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Li C, Wang X, Li H, Ahmed Z, Luo Y, Qin M, Yang Q, Long Z, Lei C, Yi K. Whole-genome resequencing reveals diversity and selective signals in the Wuxue goat. Anim Genet 2024. [PMID: 38806279 DOI: 10.1111/age.13437] [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: 10/10/2023] [Revised: 04/14/2024] [Accepted: 04/17/2024] [Indexed: 05/30/2024]
Abstract
Animal genetic resources are crucial for ensuring global food security. However, in recent years, a noticeable decline in the genetic diversity of livestock has occurred worldwide. This decline is pronounced in developing countries, where the management of these resources is insufficient. In the current study, we performed whole genome sequencing for 20 Wuxue (WX) and five Guizhou White (GW) goats. Additionally, we utilized the published genomes of 131 samples representing five different goat breeds from various regions in China. We investigated and compared the genetic diversity and selection signatures of WX goats. Whole genome sequencing analysis of the WX and GW populations yielded 120 425 063 SNPs, which resided primarily in intergenic and intron regions. Population genetic structure revealed that WX exhibited genetic resemblance to GW, Chengdu Brown, and Jintang Black and significant differentiation from the other goat breeds. In addition, three methods (nucleotide diversity, linkage disequilibrium decay, and runs of homozygosity) showed moderate genetic diversity in WX goats. We used nucleotide diversity and composite likelihood ratio methods to identify within-breed signatures of positive selection in WX goats. A total of 369 genes were identified using both detection methods, including genes related to reproduction (GRID2, ZNF276, TCF25, and SPIRE2), growth (HMGA2 and GJA3), and immunity (IRF3 and SRSF3). Overall, this study explored the adaptability of WX goats, shedding light on their genetic richness and potential to thrive in challenges posed by climatic changes and diseases. Further investigations are warranted to harness these insights to enhance more efficient and sustainable goat breeding initiatives.
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Affiliation(s)
- Chuanqing Li
- Hunan Institute of Animal and Veterinary Science, Changsha, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xianglin Wang
- Animal Husbandry and Aquatic Products Affairs Center of Xiangxi Autonomous Prefecture, Jishou, China
| | - Haobang Li
- Hunan Institute of Animal and Veterinary Science, Changsha, China
| | - Zulfiqar Ahmed
- Faculty of Veterinary and Animal Sciences, University of Poonch Rawalakot, Rawalakot, Pakistan
| | - Yang Luo
- Hunan Institute of Animal and Veterinary Science, Changsha, China
| | - Mao Qin
- Animal Husbandry and Aquatic Products Affairs Center of Xiangxi Autonomous Prefecture, Jishou, China
| | - Qiong Yang
- Animal Husbandry and Aquatic Products Affairs Center of Xiangxi Autonomous Prefecture, Jishou, China
| | - Zhangcheng Long
- Animal Husbandry and Aquatic Products Affairs Center of Xiangxi Autonomous Prefecture, Jishou, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Kangle Yi
- Hunan Institute of Animal and Veterinary Science, Changsha, China
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Gong Y, Lin Z, Wang Y, Liu Y. Research progress of non-coding RNAs regulation on intramuscular adipocytes in domestic animals. Gene 2023; 860:147226. [PMID: 36736503 DOI: 10.1016/j.gene.2023.147226] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/07/2023] [Accepted: 01/20/2023] [Indexed: 02/05/2023]
Abstract
Intramuscular fat (IMF) is the main determinant of the economic value of domestic animal meat, and has a vital impact on the sensory quality characteristics, while the content of IMF is mainly determined by the size and number of intramuscular adipocytes. In recent years, due to the development of sequencing technology and omics technology, a large number of non-coding RNAs have been identified in intramuscular adipocytes. Non-coding RNAs are a kind of RNA regulatory factors with biological functions but without translation function, which mainly include microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs). These non-coding RNAs regulate the key genes of intramuscular adipocyte growth and development at post-transcriptional level through a variety of regulatory mechanisms, and affect the number and size of intramuscular adipocytes, thus affecting the content of IMF. Here, the review summarizes the candidate non-coding RNAs (miRNAs, lncRNAs, circRNAs) and genes involved in the regulation of intramuscular adipocytes, the related regulation mechanism and signaling pathways, in order to provide reference for further clarifying the molecular regulation mechanism of non-coding RNAs on intramuscular adipocytes in domestic animals.
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Affiliation(s)
- Yanrong Gong
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Zhongzhen Lin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yan Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yiping Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.
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Li S, Zhao Z, Li Q, Li J, Pang Y. Lamprey Wound Healing and Regenerative Effects: The Collaborative Efforts of Diverse Drivers. Int J Mol Sci 2023; 24:ijms24043213. [PMID: 36834626 PMCID: PMC9965152 DOI: 10.3390/ijms24043213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/08/2023] [Accepted: 01/17/2023] [Indexed: 02/10/2023] Open
Abstract
Skin is a natural barrier between the body and the external environment, and this important multifunctional organ plays roles in body temperature regulation, sensory stimulation, mucus secretion, metabolite excretion and immune defense. Lampreys, as ancient vertebrates, rarely experience infection of damaged skin during farming and efficiently promote skin wound healing. However, the mechanism underlying these wound healing and regenerative effects is unclear. Our histology and transcriptomics results demonstrate that lampreys regenerate a nearly complete skin structure in damaged epidermis, including the secretory glands, and will almost not be infected, even if experiencing full-thickness damage. In addition, ATGL, DGL and MGL participate in the lipolysis process to provide space for infiltrating cells. A large number of red blood cells migrate to the site of injury and exert proinflammatory effects, upregulating the expression of proinflammatory factors such as IL-8 and IL-17. Based on a lamprey skin damage healing model, adipocytes and red blood cells in the subcutaneous fat layer can promote wound healing, which provides a new approach for the study of skin healing mechanisms. Transcriptome data reveal that mechanical signal transduction pathways are mainly regulated by focal adhesion kinase and that the actin cytoskeleton plays an important role in the healing of lamprey skin injuries. We identified RAC1 as a key regulatory gene that is necessary and partially sufficient for wound regeneration. Insights into the mechanisms of lamprey skin injury and healing will provide a theoretical basis for overcoming the challenges associated with chronic healing and scar healing in the clinic.
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Affiliation(s)
- Shushen Li
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China
- Lamprey Research Center, Liaoning Normal University, Dalian 116081, China
| | - Zhiyuan Zhao
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China
- Lamprey Research Center, Liaoning Normal University, Dalian 116081, China
| | - Qingwei Li
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China
- Lamprey Research Center, Liaoning Normal University, Dalian 116081, China
| | - Jun Li
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China
- Lamprey Research Center, Liaoning Normal University, Dalian 116081, China
- Correspondence: (J.L.); (Y.P.)
| | - Yue Pang
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China
- Lamprey Research Center, Liaoning Normal University, Dalian 116081, China
- Correspondence: (J.L.); (Y.P.)
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Zhang J, Xia X, Zhu Y, Lian Z, Tian H, Xiao H, Hu Q. Potential antagonistic relationship of fgf9 and rspo1 genes in WNT4 pathway to regulate the sex differentiation in Chinese giant salamander (Andrias davidianus). Front Mol Biosci 2022; 9:974348. [PMID: 36203875 PMCID: PMC9530786 DOI: 10.3389/fmolb.2022.974348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
Farmed chinese giant salamander (Andrias davidianus) was an important distinctive economically amphibian that exhibited male-biased sexual size dimorphism. Fgf9 and rspo1 genes antagonize each other in Wnt4 signal pathway to regulate mammalian gonadal differentiation has been demonstrated. However, their expression profile and function in A. davidianus are unclear. In this study, we firstly characterized fgf9 and rspo1 genes expression in developing gonad. Results showed that fgf9 expression level was higher in testes than in ovaries and increased from 1 to 6 years while rspo1 expression was higher in ovaries than in testes. In situ hybridization assay showed that both fgf9 and rspo1 genes expressed at 62 dpf in undifferentiated gonad, and fgf9 gene was mainly expressed in spermatogonia and sertoli cells in testis while strong positive signal of rspo1 was detected in granular cell in ovary. During sex-reversal, fgf9 expression was significantly higher in reversed testes and normal testes than in ovaries, and opposite expression pattern was detected for rspo1. When FH535 was used to inhibit Wnt/β-catenin pathway, expression of rspo1, wnt4 and β-catenin was down-regulated. Conversely, expression of fgf9, dmrt1, ftz-f1 and cyp17 were up-regulated. Furthermore, when rspo1 and fgf9 were knocked down using RNAi technology, respectively. We observed that female biased genes were down regulated in ovary primordial cells after rspo1 was knocked down, while the opposite expression profile was observed in testis primordial cells after fgf9 was knocked down. These results suggested that fgf9 and rspo1 played an antagonistic role to regulate sex differentiation in the process of the gonadal development and provided a foundation for further functional characterizations. The data also provided basic information for genome editing breeding to improve the Chinese giant salamander farming industry.
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Affiliation(s)
- Jiankang Zhang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Xueping Xia
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Ying Zhu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Zitong Lian
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Haifeng Tian
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Hanbing Xiao
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Qiaomu Hu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
- *Correspondence: Qiaomu Hu,
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Knežić T, Janjušević L, Djisalov M, Yodmuang S, Gadjanski I. Using Vertebrate Stem and Progenitor Cells for Cellular Agriculture, State-of-the-Art, Challenges, and Future Perspectives. Biomolecules 2022; 12:699. [PMID: 35625626 PMCID: PMC9138761 DOI: 10.3390/biom12050699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/01/2022] [Accepted: 05/07/2022] [Indexed: 12/19/2022] Open
Abstract
Global food systems are under significant pressure to provide enough food, particularly protein-rich foods whose demand is on the rise in times of crisis and inflation, as presently existing due to post-COVID-19 pandemic effects and ongoing conflict in Ukraine and resulting in looming food insecurity, according to FAO. Cultivated meat (CM) and cultivated seafood (CS) are protein-rich alternatives for traditional meat and fish that are obtained via cellular agriculture (CA) i.e., tissue engineering for food applications. Stem and progenitor cells are the building blocks and starting point for any CA bioprocess. This review presents CA-relevant vertebrate cell types and procedures needed for their myogenic and adipogenic differentiation since muscle and fat tissue are the primary target tissues for CM/CS production. The review also describes existing challenges, such as a need for immortalized cell lines, or physical and biochemical parameters needed for enhanced meat/fat culture efficiency and ways to address them.
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Affiliation(s)
- Teodora Knežić
- Center for Biosystems, BioSense Institute, University of Novi Sad, Dr. Zorana Djindjica 1, 21000 Novi Sad, Serbia; (T.K.); (L.J.); (M.D.)
| | - Ljiljana Janjušević
- Center for Biosystems, BioSense Institute, University of Novi Sad, Dr. Zorana Djindjica 1, 21000 Novi Sad, Serbia; (T.K.); (L.J.); (M.D.)
| | - Mila Djisalov
- Center for Biosystems, BioSense Institute, University of Novi Sad, Dr. Zorana Djindjica 1, 21000 Novi Sad, Serbia; (T.K.); (L.J.); (M.D.)
| | - Supansa Yodmuang
- Research Affairs, Faculty of Medicine, Chulalongkorn University, 1873 Rama 4 Rd, Pathumwan, Bangkok 10330, Thailand;
| | - Ivana Gadjanski
- Center for Biosystems, BioSense Institute, University of Novi Sad, Dr. Zorana Djindjica 1, 21000 Novi Sad, Serbia; (T.K.); (L.J.); (M.D.)
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Rendon CJ, Flood E, Thompson JM, Chirivi M, Watts SW, Contreras GA. PIEZO1 mechanoreceptor activation reduces adipogenesis in perivascular adipose tissue preadipocytes. Front Endocrinol (Lausanne) 2022; 13:995499. [PMID: 36120469 PMCID: PMC9471253 DOI: 10.3389/fendo.2022.995499] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
During hypertension, vascular remodeling allows the blood vessel to withstand mechanical forces induced by high blood pressure (BP). This process is well characterized in the media and intima layers of the vessel but not in the perivascular adipose tissue (PVAT). In PVAT, there is evidence for fibrosis development during hypertension; however, PVAT remodeling is poorly understood. In non-PVAT depots, mechanical forces can affect adipogenesis and lipogenic stages in preadipocytes. In tissues exposed to high magnitudes of pressure like bone, the activation of the mechanosensor PIEZO1 induces differentiation of progenitor cells towards osteogenic lineages. PVAT's anatomical location continuously exposes it to forces generated by blood flow that could affect adipogenesis in normotensive and hypertensive states. In this study, we hypothesize that activation of PIEZO1 reduces adipogenesis in PVAT preadipocytes. The hypothesis was tested using pharmacological and mechanical activation of PIEZO1. Thoracic aorta PVAT (APVAT) was collected from 10-wk old male SD rats (n=15) to harvest preadipocytes that were differentiated to adipocytes in the presence of the PIEZO1 agonist Yoda1 (10 µM). Mechanical stretch was applied with the FlexCell System at 12% elongation, half-sine at 1 Hz simultaneously during the 4 d of adipogenesis (MS+, mechanical force applied; MS-, no mechanical force used). Yoda1 reduced adipogenesis by 33% compared with CON and, as expected, increased cytoplasmic Ca2+ flux. MS+ reduced adipogenesis efficiency compared with MS-. When Piezo1 expression was blocked with siRNA [siPiezo1; NC=non-coding siRNA], the anti-adipogenic effect of Yoda1 was reversed in siPiezo1 cells but not in NC; in contrast, siPiezo1 did not alter the inhibitory effect of MS+ on adipogenesis. These data demonstrate that PIEZO1 activation in PVAT reduces adipogenesis and lipogenesis and provides initial evidence for an adaptive response to excessive mechanical forces in PVAT during hypertension.
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Affiliation(s)
- C. Javier Rendon
- Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, MI, United States
- *Correspondence: C. Javier Rendon,
| | - Emma Flood
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, United States
| | - Janice M. Thompson
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, United States
| | - Miguel Chirivi
- Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, MI, United States
| | - Stephanie W. Watts
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, United States
| | - G. Andres Contreras
- Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, MI, United States
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