024] [Indexed: 03/21/2024] Open
Abstract
BACKGROUND Resilience is the capacity of an animal to be minimally affected by disturbances or to rapidly return to its initial state before exposure to a disturbance. Resilient livestock are desired because of their improved health and increased economic profit. Genetic improvement of resilience may also lead to trade-offs with production traits. Recently, resilience indicators based on longitudinal data have been suggested, but they need further evaluation to determine whether they are indeed predictive of improved resilience, such as disease resilience. This study investigated different resilience indicators based on deviations between expected and observed egg production (EP) by exploring their genetic parameters, their possible trade-offs with production traits, and their relationships with antibody traits in chickens. METHODS Egg production in a nucleus breeding herd environment based on 1-week-, 2-week-, or 3-week-intervals of two purebred chicken lines, a white egg-laying (33,825 chickens) and a brown egg-laying line (34,397 chickens), were used to determine deviations between observed EP and expected average batch EP, and between observed EP and expected individual EP. These deviations were used to calculate three types of resilience indicators for two life periods of each individual: natural logarithm-transformed variance (ln(variance)), skewness, and lag-one autocorrelation (autocorrelation) of deviations from 25 to 83 weeks of age and from 83 weeks of age to end of life. Then, we estimated their genetic correlations with EP traits and with two antibody traits. RESULTS The most promising resilience indicators were those based on 1-week-intervals, as they had the highest heritability estimates (0.02-0.12) and high genetic correlations (above 0.60) with the same resilience indicators based on longer intervals. The three types of resilience indicators differed genetically from each other, which indicates that they possibly capture different aspects of resilience. Genetic correlations of the resilience indicator traits based on 1-week-intervals with EP traits were favorable or zero, which means that trade-off effects were marginal. The resilience indicator traits based on 1-week-intervals also showed no genetic correlations with the antibody traits, which suggests that they are not informative for improved immunity or vice versa in the nucleus environment. CONCLUSIONS This paper gives direction towards the evaluation and implementation of resilience indicators, i.e. to further investigate resilience indicator traits based on 1-week-intervals, in breeding programs for selecting genetically more resilient layer chickens.
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Affiliation(s)
- Tom V L Berghof
- Wageningen University & Research Animal Breeding and Genomics, PO Box 338, 6700 AH, Wageningen, The Netherlands.
- Reproductive Biotechnology, TUM School of Life Sciences, Technical University of Munich, Liesel-Beckmann-Strasse 1, 85354, Freising, Germany.
| | - Nicolas Bedere
- PEGASE, INRAE, Institut Agro, 35590, Saint Gilles, France
| | - Katrijn Peeters
- Hendrix Genetics B.V., P.O. Box 114, 5830 AC, Boxmeer, The Netherlands
| | - Marieke Poppe
- Wageningen University & Research Animal Breeding and Genomics, PO Box 338, 6700 AH, Wageningen, The Netherlands
- CRV B.V., Wassenaarweg 20, Arnhem, The Netherlands
| | - Jeroen Visscher
- Hendrix Genetics B.V., P.O. Box 114, 5830 AC, Boxmeer, The Netherlands
| | - Han A Mulder
- Wageningen University & Research Animal Breeding and Genomics, PO Box 338, 6700 AH, Wageningen, The Netherlands.
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50
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Luo X, Guo J, Zhang J, Ma Z, Li H. Overview of chicken embryo genes related to sex differentiation. PeerJ 2024; 12:e17072. [PMID: 38525278 PMCID: PMC10959104 DOI: 10.7717/peerj.17072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/18/2024] [Indexed: 03/26/2024] Open
Abstract
Sex determination in chickens at an early embryonic stage has been a longstanding challenge in poultry production due to the unique ZZ:ZW sex chromosome system and various influencing factors. This review has summarized the genes related to the sex differentiation of chicken early embryos (mainly Dmrt1, Sox9, Amh, Cyp19a1, Foxl2, Tle4z1, Jun, Hintw, Ube2i, Spin1z, Hmgcs1, Foxd1, Tox3, Ddx4, cHemgn and Serpinb11 in this article), and has found that these contributions enhance our understanding of the genetic basis of sex determination in chickens, while identifying potential gene targets for future research. This knowledge may inform and guide the development of sex screening technologies for hatching eggs and support advancements in gene-editing approaches for chicken embryos. Moreover, these insights offer hope for enhancing animal welfare and promoting conservation efforts in poultry production.
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Affiliation(s)
- Xiaolu Luo
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, Guangdong, China
| | - Jiancheng Guo
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, Guangdong, China
| | - Jiahang Zhang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, Guangdong, China
| | - Zheng Ma
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, Guangdong, China
| | - Hua Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, Guangdong, China
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