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Jiang N, Lin B, Song L, Tan G, Zhang Z, Yu K. Integrated transcriptome and proteome analyses unravel a series of early defence responses in Sarcandra glabra against Colletotrichum gloeosporioides. FUNCTIONAL PLANT BIOLOGY : FPB 2023; 50:1047-1061. [PMID: 37814360 DOI: 10.1071/fp23084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 09/20/2023] [Indexed: 10/11/2023]
Abstract
Anthracnose caused by Colletotrichum gloeosporioides critically threatens the growth and commercial cultivation of Sarcandra glabra . However, the defence responses and underlying mechanisms remain unclear. Herein, we aimed to investigate the molecular reprogramming in S. glabra leaves infected with C. gloeosporioides . Leaf tissues at 0, 24 and 48h post-inoculation (hpi) were analysed by combining RNA sequencing and Tandem Mass Tag-based liquid chromatography with tandem mass spectrometry. In total, 18 441 and 25 691 differentially expressed genes were identified at 24 and 48hpi compared to 0hpi (uninoculated control), respectively. In addition, 1240 and 1570 differentially abundant proteins were discovered at 24 and 48hpi compared to 0hpi, respectively. Correlation analysis revealed that transcription and translation levels were highly consistent regarding repeatability and expression. Analyses using databases KEGG and iPATH revealed tricitric acid cycle, glycolysis/gluconeogenesis and phenylpropanoid biosynthesis were induced, whereas photosynthesis and tryptophan were suppressed. Enzymatic activity assay results were consistent with the upregulation of defence-related enzymes including superoxide dismutases, catalases, peroxidases and chitinases. The transcriptome expression results were additionally validated by quantitative real-time polymerase chain reaction analyses. This study provides insights into the molecular reprogramming in S. glabra leaves during infection, which lay a foundation for investigating the mechanisms of host-Colletotrichum interactions and breeding disease-resistant plants.
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Affiliation(s)
- Ni Jiang
- College of Agriculture, Guangxi University, Nanning 530004, China; and Guangxi Botanical Garden of Medicinal Plants, Nanning 530023, China
| | - Birun Lin
- College of Agriculture, Guangxi University, Nanning 530004, China; and Guangdong Key Laboratory of High Technology for Plant Protection, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Lisha Song
- Guangxi Botanical Garden of Medicinal Plants, Nanning 530023, China
| | - Guiyu Tan
- Guangxi Botanical Garden of Medicinal Plants, Nanning 530023, China
| | - Zhanjiang Zhang
- Guangxi Botanical Garden of Medicinal Plants, Nanning 530023, China
| | - Kai Yu
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; and Department of Omics Technology, Nanning Current Science Biotechnology Co., Ltd., Nanning 530005, China
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Fu P, Zhang D, Yang C, Yuan X, Luo X, Zheng H, Deng Y, Liu Q, Cui K, Gao F, Shi D. Whole-genome transcriptome and DNA methylation dynamics of pre-implantation embryos reveal progression of embryonic genome activation in buffaloes. J Anim Sci Biotechnol 2023; 14:94. [PMID: 37430306 DOI: 10.1186/s40104-023-00894-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/11/2023] [Indexed: 07/12/2023] Open
Abstract
BACKGROUND During mammalian pre-implantation embryonic development (PED), the process of maternal-to-zygote transition (MZT) is well orchestrated by epigenetic modification and gene sequential expression, and it is related to the embryonic genome activation (EGA). During MZT, the embryos are sensitive to the environment and easy to arrest at this stage in vitro. However, the timing and regulation mechanism of EGA in buffaloes remain obscure. RESULTS Buffalo pre-implantation embryos were subjected to trace cell based RNA-seq and whole-genome bisulfite sequencing (WGBS) to draw landscapes of transcription and DNA-methylation. Four typical developmental steps were classified during buffalo PED. Buffalo major EGA was identified at the 16-cell stage by the comprehensive analysis of gene expression and DNA methylation dynamics. By weighted gene co-expression network analysis, stage-specific modules were identified during buffalo maternal-to-zygotic transition, and key signaling pathways and biological process events were further revealed. Programmed and continuous activation of these pathways was necessary for success of buffalo EGA. In addition, the hub gene, CDK1, was identified to play a critical role in buffalo EGA. CONCLUSIONS Our study provides a landscape of transcription and DNA methylation in buffalo PED and reveals deeply the molecular mechanism of the buffalo EGA and genetic programming during buffalo MZT. It will lay a foundation for improving the in vitro development of buffalo embryos.
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Affiliation(s)
- Penghui Fu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Guangxi Key Laboratory of Animal Breeding and Disease Control, Guangxi University, Nanning, 530004, China
- College of Animal Science and Technology, Southwest University, Chongqing, 402460, China
| | - Du Zhang
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Chunyan Yang
- Guangxi Key Laboratory of Buffalo Genetics, Reproduction and Breeding, Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Science, Nanning, 530001, China
| | - Xiang Yuan
- Guangxi Academy of Medical Sciences and the People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530016, China
| | - Xier Luo
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Haiying Zheng
- Guangxi Key Laboratory of Buffalo Genetics, Reproduction and Breeding, Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Science, Nanning, 530001, China
| | - Yanfei Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Guangxi Key Laboratory of Animal Breeding and Disease Control, Guangxi University, Nanning, 530004, China
| | - Qingyou Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Guangxi Key Laboratory of Animal Breeding and Disease Control, Guangxi University, Nanning, 530004, China
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Kuiqing Cui
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Guangxi Key Laboratory of Animal Breeding and Disease Control, Guangxi University, Nanning, 530004, China
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Fei Gao
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
- Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, DK 1870 C, Frederiksberg, Denmark.
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Guangxi Key Laboratory of Animal Breeding and Disease Control, Guangxi University, Nanning, 530004, China.
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Yu K, Xiao K, Sun QQ, Liu RF, Huang LF, Zhang PF, Xu HY, Lu YQ, Fu Q. Comparative proteomic analysis of seminal plasma exosomes in buffalo with high and low sperm motility. BMC Genomics 2023; 24:8. [PMID: 36624393 PMCID: PMC9830767 DOI: 10.1186/s12864-022-09106-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 12/30/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Exosomes are nanosized membranous vesicles secreted by various types of cells, which facilitate intercellular communication by transporting bioactive compounds. Exosomes are abundant in biological fluids including semen, and their protein composition and the potential of seminal plasma exosomes (SPEs) as fertility biomarkers were elucidated in humans, however, little information is available regarding buffalo (Bubalus bubalis). Here, we examined protein correlation between spermatozoa, seminal plasma (SP), and SPEs, and we compared and analyzed protein differences between high-motility (H-motility) and low-motility (L-motility) SPEs in buffalo. RESULTS SPEs were concentrated and purified by ultracentrifugation combined with sucrose density gradient centrifugation, followed by verification using western blotting, nanoparticle tracking analysis, and transmission electron microscopy. Protein composition in spermatozoa, SP and SPEs, and protein difference in H- and L-motility SPEs were identified by LC-MS/MS proteomic analysis and were functionally analyzed through comprehensive bioinformatics. Many SPEs proteins originated from spermatozoa and SP, and nearly one third were also present in spermatozoa and SP. A series of proteins associated with reproductive processes including sperm capacitation, spermatid differentiation, fertilization, sperm-egg recognition, membrane fusion, and acrosome reaction were integrated in a functional network. Comparative proteomic analyses showed 119 down-regulated and 41 up-regulated proteins in L-motility SPEs, compared with H-motility SPEs. Gene Ontology (GO) enrichment of differentially expressed proteins (DEPs) showed that most differential proteins were located in sperm and vesicles, with activities of hydrolase and metalloproteinase, and were involved in sperm-egg recognition, fertilization, single fertilization, and sperm-zona pellucida binding processes, etc. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that differential proteins were mainly involved in the PPRP signaling pathway, calcium signaling pathway, and cAMP signaling pathway, among others. Furthermore, 6 proteins associated with reproduction were validated by parallel reaction monitoring analysis. CONCLUSION This study provides a comprehensive description of the seminal plasma exosome proteome and may be of use for further screening of biomarkers associated with male infertility.
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Affiliation(s)
- Kai Yu
- grid.256609.e0000 0001 2254 5798State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004 China ,grid.256609.e0000 0001 2254 5798College of Animal Science and Technology, Guangxi University, Nanning, 530004 China
| | - Kai Xiao
- grid.256609.e0000 0001 2254 5798State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004 China ,grid.256609.e0000 0001 2254 5798College of Animal Science and Technology, Guangxi University, Nanning, 530004 China
| | - Qin-qiang Sun
- grid.256609.e0000 0001 2254 5798State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004 China ,grid.256609.e0000 0001 2254 5798College of Animal Science and Technology, Guangxi University, Nanning, 530004 China
| | - Run-feng Liu
- grid.256609.e0000 0001 2254 5798State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004 China ,grid.256609.e0000 0001 2254 5798College of Animal Science and Technology, Guangxi University, Nanning, 530004 China
| | - Liang-feng Huang
- grid.256609.e0000 0001 2254 5798State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004 China ,grid.256609.e0000 0001 2254 5798College of Animal Science and Technology, Guangxi University, Nanning, 530004 China
| | - Peng-fei Zhang
- grid.256609.e0000 0001 2254 5798State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004 China ,grid.256609.e0000 0001 2254 5798College of Animal Science and Technology, Guangxi University, Nanning, 530004 China
| | - Hui-yan Xu
- grid.256609.e0000 0001 2254 5798State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004 China ,grid.256609.e0000 0001 2254 5798College of Animal Science and Technology, Guangxi University, Nanning, 530004 China
| | - Yang-qing Lu
- grid.256609.e0000 0001 2254 5798State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004 China ,grid.256609.e0000 0001 2254 5798College of Animal Science and Technology, Guangxi University, Nanning, 530004 China
| | - Qiang Fu
- grid.256609.e0000 0001 2254 5798State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004 China
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Chen F, Ma B, Lin Y, Luo X, Xu T, Zhang Y, Chen F, Li Y, Zhang Y, Luo B, Zhang Q, Xie X. Comparative maternal protein profiling of mouse biparental and uniparental embryos. Gigascience 2022; 11:6691138. [PMID: 36056732 PMCID: PMC9440387 DOI: 10.1093/gigascience/giac084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/29/2022] [Accepted: 08/01/2022] [Indexed: 12/25/2022] Open
Abstract
Background Maternal proteins have important roles during early embryonic development. However, our understanding of maternal proteins is still very limited. The integrated analysis of mouse uniparental (parthenogenetic) and biparental (fertilized) embryos at the protein level creates a protein expression landscape that can be used to explore preimplantation mouse development. Results Using label-free quantitative mass spectrometry (MS) analysis, we report on the maternal proteome of mouse parthenogenetic embryos at pronucleus, 2-cell, 4-cell, 8-cell, morula, and blastocyst stages and highlight dynamic changes in protein expression. In addition, comparison of proteomic profiles of parthenogenotes and fertilized embryos highlights the different fates of maternal proteins. Enrichment analysis uncovered a set of maternal proteins that are strongly correlated with the subcortical maternal complex, and we report that in parthenogenotes, some of these maternal proteins escape the fate of protein degradation. Moreover, we identified a new maternal factor-Fbxw24, and highlight its importance in early embryonic development. We report that Fbxw24 interacts with Ddb1-Cul4b and may regulate maternal protein degradation in mouse. Conclusions Our study provides an invaluable resource for mechanistic analysis of maternal proteins and highlights the role of the novel maternal factor Fbw24 in regulating maternal protein degradation during preimplantation embryo development.
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Affiliation(s)
- Fumei Chen
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Buguo Ma
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China.,Central Laboratory, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Yongda Lin
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China.,Central Laboratory, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Xin Luo
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Tao Xu
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Yuan Zhang
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Fang Chen
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China.,Central Laboratory, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Yanfei Li
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China.,Central Laboratory, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Yaoyao Zhang
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China.,Central Laboratory, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Bin Luo
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China.,Central Laboratory, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Qingmei Zhang
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China.,Central Laboratory, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Xiaoxun Xie
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China.,Central Laboratory, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
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Huang X, Sun Q, Chen D, Yang W, Zhang J, Liu R, Zhang P, Huang L, Zhang M, Fu Q. Nlrp5 and Tle6 expression patterns in buffalo oocytes and preimplantation embryos. Reprod Domest Anim 2022; 57:481-488. [PMID: 35044003 DOI: 10.1111/rda.14084] [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: 11/26/2021] [Accepted: 01/14/2022] [Indexed: 11/30/2022]
Abstract
Maternal-effect genes (MEGs) accumulate in oocytes during oogenesis and mediate the preimplantation embryo developmental program until activation of the zygote genome. Nlrp5 and Tle6 are required for normal preimplantation and embryonic development. However, the precise function of these MEGs in buffalo (Bubalus bubalis) remains to be elucidated. The aim of this study was to characterize Nlrp5 and Tle6 sequences, and analyze their mRNA and protein expression patterns in somatic tissues, oocytes, and preimplantation embryos of buffalo. The coding sequences of each gene were successfully cloned and characterized. Real-time quantitative reverse transcription PCR results revealed an absence of Nlrp5 or Tle6 transcripts in somatic tissues, with the exception of ovary. Expression levels of Nlrp5 and Tle6 in oocytes increased from the germinal vesicle stage to metaphase II stage, and then gradually decreased during morula and blastocyst stages. Protein expression patterns were confirmed by immunofluorescence analysis. This study lays a foundation for further validation of the function of MEGs in buffalo.
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Affiliation(s)
- Xingchen Huang
- State Key Laboratory of Subtropical Agro-Bioresource Conservation and Utilization, Nanning, Guangxi Province, P. R. China, 530004
| | - Qinqiang Sun
- State Key Laboratory of Subtropical Agro-Bioresource Conservation and Utilization, Nanning, Guangxi Province, P. R. China, 530004
| | - Dongrong Chen
- State Key Laboratory of Subtropical Agro-Bioresource Conservation and Utilization, Nanning, Guangxi Province, P. R. China, 530004
| | - Weihan Yang
- State Key Laboratory of Subtropical Agro-Bioresource Conservation and Utilization, Nanning, Guangxi Province, P. R. China, 530004
| | - Junjun Zhang
- State Key Laboratory of Subtropical Agro-Bioresource Conservation and Utilization, Nanning, Guangxi Province, P. R. China, 530004
| | - Runfeng Liu
- State Key Laboratory of Subtropical Agro-Bioresource Conservation and Utilization, Nanning, Guangxi Province, P. R. China, 530004
| | - Pengfei Zhang
- State Key Laboratory of Subtropical Agro-Bioresource Conservation and Utilization, Nanning, Guangxi Province, P. R. China, 530004
| | - Liangfeng Huang
- State Key Laboratory of Subtropical Agro-Bioresource Conservation and Utilization, Nanning, Guangxi Province, P. R. China, 530004
| | - Ming Zhang
- State Key Laboratory of Subtropical Agro-Bioresource Conservation and Utilization, Nanning, Guangxi Province, P. R. China, 530004
| | - Qiang Fu
- State Key Laboratory of Subtropical Agro-Bioresource Conservation and Utilization, Nanning, Guangxi Province, P. R. China, 530004
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Li X, Zou C, Li M, Fang C, Li K, Liu Z, Li C. Transcriptome Analysis of In Vitro Fertilization and Parthenogenesis Activation during Early Embryonic Development in Pigs. Genes (Basel) 2021; 12:genes12101461. [PMID: 34680856 PMCID: PMC8535918 DOI: 10.3390/genes12101461] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 11/16/2022] Open
Abstract
Parthenogenesis activation (PA), as an important artificial breeding method, can stably preserve the dominant genotype of a species. However, the delayed development of PA embryos is still overly severe and largely leads to pre-implantation failure in pigs. The mechanisms underlying the deficiencies of PA embryos have not been completely understood. For further understanding of the molecular mechanism behind PA embryo failure, we performed transcriptome analysis among pig oocytes (meiosis II, MII) and early embryos at three developmental stages (zygote, morula, and blastocyst) in vitro fertilization (IVF) and PA group. Totally, 11,110 differentially expressed genes (DEGs), 4694 differentially expressed lincRNAs (DELs) were identified, and most DEGs enriched the regulation of apoptotic processes. Through cis- and trans-manner functional prediction, we found that hub lincRNAs were mostly involved in abnormal parthenogenesis embryonic development. In addition, twenty DE imprinted genes showed that some paternally imprinted genes in IVF displayed higher expression than that in PA. Notably, we identified that three DELs of imprinted genes (MEST, PLAGL1, and DIRAS3) were up regulated in IVF, and there was no significant change in PA group. Disordered expression of key genes for embryonic development might play key roles in abnormal parthenogenesis embryonic development. Our study indicates that embryos derived from different production techniques have varied in vitro development to the blastocyst stage, and they also affect the transcription level of corresponding genes, such as imprinted genes. This work will help future research on these genes and molecular-assisted breeding for pig parthenotes.
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Affiliation(s)
- Xin Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China; (X.L.); (C.Z.); (M.L.); (C.F.)
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Cheng Zou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China; (X.L.); (C.Z.); (M.L.); (C.F.)
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Mengxun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China; (X.L.); (C.Z.); (M.L.); (C.F.)
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Chengchi Fang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China; (X.L.); (C.Z.); (M.L.); (C.F.)
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Kui Li
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China;
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal Genetics Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhiguo Liu
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal Genetics Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence: (Z.L.); (C.L.)
| | - Changchun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China; (X.L.); (C.Z.); (M.L.); (C.F.)
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
- Correspondence: (Z.L.); (C.L.)
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7
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Sanchez DJD, Vasconcelos FR, Teles-Filho ACA, Viana AGA, Martins AMA, Sousa MV, Castro MS, Ricart CA, Fontes W, Bertolini M, Bustamante-Filho IC, Moura AA. Proteomic profile of pre-implantational ovine embryos produced in vivo. Reprod Domest Anim 2021; 56:586-603. [PMID: 33460477 DOI: 10.1111/rda.13897] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 01/12/2021] [Accepted: 01/14/2021] [Indexed: 12/11/2022]
Abstract
The present study was conducted to decipher the proteome of in vivo-produced pre-implantation ovine embryos. Ten locally adapted Morana Nova ewes received hormonal treatment and were inseminated 12 hr after ovulation. Six days later, 54 embryos (morula and blastocyst developmental state) were recovered from eight ewes and pooled to obtain sufficient protein for proteomic analysis. Extracted embryo proteins were analysed by LC-MS/MS, followed by identification based on four database searches (PEAKS, Proteome Discoverer software, SearchGUI software, PepExplorer). Identified proteins were analysed for gene ontology terms, protein clusters and interactions. Genes associated with the ovine embryo proteome were screened for miRNA targets using data sets of TargetScan (http://www.targetscan.org) and mIRBase (http://www.mirbase.org) servers. There were 667 proteins identified in the ovine embryos. Biological processes of such proteins were mainly related to cellular process and regulation, and molecular functions, to binding and catalytic activity. Analysis of the embryo proteins revealed 49 enriched functional clusters, linked to energy metabolism (TCA cycle, pyruvate and glycolysis metabolism), zona pellucida (ZP), MAPK signalling pathway, tight junction, binding of sperm to ZP, translation, proteasome, cell cycle and calcium/phospholipid binding. Sixteen miRNAs were related to 25 pre-implantation ovine embryo genes, all conserved in human, bovine and ovine species. The interaction network generated by miRNet showed four key miRNAs (hsa-mir-106b-5p; hsa-mir-30-5p; hsa-mir-103a-5p and hsa-mir-106a-5p) with potential interactions with embryo-expressed genes. Functional analysis of the network indicated that miRNAs modulate genes related to cell cycle, regulation of stem cell and embryonic cell differentiation, among others. Retrieved miRNAs also modulate the expression of genes involved in cell signalling pathways, such as MAPK, Wnt, TGF-beta, p53 and Toll-like receptor. The current study describes the first major proteomic profile of 6-day-old ovine embryos produced in vivo, setting a comprehensive foundation for our understanding of embryo physiology in the ovine species.
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Affiliation(s)
- Deisy J D Sanchez
- Department of Animal Science, Federal University of Ceará, Fortaleza, Brazil
| | - Fabio R Vasconcelos
- Department of Animal Science, Federal University of Ceará, Fortaleza, Brazil
| | | | - Arabela G A Viana
- Department of Animal Science, Federal University of Ceará, Fortaleza, Brazil
| | - Aline M A Martins
- Laboratory of Protein Chemistry and Biochemistry, University of Brasília, Brasília, Brazil
| | - Marcelo V Sousa
- Laboratory of Protein Chemistry and Biochemistry, University of Brasília, Brasília, Brazil
| | - Mariana S Castro
- Laboratory of Protein Chemistry and Biochemistry, University of Brasília, Brasília, Brazil
| | - Carlos A Ricart
- Laboratory of Protein Chemistry and Biochemistry, University of Brasília, Brasília, Brazil
| | - Wagner Fontes
- Laboratory of Protein Chemistry and Biochemistry, University of Brasília, Brasília, Brazil
| | - Marcelo Bertolini
- The School of Veterinay Medicine, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Arlindo A Moura
- Department of Animal Science, Federal University of Ceará, Fortaleza, Brazil
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Yang M, Wang Z, Wang R, Zhang X, Li M, Xin J, Qin Y, Zhang C, Meng F. Transcriptomic and proteomic analyses of the mechanisms of overwintering diapause in soybean pod borer (Leguminivora glycinivorella). PEST MANAGEMENT SCIENCE 2020; 76:4248-4257. [PMID: 32633047 DOI: 10.1002/ps.5989] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 05/24/2020] [Accepted: 07/06/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Soybean pod borer (Leguminivora glycinivorella) is an important soybean pest in north-eastern Asia, whose mature larvae overwinter in a diapause state. Disruption of winter diapause may be a valuable tool in pest management. However, the molecular mechanisms regulating diapause in this species have not yet been elucidated. RESULTS We compared the transcriptomes and proteomes between diapause and mature larvae and between mature and newly developed pupae to identify the genes and proteins associated with diapause. Thirty-seven differentially expressed genes and their proteins changed synchronously between diapause and mature larvae and 82 changed synchronously between diapause larvae and newly developed pupae. Among these, genes involved in fatty acid biosynthesis and the longevity regulating pathway were up-regulated in diapause larvae and down-regulated in newly developed pupae, suggesting that they may regulate diapause. One fatty acid synthase (FAS) gene and two small heat shock genes (HSP19.8 and HSP18.9) were chosen for further functional analysis. After RNA interference (RNAi)-mediated knockdown of FAS, the survival of mature larvae was significantly lower than that of control larvae, but the mean developmental time from first-instar larva to adult remained unchanged. RNAi-mediated knockdown of HSP19.8 and HSP18.9 severely shortened the mean developmental time, causing approximately 50% larvae to develop directly into pupae. CONCLUSION FAS and the small heat shock gene play roles in diapause regulation and larvae survival. This study provides important information that may assist in understanding the molecular regulatory mechanisms of overwintering diapause of this important agricultural insect pest. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Mingyu Yang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Zhanchun Wang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Rui Wang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Xiaoming Zhang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Mingyue Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Junjie Xin
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Yushi Qin
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Chuan Zhang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Fanli Meng
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
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Pu L, Shahzad Q, Chen F, Yao S, Tang Y, Chen D, Yu K, Xie L, Xu H, Zhang M, Lu Y. Proteomic analysis demonstrates that parthenogenetically activated swamp buffalo embryos have dysregulated energy metabolism. Reprod Domest Anim 2020; 55:1764-1773. [PMID: 33031588 DOI: 10.1111/rda.13838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 10/02/2020] [Indexed: 01/06/2023]
Abstract
The comprehensive understanding of early embryo development is essential to optimize in vitro culture conditions. Protein expression landscape of parthenogenetically produced embryo remains unexplored. This study aimed to investigate the protein expression dynamics with a particular focus on energy metabolism throughout the early developmental stages of parthenogenetic buffalo embryos. For this purpose, we performed iTRAQ-based quantitative mass spectrometry and identified 280 proteins common in all stages. A total of 933 proteins were identified during the proteomics analysis. The data depicted that morula and blastocyst had distinct protein expression dynamics as compared to 2- to 16-cell-stage embryo. KEGG pathway analysis showed 23 proteins belonging to energy metabolism appeared in the data. Study of energy metabolism-related protein's expression pattern demonstrated that there was asynchrony in proteins related to glycolysis throughout the examined developmental stages. The expression pattern of pyruvate kinase mutase (PKM), an essential protein of glycolysis, indicated a slightly decreasing trend from 2-cell-stage embryo to blastocyst, and it was supported by expression of proteins involved in lactate production (LDHA and LDHB) suggesting the decreasing rate of aerobic glycolysis (Warburg Effect) at morula and blastocyst stage. The increased Warburg Effect is considered as the hallmark of proliferating cells or embryo at the blastocyst stage. Furthermore, the proteins involved in the citric acid cycle also showed down-regulation at the blastocyst stage, indicating a lesser role of oxidative phosphorylation at this stage. Therefore, it could be divulged from the study that there may be an irregular pattern of energy metabolism in early parthenogenetic embryos. Further studies are recommended to understand this phenomenon.
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Affiliation(s)
- Liping Pu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Qaisar Shahzad
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Fumen Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Shun Yao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Yuyan Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Dongrong Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Kai Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Long Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Huiyan Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Ming Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Yangqing Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
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10
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Genomic Identification, Evolution, and Expression Analysis of Collagen Genes Family in Water Buffalo during Lactation. Genes (Basel) 2020; 11:genes11050515. [PMID: 32384775 PMCID: PMC7288458 DOI: 10.3390/genes11050515] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 04/29/2020] [Accepted: 04/30/2020] [Indexed: 11/17/2022] Open
Abstract
Collagens, as extracellular matrix proteins, support cells for structural integrity and contribute to support mammary basic structure and development. This study aims to perform the genomic identification, evolution, and expression analyses of the collagen gene family in water buffalo (Bubalus bubalis) during lactation. A total of 128 buffalo collagen protein sequences were deduced from the 45 collagen genes identified in silico from buffalo genome, which classified into six groups based on their phylogenetic relationships, conserved motifs, and gene structure analyses. The identified collagen sequences were unequally distributed on 16 chromosomes. The tandem duplicated genes were found within three chromosomes, while only one segmental event occurred between Chr3 and Chr8. Collinearity analysis revealed that a total of 36 collagen gene pairs were orthologous between buffalo and cattle genomes despite having different chromosome numbers. Comparative transcription analyses revealed that a total of 23 orthologous collagen genes were detected in the milk samples at different lactation periods between the two species. Notably, the duplicated gene pair of COL4A1-COL4A2 during lactation had a higher mRNA expression level than that of cattle, while a higher expression level of COL6A1-COL6A2 pair was found in cattle compared with that of buffalo. The present study provides useful information for investigating the potential functions of the collagen family in buffalo during lactation and helps in the functional characterization of collagen genes in additional research.
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Shahzad Q, Pu L, Ahmed Wadood A, Waqas M, Xie L, Shekhar Pareek C, Xu H, Liang X, Lu Y. Proteomics Analysis Reveals that Warburg Effect along with Modification in Lipid Metabolism Improves In Vitro Embryo Development under Low Oxygen. Int J Mol Sci 2020; 21:E1996. [PMID: 32183390 PMCID: PMC7139666 DOI: 10.3390/ijms21061996] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/10/2020] [Accepted: 03/12/2020] [Indexed: 01/13/2023] Open
Abstract
The molecular mechanism regulating embryo development under reduced oxygen tension remains elusive. This study aimed to identify the molecular mechanism impacting embryo development under low oxygen conditions. Buffalo embryos were cultured under 5% or 20% oxygen and were evaluated according to their morphological parameters related to embryo development. The protein profiles of these embryos were compared using iTRAQ-based quantitative proteomics. Physiological O2 (5%) significantly promoted blastocyst yield, hatching rate, embryo quality and cell count as compared to atmospheric O2 (20%). The embryos in the 5% O2 group had an improved hatching rate of cryopreserved blastocysts post-warming (p < 0.05). Comparative proteome profiles of hatched blastocysts cultured under 5% vs. 20% O2 levels identified 43 differentially expressed proteins (DEPs). Functional analysis indicated that DEPs were mainly associated with glycolysis, fatty acid degradation, inositol phosphate metabolism and terpenoid backbone synthesis. Our results suggest that embryos under physiological oxygen had greater developmental potential due to the pronounced Warburg Effect (aerobic glycolysis). Moreover, our proteomic data suggested that higher lipid degradation, an elevated cholesterol level and a higher unsaturated to saturated fatty acid ratio might be involved in the better cryo-survival ability reported in embryos cultured under low oxygen. These data provide new information on the early embryo protein repertoire and general molecular mechanisms of embryo development under varying oxygen levels.
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Affiliation(s)
- Qaisar Shahzad
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, Guangxi 530000, China; (Q.S.); (L.P.); (A.A.W.); (M.W.); (L.X.)
| | - Liping Pu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, Guangxi 530000, China; (Q.S.); (L.P.); (A.A.W.); (M.W.); (L.X.)
| | - Armughan Ahmed Wadood
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, Guangxi 530000, China; (Q.S.); (L.P.); (A.A.W.); (M.W.); (L.X.)
| | - Muhammad Waqas
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, Guangxi 530000, China; (Q.S.); (L.P.); (A.A.W.); (M.W.); (L.X.)
| | - Long Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, Guangxi 530000, China; (Q.S.); (L.P.); (A.A.W.); (M.W.); (L.X.)
| | - Chandra Shekhar Pareek
- Institute of Veterinary Medicine, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, 87-100 Torun, Poland;
- Division of Functional genomics in biological and biomedical research, Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, 87-100 Torun, Poland
| | - Huiyan Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, Guangxi 530000, China; (Q.S.); (L.P.); (A.A.W.); (M.W.); (L.X.)
| | - Xianwei Liang
- Guangxi Key Laboratory of Buffalo Genetics and Breeding, Buffalo Research Institute, Chinese 10 Academy of Agriculture Science, Nanning 530001, China;
| | - Yangqing Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, Guangxi 530000, China; (Q.S.); (L.P.); (A.A.W.); (M.W.); (L.X.)
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12
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Peng R, Wang L, Gao W, Zhu F, Hu F, Zeng W, Shi L, Chen X, Cai J, Zhang D, Xia Z, Yang Z. The 5.8S pre-rRNA maturation factor, M-phase phosphoprotein 6, is a female fertility factor required for oocyte quality and meiosis. Cell Prolif 2020; 53:e12769. [PMID: 32003502 PMCID: PMC7106954 DOI: 10.1111/cpr.12769] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 12/07/2019] [Accepted: 01/04/2020] [Indexed: 11/30/2022] Open
Abstract
OBJECTIVES M-phase phosphoprotein 6 (MPP6) is important for 5.8S pre-rRNA maturation in somatic cells and was screened as a female fertility factor. However, whether MPP6 functions in oocyte meiosis and fertility is not yet known. We aimed to address this. MATERIALS AND METHODS Mouse oocytes with surrounded nucleus (SN) or non-surrounded nucleus (NSN) were used for all experiments. Peptide nanoparticle-mediated antibody transfection was used to deplete MPP6. Immunofluorescence staining, immunohistochemistry and live tracker staining were used to examine MPP6 localization and characterize phenotypes after control or MPP6 depletion. High-fidelity PCR and fluorescence in situ hybridization (FISH) were used to examine the localization and level of 5.8S rRNAs. Western blot was used to examine the protein level. MPP6-EGFP mRNA microinjection was used to do the rescue. RESULTS MPP6 was enriched within ovaries and oocytes. MPP6 depletion significantly impeded oocyte meiosis. MPP6 depletion increased 5.8S pre-rRNA. The mRNA levels of MPP6 and 5.8S rRNA decreased within ageing oocytes, and MPP6 mRNA injection partially increased 5.8S rRNA maturation and improved oocyte quality. CONCLUSIONS MPP6 is required for 5.8S rRNA maturation, meiosis and quality control in mouse oocytes, and MPP6 level might be a marker for oocyte quality.
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Affiliation(s)
- Rui‐Rui Peng
- Center for Reproductive MedicineShandong Provincial Hospital Affiliated to Shandong UniversityJinanChina
- State Key Lab of Reproductive MedicineNanjing Medical UniversityNanjingChina
| | - Li‐Li Wang
- State Key Lab of Reproductive MedicineNanjing Medical UniversityNanjingChina
| | - Wen‐Yi Gao
- State Key Lab of Reproductive MedicineNanjing Medical UniversityNanjingChina
| | - Feng‐Yu Zhu
- State Key Lab of Reproductive MedicineNanjing Medical UniversityNanjingChina
| | - Fan Hu
- State Key Lab of Reproductive MedicineNanjing Medical UniversityNanjingChina
| | - Wen‐Tao Zeng
- Animal Core FacilityNanjing Medical UniversityNanjingChina
| | - Li‐Ya Shi
- The Second Affiliated HospitalNanjing Medical UniversityNanjingChina
| | - Xi‐Chen Chen
- Analysis and Test CenterNanjing Medical UniversityNanjingChina
| | - Jing‐Yang Cai
- State Key Lab of Reproductive MedicineNanjing Medical UniversityNanjingChina
| | - Dong Zhang
- State Key Lab of Reproductive MedicineNanjing Medical UniversityNanjingChina
- Animal Core FacilityNanjing Medical UniversityNanjingChina
| | - Zheng‐Rong Xia
- Analysis and Test CenterNanjing Medical UniversityNanjingChina
| | - Zhi‐Xia Yang
- State Key Lab of Reproductive MedicineNanjing Medical UniversityNanjingChina
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