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Zimmerman SJ, Aldridge CL, Schroeder MA, Fike JA, Cornman RS, Oyler-McCance SJ. The potential influence of genome-wide adaptive divergence on conservation translocation outcome in an isolated greater sage-grouse population. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2024; 38:e14254. [PMID: 38563102 DOI: 10.1111/cobi.14254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 12/20/2023] [Accepted: 01/20/2024] [Indexed: 04/04/2024]
Abstract
Conservation translocations are an important conservation tool commonly employed to augment declining or reestablish extirpated populations. One goal of augmentation is to increase genetic diversity and reduce the risk of inbreeding depression (i.e., genetic rescue). However, introducing individuals from significantly diverged populations risks disrupting coadapted traits and reducing local fitness (i.e., outbreeding depression). Genetic data are increasingly more accessible for wildlife species and can provide unique insight regarding the presence and retention of introduced genetic variation from augmentation as an indicator of effectiveness and adaptive similarity as an indicator of source and recipient population suitability. We used 2 genetic data sets to evaluate augmentation of isolated populations of greater sage-grouse (Centrocercus urophasianus) in the northwestern region of the species range (Washington, USA) and to retrospectively evaluate adaptive divergence among source and recipient populations. We developed 2 statistical models for microsatellite data to evaluate augmentation outcomes. We used one model to predict genetic diversity after augmentation and compared these predictions with observations of genetic change. We used the second model to quantify the amount of observed reproduction attributed to transplants (proof of population integration). We also characterized genome-wide adaptive divergence among source and recipient populations. Observed genetic diversity (HO = 0.65) was higher in the recipient population than predicted had no augmentation occurred (HO = 0.58) but less than what was predicted by our model (HO = 0.75). The amount of shared genetic variation between the 2 geographically isolated resident populations increased, which is evidence of periodic gene flow previously assumed to be rare. Among candidate adaptive genes associated with elevated fixation index (FST) (143 genes) or local environmental variables (97 and 157 genes for each genotype-environment association method, respectively), we found clusters of genes with related functions that may influence the ability of transplants to use local resources and navigate unfamiliar environments and their reproductive potential, all possible reasons for low genetic retention from augmentation.
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Affiliation(s)
- Shawna J Zimmerman
- Fort Collins Science Center, U.S. Geological Survey, Fort Collins, Colorado, USA
| | - Cameron L Aldridge
- Fort Collins Science Center, U.S. Geological Survey, Fort Collins, Colorado, USA
| | | | - Jennifer A Fike
- Fort Collins Science Center, U.S. Geological Survey, Fort Collins, Colorado, USA
| | - Robert Scott Cornman
- Fort Collins Science Center, U.S. Geological Survey, Fort Collins, Colorado, USA
| | - Sara J Oyler-McCance
- Fort Collins Science Center, U.S. Geological Survey, Fort Collins, Colorado, USA
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2
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Isa AM, Sun Y, Wang Y, Li Y, Yuan J, Ni A, Ma H, Shi L, Tesfay HH, Zong Y, Wang P, Ge P, Chen J. Transcriptome analysis of ovarian tissues highlights genes controlling energy homeostasis and oxidative stress as potential drivers of heterosis for egg number and clutch size in crossbred laying hens. Poult Sci 2024; 103:103163. [PMID: 37980751 PMCID: PMC10684806 DOI: 10.1016/j.psj.2023.103163] [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: 07/18/2023] [Revised: 09/15/2023] [Accepted: 09/29/2023] [Indexed: 11/21/2023] Open
Abstract
Heterosis is the major benefit of crossbreeding and has been exploited in laying hens breeding for a long time. This genetic phenomenon has been linked to various modes of nonadditive gene action. However, the molecular mechanism of heterosis for egg production in laying hens has not been fully elucidated. To fill this research gap, we sequenced mRNAs and lncRNAs of the ovary stroma containing prehierarchical follicles in White Leghorn, Rhode Island Red chickens as well as their reciprocal crossbreds that demonstrated heterosis for egg number and clutch size. We further delineated the modes of mRNAs and lncRNAs expression to identify their potential functions in the observed heterosis. Results showed that dominance was the principal mode of nonadditive expression exhibited by mRNAs and lncRNAs in the prehierarchical follicles of crossbred hens. Specifically, low-parent dominance was the main mode of mRNA expression, while high-parent dominance was the predominant mode of lncRNA expression. Important pathways enriched by genes that showed higher expression in crossbreds compared to either one or both parental lines were cell adhesion molecules, tyrosine and purine metabolism. In contrast, ECM-receptor interaction, focal adhesion, PPAR signaling, and ferroptosis were enriched in genes with lower expression in the crossbred. Protein network interaction identified nonadditively expressed genes including apolipoprotein B (APOB), transferrin, acyl-CoA synthetase medium-chain family member (APOBEC) 3, APOBEC1 complementation factor, and cathepsin S as hub genes. Among these potential hub genes, APOB was the only gene with underdominance expression common to the 2 reciprocal crossbred lines, and has been linked to oxidative stress. LncRNAs with nonadditive expression in the crossbred hens targeted natriuretic peptide receptor 1, epidermal differentiation protein beta, spermatogenesis-associated gene 22, sperm-associated antigen 16, melanocortin 2 receptor, dolichol kinase, glycine amiinotransferase, and prolactin releasing hormone receptor. In conclusion, genes with nonadditive expression in the crossbred may play crucial roles in follicle growth and atresia by improving follicle competence and increasing oxidative stress, respectively. These 2 phenomena could underpin heterosis for egg production in crossbred laying hens.
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Affiliation(s)
- Adamu Mani Isa
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Department of Animal Science, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Yanyan Sun
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yuanmei Wang
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yunlei Li
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jingwei Yuan
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Aixin Ni
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hui Ma
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lei Shi
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hailai Hagos Tesfay
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yunhe Zong
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Panlin Wang
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Pingzhuang Ge
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jilan Chen
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Zuo Q, Gong W, Yao Z, Xia Q, Zhang Y, Li B. Identification of key events and regulatory networks in the formation process of primordial germ cell based on proteomics. J Cell Physiol 2023; 238:610-630. [PMID: 36745473 DOI: 10.1002/jcp.30952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 12/12/2022] [Accepted: 01/09/2023] [Indexed: 02/07/2023]
Abstract
Currently, studies have analyzed the formation mechanism of primordial germ cell (PGC) at the transcriptional level, but few at the protein level, which made the mechanism study of PGC formation not systematic. Here, we screened differential expression proteins (DEPs) regulated PGC formation by label-free proteomics with a novel sampling strategy of embryonic stem cells and PGC. Analysis of DEPs showed that multiple key events were involved, such as the transition from glycolysis to oxidative phosphorylation, activation of autophagy, low DNA methylation ensured the normal formation of PGC, beyond that, protein ubiquitination also played an important role in PGC formation. Importantly, the progression of such events was attributed to the inconsistency between transcription and translation. Interestingly, MAPK, PPAR, Wnt, and JAK signaling pathways not only interact with each other but also interact with different events to participate in the formation of PGC, which formed the PGC regulatory network. According to the regulatory network, the efficiency of PGC formation in induction system can be significantly improved. In conclusion, our results indicate that chicken PGC formation is a complex process involving multiple events and signals, which provide technical support for the specific application in PGC research.
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Affiliation(s)
- Qisheng Zuo
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, P.R. China
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, P.R. China
| | - Wei Gong
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, P.R. China
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, P.R. China
| | - Zeling Yao
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, P.R. China
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, P.R. China
| | - Qian Xia
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, P.R. China
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, P.R. China
| | - Yani Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, P.R. China
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, P.R. China
| | - Bichun Li
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, P.R. China
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, P.R. China
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Ichikawa K, Horiuchi H. Fate Decisions of Chicken Primordial Germ Cells (PGCs): Development, Integrity, Sex Determination, and Self-Renewal Mechanisms. Genes (Basel) 2023; 14:genes14030612. [PMID: 36980885 PMCID: PMC10048776 DOI: 10.3390/genes14030612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/24/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023] Open
Abstract
Primordial germ cells (PGCs) are precursor cells of sperm and eggs. The fate decisions of chicken PGCs in terms of their development, integrity, and sex determination have unique features, thereby providing insights into evolutionary developmental biology. Additionally, fate decisions in the context of a self-renewal mechanism have been applied to establish culture protocols for chicken PGCs, enabling the production of genome-edited chickens and the conservation of genetic resources. Thus, studies on the fate decisions of chicken PGCs have significantly contributed to both academic and industrial development. Furthermore, studies on fate decisions have rapidly advanced owing to the recent development of essential research technologies, such as genome editing and RNA sequencing. Here, we reviewed the status of fate decisions of chicken PGCs and provided insight into other important research issues that require attention.
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Affiliation(s)
- Kennosuke Ichikawa
- Genome Editing Innovation Center, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima 739-0046, Hiroshima, Japan
- Correspondence:
| | - Hiroyuki Horiuchi
- Genome Editing Innovation Center, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima 739-0046, Hiroshima, Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima 739-8528, Hiroshima, Japan
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Do DN, Suravajhala P. Editorial: Role of Non-Coding RNAs in Animals. Animals (Basel) 2023; 13:ani13050805. [PMID: 36899662 PMCID: PMC10000048 DOI: 10.3390/ani13050805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/10/2023] [Accepted: 02/21/2023] [Indexed: 02/25/2023] Open
Abstract
The importance of non-coding RNAs (ncRNAs), such as microRNAs (miRNA), long non-coding RNAs (lncRNA), and circular RNAs (circRNA), in gene regulation is increasingly being appreciated in many species [...].
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Affiliation(s)
- Duy Ngoc Do
- Faculty of Veterinary Medicine, Viet Nam National University of Agriculture, Hanoi 100000, Vietnam
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS B2N 5E3, Canada
- Correspondence: (D.N.D.); (P.S.)
| | - Prashanth Suravajhala
- Bioclues.org, Hyderabad 500072, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana 690525, India
- Correspondence: (D.N.D.); (P.S.)
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Jing Y, Cheng B, Wang H, Bai X, Zhang Q, Wang N, Li H, Wang S. The landscape of the long non-coding RNAs and circular RNAs of the abdominal fat tissues in the chicken lines divergently selected for fatness. BMC Genomics 2022; 23:790. [PMID: 36456907 PMCID: PMC9714206 DOI: 10.1186/s12864-022-09045-y] [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: 06/13/2022] [Accepted: 11/24/2022] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Excessive deposition of abdominal fat poses serious problems in broilers owing to rapid growth. Recently, the evolution of the existing knowledge on long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) have established their indispensable roles in multiple physiological metabolic processes, including adipogenesis and fat deposition. However, not much has been explored on their profiles in the abdominal fat tissues of broilers to date. In the study, we aimed to characterize the vital candidates of lncRNAs and circRNAs and their underlying regulations for abdominal fat deposition in broilers. RESULTS The present study sequenced the lncRNAs and circRNAs expression profiles in the abdominal fat tissues isolated from 7-week-old broilers, who were divergently selected for their fatness. It identified a total of 3359 lncRNAs and 176 circRNAs, demonstrating differential expressed (DE) 30 lncRNAs and 17 circRNAs between the fat- and lean-line broilers (|log2FC| ≥ 1, P < 0.05). Subsequently, the 20 cis-targets and 48 trans-targets of the candidate DE lncRNAs were identified for depositing abdominal fat by adjacent gene analysis and co-expression analysis, respectively. In addition, the functional enrichment analysis showed the DE lncRNAs targets and DE circRNAs host genes to be mainly involved in the cellular processes, amino/fatty acid metabolism, and immune inflammation-related pathways and GO terms. Finally, the vital 16 DE lncRNAs located in cytoplasm and specifically expressed in fat/lean line and their targets were used to construct the lncRNA-miRNA-mRNA competing endogenous RNA (ceRNA) regulatory network, comprising 7 DE lncRNAs, 28 miRNAs, 11 DE mRNAs. Notably, three lncRNAs including XR_001468036.2, XR_003077610.1 and XR_001466431.2 with the most connected degrees might play hub regulatory roles in abdominal fat deposition of broilers. CONCLUSIONS This study characterized the whole expression difference of lncRNAs and circRNAs between the two lines broilers with divergently ability of abdominal fat. The vital candidate DE lncRNAs/circRNAs and ceRNA regulations were identified related to the deposition of abdominal fat in chicken. These results might further improve our understanding of regulating the non-coding RNAs in obesity.
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Affiliation(s)
- Yang Jing
- grid.418524.e0000 0004 0369 6250Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, 150030 People’s Republic of China ,grid.453075.0Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, 150030 People’s Republic of China ,grid.412243.20000 0004 1760 1136College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030 People’s Republic of China
| | - Bohan Cheng
- grid.418524.e0000 0004 0369 6250Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, 150030 People’s Republic of China ,grid.453075.0Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, 150030 People’s Republic of China ,grid.412243.20000 0004 1760 1136College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030 People’s Republic of China
| | - Haoyu Wang
- grid.418524.e0000 0004 0369 6250Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, 150030 People’s Republic of China ,grid.453075.0Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, 150030 People’s Republic of China ,grid.412243.20000 0004 1760 1136College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030 People’s Republic of China
| | - Xue Bai
- grid.418524.e0000 0004 0369 6250Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, 150030 People’s Republic of China ,grid.453075.0Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, 150030 People’s Republic of China ,grid.412243.20000 0004 1760 1136College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030 People’s Republic of China
| | - Qi Zhang
- grid.418524.e0000 0004 0369 6250Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, 150030 People’s Republic of China ,grid.453075.0Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, 150030 People’s Republic of China ,grid.412243.20000 0004 1760 1136College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030 People’s Republic of China
| | - Ning Wang
- grid.418524.e0000 0004 0369 6250Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, 150030 People’s Republic of China ,grid.453075.0Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, 150030 People’s Republic of China ,grid.412243.20000 0004 1760 1136College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030 People’s Republic of China
| | - Hui Li
- grid.418524.e0000 0004 0369 6250Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, 150030 People’s Republic of China ,grid.453075.0Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, 150030 People’s Republic of China ,grid.412243.20000 0004 1760 1136College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030 People’s Republic of China
| | - Shouzhi Wang
- grid.418524.e0000 0004 0369 6250Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, 150030 People’s Republic of China ,grid.453075.0Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, 150030 People’s Republic of China ,grid.412243.20000 0004 1760 1136College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030 People’s Republic of China
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Comparative Transcriptome Analysis Provided a New Insight into the Molecular Mechanisms of Epididymis Regulating Semen Volume in Drakes. Animals (Basel) 2022; 12:ani12213023. [PMID: 36359147 PMCID: PMC9655896 DOI: 10.3390/ani12213023] [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: 09/30/2022] [Revised: 10/29/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
Semen volume is an important factor in artificial insemination (AI) of ducks. In drakes, seminal plasma that is produced by the epididymis determines the semen volume. However, the mechanism of epididymis regulating semen volume of drakes remains unclear. Therefore, the aim of the present study was to preliminarily reveal the mechanism regulating the semen volume through comparing the epididymal histomorphology and mRNA expression profiles between drakes with high-volume semen (HVS) and low-volume semen (LVS). Phenotypically, drakes in the HVS group produced more sperm than drakes in the LVS group. In addition, compared with the HVS group, the ductal square of ductuli conjugentes (DC) and dutus epididymidis (DE) in epididymis was significantly smaller in the LVS group, and the lumenal diameter and epithelial thickness of DC/DE were significantly shorter in the LVS group. In transcriptional regulation, 72 different expression genes (DEGs) were identified from the epididymis between HVS and LVS groups. Gene Ontology (GO) analysis indicated that the DEGs were mainly related to hormone secretion, neurotransmitter synthesis/transport, transmembrane signal transduction, transmembrane transporter activity, and nervous system development (p < 0.05). Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analysis showed that the DEGs were significantly enriched in pathways associated with hormone and neurotransmitter transmission (p < 0.05). In addition, further analysis of the top five pathways enriched by KEGG, nine key candidate genes (including SLC18A2, SNAP25, CACNA1B, GABRG2, DRD3, CAMK2A, NR5A1, and STAR) were identified, which could play a crucial role in the formation of semen. These data provide new insights into the molecular mechanism regulating semen volume of drakes and make feasible the breeding of drakes by semen volume.
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Zuo Q, Jing J, Zhou J, Zhang Y, Wei W, Chen G, Li B. Dual regulatory actions of LncBMP4 on BMP4 promote chicken primordial germ cell formation. EMBO Rep 2022; 23:e52491. [PMID: 34747116 PMCID: PMC8728602 DOI: 10.15252/embr.202152491] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 09/22/2021] [Accepted: 10/18/2021] [Indexed: 01/07/2023] Open
Abstract
The unique characteristics of chicken primordial germ cells (PGCs) provide potential strategies for transgenic animal generation; however, insufficient PGC availability has limited their application. Regulation of bone morphogenic protein 4 (BMP4), a crucial factor for PGCs formation, may provide new strategies for PGC generation. We here identify a long noncoding RNA (lncRNA) that targets BMP4 (LncBMP4). LncBMP4 has similar functions as BMP4, in that it facilitates the formation and migration of PGCs. LncBMP4 promotes BMP4 expression by adsorbing the miRNA gga-mir-12211, thus reducing its inhibitory effect on BMP4 expression. In addition, the small peptide EPC5 encoded by LncBMP4 promotes the transcription of BMP4. The competing endogenous RNA (ceRNA) effect of LncBMP4 requires N6-methyladenosine (m6A) modification, in a dose-dependent manner, and high levels of m6A modification hinder EPC5 translation. Understanding the molecular mechanisms through which LncBMP4 promotes BMP4 expression during PGC formation may provide new avenues for efficient PGC generation.
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Affiliation(s)
- Qisheng Zuo
- Joint International Research Laboratory of Agriculture and Agri‐Product Safety of Ministry of Education of ChinaYangzhou UniversityYangzhouChina
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu ProvinceCollege of Animal Science and TechnologyYangzhou UniversityYangzhouChina
| | - Jin Jing
- Joint International Research Laboratory of Agriculture and Agri‐Product Safety of Ministry of Education of ChinaYangzhou UniversityYangzhouChina
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu ProvinceCollege of Animal Science and TechnologyYangzhou UniversityYangzhouChina
| | - Jing Zhou
- Joint International Research Laboratory of Agriculture and Agri‐Product Safety of Ministry of Education of ChinaYangzhou UniversityYangzhouChina
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu ProvinceCollege of Animal Science and TechnologyYangzhou UniversityYangzhouChina
| | - Yani Zhang
- Joint International Research Laboratory of Agriculture and Agri‐Product Safety of Ministry of Education of ChinaYangzhou UniversityYangzhouChina
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu ProvinceCollege of Animal Science and TechnologyYangzhou UniversityYangzhouChina
| | - Wanhong Wei
- Department of Biological SciencesCollege of Bioscience and BiotechnologyYangzhou UniversityYangzhouChina
| | - Guohong Chen
- Joint International Research Laboratory of Agriculture and Agri‐Product Safety of Ministry of Education of ChinaYangzhou UniversityYangzhouChina
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu ProvinceCollege of Animal Science and TechnologyYangzhou UniversityYangzhouChina
| | - Bichun Li
- Joint International Research Laboratory of Agriculture and Agri‐Product Safety of Ministry of Education of ChinaYangzhou UniversityYangzhouChina
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu ProvinceCollege of Animal Science and TechnologyYangzhou UniversityYangzhouChina
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9
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Long Noncoding RNAs: Recent Insights into Their Role in Male Infertility and Their Potential as Biomarkers and Therapeutic Targets. Int J Mol Sci 2021; 22:ijms222413579. [PMID: 34948376 PMCID: PMC8708977 DOI: 10.3390/ijms222413579] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 12/21/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are composed of nucleotides located in the nucleus and cytoplasm; these are transcribed by RNA polymerase II and are greater than 200 nt in length. LncRNAs fulfill important functions in a variety of biological processes, including genome imprinting, cell differentiation, apoptosis, stem cell pluripotency, X chromosome inactivation and nuclear transport. As high throughput sequencing technology develops, a substantial number of lncRNAs have been found to be related to a variety of biological processes, such as development of the testes, maintaining the self-renewal and differentiation of spermatogonial stem cells, and regulating spermatocyte meiosis. These indicate that lncRNAs can be used as biomarkers and potential therapeutic targets for male infertility. However, only a few comprehensive reviews have described the role of lncRNAs in male reproduction. In this paper, we summarize recent findings relating to the role of lncRNAs in spermatogenesis, their potential as biomarkers for male infertility and the relationship between reproductive arrest and transgenerational effects. Finally, we suggest specific targets for the treatment of male infertility from the perspective of lncRNAs.
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10
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Sun C, Jin K, Zuo Q, Sun H, Song J, Zhang Y, Chen G, Li B. Characterization of Alternative Splicing (AS) Events during Chicken ( Gallus gallus) Male Germ-Line Stem Cell Differentiation with Single-Cell RNA-seq. Animals (Basel) 2021; 11:ani11051469. [PMID: 34065391 PMCID: PMC8160964 DOI: 10.3390/ani11051469] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 12/27/2022] Open
Abstract
Simple Summary Studies have shown that alternative splicing (AS) has been utilized in a wide variety of life processes. However, there are very few studies on AS during germ cell development. In this study, we preliminarily investigated the variation of variable shear events during the formation of chicken germ cells through the RNA-seq data analysis of embryonic stem cells (ESCs), gonad PGCs (gPGCs), and spermatogonia stem cells (SSCs), and the critical AS mode for several crucial stage-specific genes, which were identified during germ cell development. The results of this study lay a theoretical foundation for further analysis of the regulation mechanism of key genes involved in germ cell formation. Abstract Alternative splicing (AS) is a ubiquitous, co-transcriptional, and post-transcriptional regulation mechanism during certain developmental processes, such as germ cell differentiation. A thorough understanding of germ cell differentiation will help us to open new avenues for avian reproduction, stem cell biology, and advances in medicines for human consumption. Here, based on single-cell RNA-seq, we characterized genome-wide AS events in manifold chicken male germ cells: embryonic stem cells (ESCs), gonad primordial germ cells (gPGCs), and spermatogonia stem cells (SSCs). A total of 38,494 AS events from 15,338 genes were detected in ESCs, with a total of 48,955 events from 14,783 genes and 49,900 events from 15,089 genes observed in gPGCs and SSCs, respectively. Moreover, this distribution of AS events suggests the diverse splicing feature of ESCs, gPGCs, and SSCs. Finally, several crucial stage-specific genes, such as NANOG, POU5F3, LIN28B, BMP4, STRA8, and LHX9, were identified in AS events that were transmitted in ESCs, gPGCs, and SSCs. The gene expression results of the RNA-seq data were validated by qRT-PCR. In summary, we provided a comprehensive atlas of the genome-wide scale of the AS event landscape in male chicken germ-line cells and presented its distribution for the first time. This research may someday improve treatment options for men suffering from male infertility.
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Affiliation(s)
- Changhua Sun
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (C.S.); (K.J.); (Q.Z.); (H.S.); (Y.Z.); (G.C.)
- Department of Food Technology, College of Biochemical Engineering, Yangzhou Polytechnic College, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Kai Jin
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (C.S.); (K.J.); (Q.Z.); (H.S.); (Y.Z.); (G.C.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Qisheng Zuo
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (C.S.); (K.J.); (Q.Z.); (H.S.); (Y.Z.); (G.C.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Hongyan Sun
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (C.S.); (K.J.); (Q.Z.); (H.S.); (Y.Z.); (G.C.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Jiuzhou Song
- Animal & Avian Sciences, University of Maryland, College Park, MD 20741, USA;
| | - Yani Zhang
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (C.S.); (K.J.); (Q.Z.); (H.S.); (Y.Z.); (G.C.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Guohong Chen
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (C.S.); (K.J.); (Q.Z.); (H.S.); (Y.Z.); (G.C.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Bichun Li
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (C.S.); (K.J.); (Q.Z.); (H.S.); (Y.Z.); (G.C.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Correspondence:
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