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Sun Y, Li Y, Jiang X, Wu Q, Lin R, Chen H, Zhang M, Zeng T, Tian Y, Xu E, Zhang Y, Lu L. Genome-wide association study identified candidate genes for egg production traits in the Longyan Shan-ma duck. Poult Sci 2024; 103:104032. [PMID: 39003796 DOI: 10.1016/j.psj.2024.104032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/19/2024] [Accepted: 06/22/2024] [Indexed: 07/16/2024] Open
Abstract
Egg production is an important economic trait in layer ducks and understanding the genetics basis is important for their breeding. In this study, a genome-wide association study (GWAS) for egg production traits in 303 female Longyan Shan-ma ducks was performed based on a genotyping-by-sequencing strategy. Sixty-two single nucleotide polymorphisms (SNPs) associated with egg weight traits were identified (P < 9.48 × 10-5), including 8 SNPs at 5% linkage disequilibrium (LD)-based Bonferroni-corrected genome-wide significance level (P < 4.74 × 10-6). One hundred and nineteen SNPs were associated with egg number traits (P < 9.48 × 10-5), including 13 SNPs with 5% LD-based Bonferroni-corrected genome-wide significance (P < 4.74 × 10-6). These SNPs annotated 146 target genes which contained known candidate genes for egg production traits, such as prolactin and prolactin releasing hormone receptor. This study identified that these associated genes were significantly enriched in egg production-related pathways (P < 0.05), such as the oxytocin signaling, MAPK signaling, and calcium signaling pathways. It was notable that 18 genes were differentially expressed in ovarian tissues between higher and lower egg production in Shan-ma ducks. The identified potential candidate genes and pathways provide insight into the genetic basis underlying the egg production trait of layer ducks.
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Affiliation(s)
- Yanfa Sun
- College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, P.R. China
| | - Yan Li
- College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, P.R. China
| | - Xiaobing Jiang
- Fujian Provincial Animal Husbandry Headquarters, Fuzhou, Fujian 350003, P.R. China
| | - Qiong Wu
- College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, P.R. China
| | - Rulong Lin
- Longyan Shan-ma Duck Original Breeding Farm, Agricultural Bureau of Xinluo District, Longyan, 364031, P.R. China
| | - Hongping Chen
- Longyan Shan-ma Duck Original Breeding Farm, Agricultural Bureau of Xinluo District, Longyan, 364031, P.R. China
| | - Min Zhang
- College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, P.R. China
| | - Tao Zeng
- Institute of Animal Science and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, P.R. China
| | - Yong Tian
- Institute of Animal Science and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, P.R. China
| | - Enrong Xu
- College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, P.R. China
| | - Yeqiong Zhang
- College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, P.R. China
| | - Lizhi Lu
- Institute of Animal Science and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, P.R. China..
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Lun X, Shi Y, Wang Y, Zhao N, Liu Q, Meng F, Song X, Wang J, Lu L. Transcriptome analysis of Kunming mice responses to the bite of Xenopsylla cheopis. Parasit Vectors 2024; 17:250. [PMID: 38849919 PMCID: PMC11157846 DOI: 10.1186/s13071-024-06331-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 05/24/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND Flea bites could trigger a series of complex molecular responses in the host. However, our understanding of the responses at the molecular level is still relatively limited. This study quantifies the changes in gene expression in mice after flea bites by RNA sequencing (RNA-seq) from their spleens, revealing the potential biological effects of host response to flea bites. METHODS RNA-seq was used for transcriptome analysis to screen for differentially expressed genes (DEGs) between the control mice group and the flea bite mice group. Gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed on DEGs. Protein-protein interaction (PPI) network analysis on DEGs related to immune processes was performed. Finally, we randomly selected several genes from the screened DEGs to validate the results from the transcriptome data by real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR). RESULTS A total of 521 DEGs were identified, including 277 upregulated and 244 downregulated. There were 258 GO terms significantly enriched by upregulated DEGs and 419 GO terms significantly enriched by downregulated DEGs. Among the upregulated DEGs, 22 GO terms were associated with immune cells (e.g., B cells and T cells) and immune regulatory processes, while among the downregulated DEGs, 58 GO terms were associated with immune cells and immune regulatory processes. Through PPI analysis, we found that CD40 molecules with significantly downregulated expression levels after flea bites may play an important role in host immune regulation. Through KEGG pathway enrichment analysis, a total of 26 significantly enriched KEGG pathways were identified. The RT-qPCR analysis results indicated that the transcriptome sequencing results were reliable. CONCLUSIONS Through in-depth analysis of transcriptome changes in mice caused by flea bites, we revealed that flea bites could stimulate a series of biological and immunological responses in mice. These findings not only provided a deeper understanding of the impact of flea bites on the host but also provided a basis for further research on the interaction between ectoparasites and the host. We believe that digging deeper into the significance of these transcriptome changes will help reveal more about the adaptive response of the host to ectoparasites.
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Affiliation(s)
- Xinchang Lun
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China
| | - Yuan Shi
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China
- School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China
| | - Yiguan Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China
| | - Ning Zhao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China
| | - Qiyong Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China
| | - Fengxia Meng
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China
| | - Xiuping Song
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China
| | - Jun Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China
| | - Liang Lu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China.
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Cammayo-Fletcher PLT, Flores RA, Nguyen BT, Altanzul B, Fernandez-Colorado CP, Kim WH, Devi RM, Kim S, Min W. Identification of Critical Immune Regulators and Potential Interactions of IL-26 in Riemerella anatipestifer-Infected Ducks by Transcriptome Analysis and Profiling. Microorganisms 2024; 12:973. [PMID: 38792803 PMCID: PMC11123779 DOI: 10.3390/microorganisms12050973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/02/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
Riemerella anatipestifer (RA) is an economically important pathogen in the duck industry worldwide that causes high mortality and morbidity in infected birds. We previously found that upregulated IL-17A expression in ducks infected with RA participates in the pathogenesis of the disease, but this mechanism is not linked to IL-23, which primarily promotes Th17 cell differentiation and proliferation. RNA sequencing analysis was used in this study to investigate other mechanisms of IL-17A upregulation in RA infection. A possible interaction of IL-26 and IL-17 was discovered, highlighting the potential of IL-26 as a novel upstream cytokine that can regulate IL-17A during RA infection. Additionally, this process identified several important pathways and genes related to the complex networks and potential regulation of the host immune response in RA-infected ducks. Collectively, these findings not only serve as a roadmap for our understanding of RA infection and the development of new immunotherapeutic approaches for this disease, but they also provide an opportunity to understand the immune system of ducks.
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Affiliation(s)
- Paula Leona T. Cammayo-Fletcher
- College of Veterinary Medicine & Institute of Animal Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea; (P.L.T.C.-F.); (R.A.F.); (B.T.N.); (B.A.); (W.H.K.); (S.K.)
| | - Rochelle A. Flores
- College of Veterinary Medicine & Institute of Animal Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea; (P.L.T.C.-F.); (R.A.F.); (B.T.N.); (B.A.); (W.H.K.); (S.K.)
| | - Binh T. Nguyen
- College of Veterinary Medicine & Institute of Animal Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea; (P.L.T.C.-F.); (R.A.F.); (B.T.N.); (B.A.); (W.H.K.); (S.K.)
| | - Bujinlkham Altanzul
- College of Veterinary Medicine & Institute of Animal Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea; (P.L.T.C.-F.); (R.A.F.); (B.T.N.); (B.A.); (W.H.K.); (S.K.)
| | - Cherry P. Fernandez-Colorado
- Department of Veterinary Paraclinical Sciences, College of Veterinary Medicine, University of the Philippines Los Baños, Los Baños 4031, Philippines;
| | - Woo H. Kim
- College of Veterinary Medicine & Institute of Animal Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea; (P.L.T.C.-F.); (R.A.F.); (B.T.N.); (B.A.); (W.H.K.); (S.K.)
| | - Rajkumari Mandakini Devi
- Department of Veterinary Microbiology, College of Veterinary Sciences & Animal Husbandry, Central Agricultural University (1), Jalukie 797110, India;
| | - Suk Kim
- College of Veterinary Medicine & Institute of Animal Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea; (P.L.T.C.-F.); (R.A.F.); (B.T.N.); (B.A.); (W.H.K.); (S.K.)
| | - Wongi Min
- College of Veterinary Medicine & Institute of Animal Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea; (P.L.T.C.-F.); (R.A.F.); (B.T.N.); (B.A.); (W.H.K.); (S.K.)
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Chang Y, Guo R, Zeng T, Sun H, Tian Y, Han X, Cao Y, Xu L, Duan M, Lu L, Chen L. Analysis of Transcriptomic Differences in the Ovaries of High- and Low-Laying Ducks. Genes (Basel) 2024; 15:181. [PMID: 38397170 PMCID: PMC10887599 DOI: 10.3390/genes15020181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 01/21/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
The egg-laying performance of Shan Ma ducks (Anas Platyrhynchos) is a crucial economic trait. Nevertheless, limited research has been conducted on the egg-laying performance of this species. We examined routine blood indicators and observed higher levels of metabolic and immune-related factors in the high-egg-production group compared with the low-egg-production group. Furthermore, we explored the ovarian transcriptome of both high- and low-egg-production groups of Shan Ma ducks using Illumina NovaSeq 6000 sequencing. A total of 1357 differentially expressed genes (DEGs) were identified, with 686 down-regulated and 671 up-regulated in the high-egg-production (HEP) ducks and low-egg-production (LEP) ducks. Several genes involved in the regulation of ovarian development, including neuropeptide Y (NPY), cell cycle protein-dependent kinase 1 (CDK1), and transcription factor 1 (E2F1), exhibited significant differential expressions at varying stages of egg production. Pathway functional analysis revealed that the DEGs were primarily associated with the steroid biosynthesis pathway, and the neuroactive ligand-receptor interaction pathway exhibited higher activity in the HEP group compared to the LEP group. This study offers valuable information about and novel insights into high egg production.
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Affiliation(s)
- Yuguang Chang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Science & Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.C.); (T.Z.); (H.S.); (Y.T.); (Y.C.); (L.X.); (M.D.); (L.L.)
| | - Rongbing Guo
- College of Animal Sciences and Veterinary Medicine, Zhejiang A&F University, Hangzhou 311300, China;
| | - Tao Zeng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Science & Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.C.); (T.Z.); (H.S.); (Y.T.); (Y.C.); (L.X.); (M.D.); (L.L.)
| | - Hanxue Sun
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Science & Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.C.); (T.Z.); (H.S.); (Y.T.); (Y.C.); (L.X.); (M.D.); (L.L.)
| | - Yong Tian
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Science & Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.C.); (T.Z.); (H.S.); (Y.T.); (Y.C.); (L.X.); (M.D.); (L.L.)
| | - Xue Han
- Institute of Animal Husbandry and Veterinary Science, Guizhou Academy of Agricultural Sciences, Guiyang 550000, China;
| | - Yongqing Cao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Science & Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.C.); (T.Z.); (H.S.); (Y.T.); (Y.C.); (L.X.); (M.D.); (L.L.)
| | - Ligen Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Science & Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.C.); (T.Z.); (H.S.); (Y.T.); (Y.C.); (L.X.); (M.D.); (L.L.)
| | - Mingcai Duan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Science & Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.C.); (T.Z.); (H.S.); (Y.T.); (Y.C.); (L.X.); (M.D.); (L.L.)
| | - Lizhi Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Science & Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.C.); (T.Z.); (H.S.); (Y.T.); (Y.C.); (L.X.); (M.D.); (L.L.)
| | - Li Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Science & Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.C.); (T.Z.); (H.S.); (Y.T.); (Y.C.); (L.X.); (M.D.); (L.L.)
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Zhang L, Xie J, Sun G, Ji R, Li X, Zhang X, Wang J. Identification of differentially expressed genes and signaling pathways in Gaoyou duck ovary at different physiological stages. Front Vet Sci 2023; 10:1190998. [PMID: 37206435 PMCID: PMC10189055 DOI: 10.3389/fvets.2023.1190998] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 04/03/2023] [Indexed: 05/21/2023] Open
Abstract
Introduction Gaoyou duck is famous in China and abroad for its good production of double-yolk eggs. However, there has been no systematic research on the egg-laying characteristics of the Gaoyou duck, which limits the development and utilization of breed resource. Methods To identify the essential genes related to ovarian development, the transcriptome profiles of the ovaries of Gaoyou ducks at different physiological stages were analyzed. The transcriptome profiles of the ovaries of Gaoyou ducks at 150 d (before laying), 240 d (egg laying) and 500 d (nesting) were constructed, and the differentially expressed genes (DEGs) underwent GO (gene ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses. Results The 6 randomly selected DEGs were verified by real-time fluorescent quantitative PCR that their relative expression was consistent with the transcriptional expression profile. Furthermore, KEGG analysis found that 8 candidate signaling pathways were essential for ovarian development, including the MAPK signaling pathway, Progesterone-mediated oocyte maturation, Cell adhesion molecules (CAMs), NOD-like receptor signaling pathway, ECM-receptor interaction, Focal adhesion, TGF-beta signaling path-way and Phagosome. Finally, 5 key DEGs were identified to participate in ovarian development, including TGIF1, TGFBR2, RAF1, PTK2 and FGF10. Discussion Our findings reveal the mechanisms under-lying the molecular regulation of related genes in Gaoyou duck ovarian development.
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