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Fu Y, Li G, Fu X, Xing S, Zhao ZJ. RNA-Seq Analysis Reveals Altered Expression of Cell Adhesion-Related Genes Following PZR Knockout in Lung Cancer Cells. Appl Biochem Biotechnol 2024; 196:2122-2136. [PMID: 37470934 DOI: 10.1007/s12010-023-04664-x] [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] [Accepted: 07/04/2023] [Indexed: 07/21/2023]
Abstract
Protein zero related (PZR) serves as a substrate and anchor protein for SHP-2, the product of the proto-oncogene PTPN11 that is frequently mutated in cancers. The expression level of PZR is elevated in various cancers, which is correlated with an unfavorable prognosis. The role of PZR in lung cancer is not fully studied. To investigate how PZR affects signaling pathways involved in LUAD development, we utilized the CRISPR technology to knock out PZR expression in SPC-A1 lung adenocarcinoma cells and then conducted RNA sequencing to profile the transcriptome. Our results showed that 226 genes exhibited differential expressions in PZR-knockout SPC-A1 cells vs wild-type cells. Many of the genes encode proteins involved in cell adhesion, migration, actin cytoskeleton organization, and regulation of cell shape. Furthermore, our experimental data showed that PZR-knockout SPC-A1 cells displayed faster attachment to tissue culture dishes and slower detachment from the dishes upon EDTA treatment. The data suggest an important role of PZR in cell-matrix interaction and may provide new insights into the signaling events that regulate cancer development.
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Affiliation(s)
- Ying Fu
- Edmond H. Fischer Signal Transduction Laboratory, School of Life Sciences, Jilin University, Changchun, China
| | - Guodong Li
- Department of Colorectal and Anal Surgery, the Second Hospital, Jilin University, Changchun, China
| | - Xueqi Fu
- Edmond H. Fischer Signal Transduction Laboratory, School of Life Sciences, Jilin University, Changchun, China
| | - Shu Xing
- Edmond H. Fischer Signal Transduction Laboratory, School of Life Sciences, Jilin University, Changchun, China.
| | - Zhizhuang Joe Zhao
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
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2
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Zhang D, Yue Y, Yuan C, An X, Guo T, Chen B, Liu J, Lu Z. DIA-Based Proteomic Analysis Reveals MYOZ2 as a Key Protein Affecting Muscle Growth and Development in Hybrid Sheep. Int J Mol Sci 2024; 25:2975. [PMID: 38474221 DOI: 10.3390/ijms25052975] [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: 12/18/2023] [Revised: 02/12/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
Hybridization of livestock can be used to improve varieties, and different hybrid combinations produce unique breeding effects. In this study, male Southdown and Suffolk sheep were selected to hybridize with female Hu sheep to explore the effects of male parentage on muscle growth and the development of offspring. Using data-independent acquisition technology, we identified 119, 187, and 26 differentially abundant proteins (DAPs) between Hu × Hu (HH) versus Southdown × Hu (NH), HH versus Suffolk × Hu (SH), and NH versus SH crosses. Two DAPs, MYOZ2 and MYOM3, were common to the three hybrid groups and were mainly enriched in muscle growth and development-related pathways. At the myoblast proliferation stage, MYOZ2 expression decreased cell viability and inhibited proliferation. At the myoblast differentiation stage, MYOZ2 expression promoted myoblast fusion and enhanced the level of cell fusion. These findings provide new insights into the key proteins and metabolic pathways involved in the effect of male parentage on muscle growth and the development of hybrid offspring in sheep.
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Affiliation(s)
- Dan Zhang
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Yaojing Yue
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Chao Yuan
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Xuejiao An
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Tingting Guo
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Bowen Chen
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Jianbin Liu
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Zengkui Lu
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
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3
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Shi B, Zhang Z, Lv X, An K, Li L, Xia Z. Screening of Genes Related to Fat Deposition of Pekin Ducks Based on Transcriptome Analysis. Animals (Basel) 2024; 14:268. [PMID: 38254437 PMCID: PMC10812498 DOI: 10.3390/ani14020268] [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: 11/18/2023] [Revised: 01/04/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
Subcutaneous fat deposition is an important index with which to evaluate meat-producing ducks, and affects their meat quality and feed conversion rate. Studying the differentially expressed genes in subcutaneous fat will help to comprehensively understand the potential mechanisms regulating fat deposition in ducks. In this study, 72 Nankou 1 Pekin Ducks and 72 Jingdian Pekin Ducks (half male and half female) at 42 days of age were selected for slaughter performance and transcriptome analysis. The results showed that the breast-muscle yield of Nankou 1 ducks was significantly higher than that of Jingdian ducks, but that the abdominal fat yield and subcutaneous fat yield were higher than that of Jingdian ducks. Thousands of DEGs, including many important genes involved in fat metabolism regulation, were detected by transcriptome. KEGG enrichment analysis showed that the DEGs were significantly enriched on pathways such as regulation of lipolysis in adipocytes, primary bile acid biosynthesis, and biosynthesis of unsaturated fatty acids. SCD, FGF7, LTBP1, PNPLA3, ADCY2, and ACOT8 were selected as candidate genes for regulating subcutaneous fat deposition. The results indicated that Nankou 1 had superior fat deposition ability compared to Jingdian ducks, and that the candidate genes regulated fat deposition by regulating fat synthesis and decomposition.
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Affiliation(s)
- Bozhi Shi
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (B.S.); (Z.Z.); (K.A.)
| | - Ziyue Zhang
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (B.S.); (Z.Z.); (K.A.)
| | - Xueze Lv
- Beijing General Station of Animal Husbandry, Beijing 100107, China;
| | - Keying An
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (B.S.); (Z.Z.); (K.A.)
| | - Lei Li
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650500, China
| | - Zhaofei Xia
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (B.S.); (Z.Z.); (K.A.)
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Patra AK, Dos Santos Ribeiro LP, Yirga H, Puchala R, Goetsch AL. Influence of the concentration and nature of total dissolved solids in brackish groundwater on water intake, nutrient utilization, energy metabolism, ruminal fermentation, and blood constituents in different breeds of mature goats and sheep. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167949. [PMID: 37865254 DOI: 10.1016/j.scitotenv.2023.167949] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 09/29/2023] [Accepted: 10/18/2023] [Indexed: 10/23/2023]
Abstract
Brackish water is being progressively utilized in livestock farming across the globe where freshwater is scarce, potentially leading to detrimental consequences for animal health and performance. This study was conducted to determine effects of different brackish groundwater types on water and feed intake, nutrient utilization, ruminal fluid characteristics, and blood constituent concentrations in different breeds of goats and sheep in a 6 (animal types; AT) × 6 (water treatments; WT) Latin square design. Six AT (Boer, Spanish, and Tennessee Stiff-Leg does and Dorper, Katahdin, and St. Croix ewes) consumed drinking water differing in total dissolved solids (TDS) and mineral composition. Six WT were fresh water (FRW; 287 mg TDS/kg), a natural brackish water (BR) alone (100-BR; 5734 mg TDS/kg), BR with concentrations of all minerals increased by about 100 % (200-BR; 10,603 mg TDS/kg), FRW added with NaCl having similar TDS level (6654 mg/kg) as 100-BR (100-SL), FRW added with NaCl having similar TDS (12,197 mg/kg) as 200-BR (200-SL), and water with similar TDS (10,643 mg/kg) level as 200-BR by adding NaCl to 100-BR (200-BR/SL). Water treatment only affected (P < 0.05) water intake, total volatile fatty acids in ruminal fluid, blood phosphorus, blood aldosterone, and plasma osmolality. Water intake was greater (P < 0.05), but total ruminal volatile fatty acid concentrations were lower (P < 0.05) for 200-SL than other WT. Plasma osmolality and aldosterone concentrations were lower (P < 0.05) for 200-SL and 200-BR/SL than FRW. There were no significant interactions between WT and AT for any variable. Water and feed intake, digestibilities, ruminal ammonia concentration, and methane emission were similar among AT (P > 0.05). There were differences (P < 0.05) among AT for many ruminal fermentation and blood characteristics. Although there were some differences among WT, no AT seemed adversely affected by water with a TDS level near or slightly above 10,000 mg/kg regardless of mineral sources.
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Affiliation(s)
- Amlan Kumar Patra
- American Institute for Goat Research, Langston University, Langston, Oklahoma 73050, USA.
| | | | - Hirut Yirga
- American Institute for Goat Research, Langston University, Langston, Oklahoma 73050, USA
| | - Ryszard Puchala
- American Institute for Goat Research, Langston University, Langston, Oklahoma 73050, USA
| | - Arthur Louis Goetsch
- American Institute for Goat Research, Langston University, Langston, Oklahoma 73050, USA
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Li H, Feng YH, Xia C, Chen Y, Lu XY, Wei Y, Qian LL, Zhu MY, Gao GY, Meng YF, You YL, Tian Q, Liang KQ, Li YT, Lv CT, Rui XY, Wei MY, Zhang B. Physiological and transcriptomic analysis dissects the molecular mechanism governing meat quality during postmortem aging in Hu sheep ( Ovis aries). Front Nutr 2024; 10:1321938. [PMID: 38249602 PMCID: PMC10799347 DOI: 10.3389/fnut.2023.1321938] [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: 10/15/2023] [Accepted: 12/11/2023] [Indexed: 01/23/2024] Open
Abstract
Introduction Hu sheep, known for its high quality and productivity, lack fundamental scientific research in China. Methods This study focused on the effects of 24 h postmortem aging on the meat physiological and transcriptomic alteration in Hu sheep. Results The results showed that the 24 h aging process exerts a substantial influence on the mutton color, texture, and water content as compared to untreated group. Transcriptomic analysis identified 1,668 differentially expressed genes. Functional enrichment analysis highlighted the importance of glycolysis metabolism, protein processing in endoplasmic reticulum, and the FcγR-mediated phagocytosis pathway in mediating meat quality modification following postmortem aging. Furthermore, protein-protein interaction analysis uncovered complex regulatory networks involving glycolysis, the MAPK signaling pathway, protein metabolism, and the immune response. Discussion Collectively, these findings offer valuable insights into the molecular mechanisms underlying meat quality changes during postmortem aging in Hu sheep, emphasizing the potential for improving quality control strategies in mutton production.
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Affiliation(s)
- Huan Li
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Yan-Hui Feng
- College of Food Engineering, Anhui Science and Technology University, Chuzhou, Anhui, China
| | - Chao Xia
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Yu Chen
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Xin-Yi Lu
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Yue Wei
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Le-Le Qian
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Meng-Yao Zhu
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Guo-Yv Gao
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Ya-Fei Meng
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Yv-Le You
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Qi Tian
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Kun-Qi Liang
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Yun-Tao Li
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Chao-Tian Lv
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Xiang-Yun Rui
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Ming-Yue Wei
- School of Ecology, Resources and Environment, Dezhou University, Dezhou, Shandong, China
| | - Bin Zhang
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
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6
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Hosseini SF, Bakhtiarizadeh MR, Salehi A. Meta-analysis of RNA-Seq datasets highlights novel genes/pathways involved in fat deposition in fat-tail of sheep. Front Vet Sci 2023; 10:1159921. [PMID: 37252399 PMCID: PMC10213422 DOI: 10.3389/fvets.2023.1159921] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 04/11/2023] [Indexed: 05/31/2023] Open
Abstract
Introduction Fat-tail in sheep is considered as an important energy reservoir to provide energy as a survival buffer during harsh challenges. However, fat-tail is losing its importance in modern sheep industry systems and thin-tailed breeds are more desirable. Using comparative transcriptome analysis to compare fat-tail tissue between fat- and thin-tailed sheep breeds provides a valuable approach to study the complex genetic factors associated with fat-tail development. However, transcriptomic studies often suffer from issues with reproducibility, which can be improved by integrating multiple studies based on a meta-analysis. Methods Hence, for the first time, an RNA-Seq meta-analysis on sheep fat-tail transcriptomes was performed using six publicly available datasets. Results and discussion A total of 500 genes (221 up-regulated, 279 down-regulated) were identified as differentially expressed genes (DEGs). A jackknife sensitivity analysis confirmed the robustness of the DEGs. Moreover, QTL and functional enrichment analysis reinforced the importance of the DEGs in the underlying molecular mechanisms of fat deposition. Protein-protein interactions (PPIs) network analysis revealed the functional interactions among the DEGs and the subsequent sub-network analysis led to identify six functional sub-networks. According to the results of the network analysis, down-regulated DEGs in green and pink sub-networks (like collagen subunits IV, V, and VI, integrins 1 and 2, SCD, SCD5, ELOVL6, ACLY, SLC27A2, and LPIN1) may impair lipolysis or fatty acid oxidation and cause fat accumulation in tail. On the other hand, up-regulated DEGs, especially those are presented in green and pink sub-networks (like IL6, RBP4, LEPR, PAI-1, EPHX1, HSD11B1, and FMO2), might contribute to a network controlling fat accumulation in the tail of sheep breed through mediating adipogenesis and fatty acid biosynthesis. Our results highlighted a set of known and novel genes/pathways associated with fat-tail development, which could improve the understanding of molecular mechanisms behind fat deposition in sheep fat-tail.
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Hao Z, Jin X, Wang J, Luo Y, Hu J, Liu X, Li S, Zhao F, Li M. Functional differentiation of the ovine preadipocytes -insights from gene expression profiling. Funct Integr Genomics 2023; 23:97. [PMID: 36952056 DOI: 10.1007/s10142-023-01034-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 03/24/2023]
Abstract
The preadipocytes differentiation is a vital process of lipogenesis; exploring the molecular mechanisms of lipogenesis contributes to improve the meat quality and final commercial income. Lipogenesis has been widely reported in other livestock, but little is known about the gene expression profiles at different stages during preadipocytes differentiation in sheep. In this study, ovine preadipocytes were cultured in vitro and then induced to begin differentiation. Then, the gene expression profiles of preadipocytes collected on day 0 (D0), day 2 (D2), and day 8 (D8) of differentiation were analyzed by RNA-seq technology. According to the findings, 2254 differentially expressed genes (DEGs) were found in D2 vs D0; 1817 DEGs and 1902 DEGs were found in D8 vs D0 and D8 vs D2, respectively. The DEGs were found to be enriched in several biological processes, including focal adhesion, ECM-receptor interaction, PI3K-Akt signaling pathway, steroid biosynthesis, and MAPK signaling pathway, according to Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. The regulatory network of the DEGs related to ovine preadipocytes differentiation was systematically constructed, which showed that hub genes might modulate ovine preadipocytes differentiation. In summary, preadipocyte differentiation is regulated by several key genes, including ACACB, CXCL6, SREBF1, INSIG1, APOE, GJA1, CDH11, SYNE1, PCSK1, S100A4, FN1, PLIN2, CXCL6, FN1, PTX3, and FABP3. This study provides a deeper knowledge of the roles of genes in sheep lipogenesis by revealing global gene expression profiles during preadipocyte differentiation.
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Affiliation(s)
- Zhiyun Hao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiayang Jin
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
| | - Jiqing Wang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China.
| | - Yuzhu Luo
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiang Hu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiu Liu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Shaobin Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Fangfang Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Mingna Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
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Miao X, Luo Q, Zhao H, Qin X. Comparison of alternative splicing (AS) events in adipose tissue of polled dorset versus small tail han sheep. Heliyon 2023; 9:e14938. [PMID: 37095997 PMCID: PMC10121611 DOI: 10.1016/j.heliyon.2023.e14938] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 04/03/2023] Open
Abstract
Background During the alternative splicing (AS), the exons of primary transcripts are spliced in various arrangements, resulting in structurally and functionally distinct mRNAs and proteins. This study aimed to examine genes with AS events from Small Tail Han sheep and Dorset sheep to explore the mechanism of adipose developments. Methods This study identified the genes with AS events in adipose tissues of two different sheep with next-generation sequencing. In this paper, genes with significantly different AS events were performed gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Results 364 genes with 411 A S events showed significant differences in adipose tissues between the two breeds; 108 genes with 120 A S events were extremely significant differences between the two breeds. We identified several novel genes that are related with adipose growth and development. The results of KEGG and GO analysis indicated that oocyte meiosis, mitogen-activated protein kinase (Wnt), mitogen-activated protein kinase (MAPK) signaling pathway, etc. Were closely related to the adipose tissue developments. Conclusions This paper revealed that the genes with AS events are important for adipose tissues in sheep, exploring the mechanisms of AS events associated with adipose tissue developments in sheep of different breeds.
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Alsoufi MA, Liu Y, Cao C, Zhao J, Kang J, Li M, Wang K, He Y, Ge C. Integrated Transcriptomics Profiling in Chahua and Digao Chickens' Breast for Assessment Molecular Mechanism of Meat Quality Traits. Genes (Basel) 2022; 14:95. [PMID: 36672833 PMCID: PMC9859260 DOI: 10.3390/genes14010095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/27/2022] [Accepted: 12/02/2022] [Indexed: 12/31/2022] Open
Abstract
Meat quality traits are an important economic trait and remain a major argument, from the producer to the consumer. However, there are a few candidate genes and pathways of chicken meat quality traits that were reported for chicken molecular breeding. The purpose of the present study is to identify the candidate genes and pathways associated with meat quality underlying variations in meat quality. Hence, transcriptome profiles of breast tissue in commercial Digao (DG, 5 male) and Chahua (CH, 5 male) native chicken breeds were analyzed at the age of 100 days. The results found 3525 differentially expressed genes (DEGs) in CH compared to DG with adjusted p-values of ≤0.05 and log2FC ≥ 0.1 FDR ≤ 0.05. Functional analysis of GO showed that the DEGs are mainly involved in the two types of processes of meat quality, such as positive regulation of the metabolic process, extracellular structure organization, collagen trimer, cellular amino acid metabolic process, cellular amino acid catabolic process, and heme binding. Functional analysis of KEGG showed that the DEGs are mainly involved in the two types of processes of meat quality, such as oxidative phosphorylation, carbon metabolism, valine, leucine, and isoleucine degradation, and fatty acid degradation. Many of the DEGs are well known to be related to meat quality, such as COL28A1, COL1A2, MB, HBAD, HBA1, ACACA, ACADL, ACSL1, ATP8A1, CAV1, FADS2, FASN, DCN, CHCHD10, AGXT2, ALDH3A2, and MORN4. Therefore, the current study detected multiple pathways and genes that could be involved in the control of the meat quality traits of chickens. These findings should be used as an essential resource to improve the accuracy of selection for meat traits in chickens using marker-assisted selection based on differentially expressed genes.
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Affiliation(s)
- Mohammed Abdulwahid Alsoufi
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
- Department of Animal Production, Faculty of Agriculture, Sana’a University, Alwehdah Street, Sana’a P.O. Box 19509, Yemen
| | - Yong Liu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Changwei Cao
- Department of Food Science and Engineering, College of Biological Sciences, Southwest Forestry University, Kunming 650224, China
| | - Jinbo Zhao
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Jiajia Kang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Mengyuan Li
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Kun Wang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Yang He
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Changrong Ge
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
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10
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Integrative Analysis of miRNAs Involved in Fat Deposition in Different Pig Breeds. Genes (Basel) 2022; 14:genes14010094. [PMID: 36672834 PMCID: PMC9859024 DOI: 10.3390/genes14010094] [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: 11/19/2022] [Revised: 12/17/2022] [Accepted: 12/20/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND miRNAs are a set of small, noncoding RNAs that bind to partially complementary sequences on target mRNAs. This leads to the post-transcriptional regulation of gene expression. Many studies have shown that microRNAs play critical roles in adipose cell differentiation and fat metabolism. The aim of this study was to explore the regulatory functions of miRNAs in fat deposition for the prevention and therapy of lipid metabolism-related diseases. METHODS The significant differences in the fat deposition of Laiwu (LW) pigs and Large White (LY) pigs were studied. To investigate the genetic relationships of miRNAs that regulate fat deposition, we performed a genome-wide analysis of miRNAs derived from subcutaneous adipose tissue of LW and LY pigs using RNA-seq. RESULTS There were 39 known miRNAs and 56 novel miRNAs significantly differential expressed between the two breeds of pigs. In the analysis of the Gene Ontology and KEGG pathways, predicted targets of these differentially expressed miRNAs were involved in several fat-associated pathways, such as the peroxisome proliferator-activated receptor (PPAR), mitogen-activated protein kinases (MAPK) and Wnt signaling pathways. In addition, ssc-miR-133a-3p, ssc-miR-486 and ssc-miR-1 each had a great impact on the development of porcine subcutaneous fat through the PPAR signaling pathway. CONCLUSIONS We explored the role of differentially expressed miRNAs and studied the mechanisms of adipogenesis and fat deposition between two different pig breeds. In addition, these results also contribute to research relevant to human obesity.
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Yan Z, Feng C, Jin X, Wang F, Liu C, Li N, Qiao Y, Bai Y, Wu F, Giesy JP. Organophosphate esters cause thyroid dysfunction via multiple signaling pathways in zebrafish brain. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2022; 12:100198. [PMID: 36157343 PMCID: PMC9500371 DOI: 10.1016/j.ese.2022.100198] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/01/2022] [Accepted: 06/01/2022] [Indexed: 05/04/2023]
Abstract
Organophosphate esters (OPEs) are widespread in various environmental media, and can disrupt thyroid endocrine signaling pathways. Mechanisms by which OPEs disrupt thyroid hormone (TH) signal transduction are not fully understood. Here, we present in vivo-in vitro-in silico evidence establishing OPEs as environmental THs competitively entering the brain to inhibit growth of zebrafish via multiple signaling pathways. OPEs can bind to transthyretin (TTR) and thyroxine-binding globulin, thereby affecting the transport of TH in the blood, and to the brain by TTR through the blood-brain barrier. When GH3 cells were exposed to OPEs, cell proliferation was significantly inhibited given that OPEs are competitive inhibitors of TH. Cresyl diphenyl phosphate was shown to be an effective antagonist of TH. Chronic exposure to OPEs significantly inhibited the growth of zebrafish by interfering with thyroperoxidase and thyroglobulin to inhibit TH synthesis. Based on comparisons of modulations of gene expression with the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases, signaling pathways related to thyroid endocrine functions, such as receptor-ligand binding and regulation of hormone levels, were identified as being affected by exposure to OPEs. Effects were also associated with the biosynthesis and metabolism of lipids, and neuroactive ligand-receptor interactions. These findings provide a comprehensive understanding of the mechanisms by which OPEs disrupt thyroid pathways in zebrafish.
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Key Words
- AChE, acetylcholinesterase
- ANOVA, analysis of variance
- BCF, bioconcentration factor
- BFR, brominated flame retardant
- CD-FBS, charcoal-dextran-treated fetal bovine serum
- CDP, cresyl diphenyl phosphate
- Competitive inhibition assay
- DEG, differentially expressed gene
- DKA, β-diketone antibiotic
- DMSO, dimethyl sulfoxide
- EAS, estrogen
- FBS, fetal bovine serum
- GAPDH, glyceraldehyde-3-phosphate dehydrogenase
- GO, Gene Ontology
- HPLC-MS/MS, high-performance liquid chromatograph interfaced with a mass spectrometer
- HPT, hypothalamic–pituitary–thyroid
- HS, horse serum
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- MAPK, mitogen-activated protein kinase
- Molecular docking simulation
- NIS, Na+/I− symporter
- OD490, optical density
- OPE, organophosphate ester
- OPFR, organophosphate flame retardant
- Organophosphate ester
- P/S, penicillin–streptomycin
- PBDE, polybrominated diphenyl ether
- PBS, phosphate-buffered saline
- RIC20/50, concentration inhibiting 20%/50%
- T4, thyroxin
- TBG, thyroxine-binding globulin
- TCIPP, tris(2-chloroisopropyl) phosphate
- TDCIPP, tris(1,3-dichloro-2-propyl) phosphate (TDCIPP)
- TDCIPP-d15, tris(1,3-dichloroisopropyl) phosphate-D15
- TG, thyroglobulin
- TH, thyroid hormone
- THR, thyroid hormone receptor
- TIPP, tris(isopropyl) phosphate
- TPHP, triphenyl phosphate
- TPO, thyroperoxidase
- TRβ, thyroid hormone receptor β
- TTR, transthyretin
- Thyroid endocrine function
- Transcriptome sequencing
- androgen, and steroidogenesis
- cga, glycoprotein hormone
- qRT-PCR, quantitative real-time PCR
- tshβa, thyroid-stimulating hormone beta subunit a
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Affiliation(s)
- Zhenfei Yan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
- College of Environment, Hohai University, Nanjing, 210098, China
| | - Chenglian Feng
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
- Corresponding author.
| | - Xiaowei Jin
- China National Environmental Monitoring Centre, Beijing, 100012, China
- Corresponding author.
| | - Fangkun Wang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian, 271018, China
| | - Cong Liu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian, 271018, China
| | - Na Li
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yu Qiao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Yingchen Bai
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Fengchang Wu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
- College of Environment, Hohai University, Nanjing, 210098, China
| | - John P. Giesy
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK, Canada
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Environmental Sciences, Baylor University, Waco, TX, USA
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12
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Kalds P, Zhou S, Gao Y, Cai B, Huang S, Chen Y, Wang X. Genetics of the phenotypic evolution in sheep: a molecular look at diversity-driving genes. Genet Sel Evol 2022; 54:61. [PMID: 36085023 PMCID: PMC9463822 DOI: 10.1186/s12711-022-00753-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 08/29/2022] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND After domestication, the evolution of phenotypically-varied sheep breeds has generated rich biodiversity. This wide phenotypic variation arises as a result of hidden genomic changes that range from a single nucleotide to several thousands of nucleotides. Thus, it is of interest and significance to reveal and understand the genomic changes underlying the phenotypic variation of sheep breeds in order to drive selection towards economically important traits. REVIEW Various traits contribute to the emergence of variation in sheep phenotypic characteristics, including coat color, horns, tail, wool, ears, udder, vertebrae, among others. The genes that determine most of these phenotypic traits have been investigated, which has generated knowledge regarding the genetic determinism of several agriculturally-relevant traits in sheep. In this review, we discuss the genomic knowledge that has emerged in the past few decades regarding the phenotypic traits in sheep, and our ultimate aim is to encourage its practical application in sheep breeding. In addition, in order to expand the current understanding of the sheep genome, we shed light on research gaps that require further investigation. CONCLUSIONS Although significant research efforts have been conducted in the past few decades, several aspects of the sheep genome remain unexplored. For the full utilization of the current knowledge of the sheep genome, a wide practical application is still required in order to boost sheep productive performance and contribute to the generation of improved sheep breeds. The accumulated knowledge on the sheep genome will help advance and strengthen sheep breeding programs to face future challenges in the sector, such as climate change, global human population growth, and the increasing demand for products of animal origin.
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Affiliation(s)
- Peter Kalds
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- Department of Animal and Poultry Production, Faculty of Environmental Agricultural Sciences, Arish University, El-Arish, 45511 Egypt
| | - Shiwei Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100 China
| | - Yawei Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Bei Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Shuhong Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Yulin Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs, Yangling, 712100 China
| | - Xiaolong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs, Yangling, 712100 China
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Liu T, Li F, Wang W, Wang X, Ma Z, Li C, Weng X, Zheng C. Early feeding strategies in lambs affect rumen development and growth performance, with advantages persisting for two weeks after the transition to fattening diets. Front Vet Sci 2022; 9:925649. [PMID: 35968009 PMCID: PMC9366302 DOI: 10.3389/fvets.2022.925649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/04/2022] [Indexed: 11/27/2022] Open
Abstract
This study aimed to explore the effects of early feeding strategies on the growth and rumen development of lambs from pre-weaning to the transition to fattening diets. Ninety-six newborn, male lambs with similar body weights were randomly assigned to three treatments: fed starter at 42 days old + weaned at 56 days old (Ctrl, n = 36), fed starter at 7 days old + weaned at 56 days old (ES, n = 36), and fed starter at 7 days old + weaned at 28 days old (ES + EW, n = 24). The fattening diets of all lambs were gradually replaced from 60 to 70 days of age. Six randomly selected lambs from each treatment were slaughtered at 14, 28, 42, 56, 70, and 84 days of age. The results showed that the richness and diversity of rumen microbiota of lambs in the Ctrl group were distinct from those of lambs in the other groups at 42 days of age. Moreover, transcriptome analysis revealed 407, 219, and 1,211 unique differentially expressed genes (DEGs) in the rumen tissue of ES vs. Ctrl, ES vs. ES + EW, and ES + EW vs. Ctrl groups, respectively, at 42 days of age. Different early feeding strategies resulted in differences in ruminal anatomy, morphology, and fermentation in lambs from 42 to 84 days of age (P < 0.05). Lambs in the ES + EW group had a higher average starter diet intake than those in the other groups (P < 0.05) from 28 to 56 days of age, which affected their growth performance. After 42 days of age, the body and carcass weights of lambs in the ES and ES + EW groups were higher than those in the Ctrl group (P < 0.05). These findings demonstrate that feeding lambs with a starter diet at 7 days of age and weaning them at 28 days of age can promote rumen development and improve growth performance, and this advantage persists for up to 2 weeks after transition to the fattening diet.
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Affiliation(s)
- Ting Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Fadi Li
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Weimin Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xiaojuan Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Zhiyuan Ma
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Chong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiuxiu Weng
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Chen Zheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- *Correspondence: Chen Zheng
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14
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Differential regulation of mRNAs and lncRNAs related to lipid metabolism in Duolang and Small Tail Han sheep. Sci Rep 2022; 12:11157. [PMID: 35778462 PMCID: PMC9249921 DOI: 10.1038/s41598-022-15318-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 06/22/2022] [Indexed: 11/21/2022] Open
Abstract
The function of long non-coding RNA (lncRNA) can be achieved through the regulation of target genes, and the deposition of fat is regulated by lncRNA. Fat has an important effect on meat quality. However, there are relatively few studies on lncRNAs in the subcutaneous adipose tissue of Duolang sheep and Small Tail Han sheep. In this study, RNA-Seq technology and bioinformatics methods were used to identify and analyze the lncRNA and mRNA in the subcutaneous adipose tissue of the two breeds of sheep. The results showed that 107 lnRNAs and 1329 mRNAs were differentially expressed. The differentially expressed genes and lncRNA target genes were significantly enriched in the biosynthesis of unsaturated fatty acids signaling pathway, fatty acid metabolism, adipocyte differentiation and other processes related to fat deposition. Among them, LOC105616076, LOC114118103, LOC105607837, LOC101116622, and LOC105603235 target FADS1, SCD, ELOVL6, HSD17B12 and HACD2, respectively. They play a key regulatory role in the biosynthesis of unsaturated fatty acids. This study lays a foundation for the study of the molecular mechanism of lncRNA on fat development, and has reference value for studying the differences in fat deposition between Duolang sheep and Small Tail Han sheep.
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15
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Yang C, Wang Z, Song Q, Dong B, Bi Y, Bai H, Jiang Y, Chang G, Chen G. Transcriptome Sequencing to Identify Important Genes and lncRNAs Regulating Abdominal Fat Deposition in Ducks. Animals (Basel) 2022; 12:ani12101256. [PMID: 35625102 PMCID: PMC9138122 DOI: 10.3390/ani12101256] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 05/02/2022] [Accepted: 05/10/2022] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Abdominal fat deposition affects the quality of duck meat and the feed conversion ratio. Here, we performed transcriptome sequencing of the abdominal adipose tissue of ducks with high and low abdominal fat rate by RNA sequencing, exploring the key regulatory genes and lncRNAs related to abdominal fat deposition. As a result, several candidate genes, lncRNAs, and pathways related to abdominal fat deposition in ducks were retrieved. This study lays the foundations for exploring molecular mechanisms underlying the regulation of abdominal fat deposition in ducks, providing a theoretical reference for breeding high-quality meat-producing ducks. Abstract Abdominal fat deposition is an important trait in meat-producing ducks. F2 generations of 304 Cherry Valley and Runzhou Crested White ducks were studied to identify genes and lncRNAs affecting abdominal fat deposition. RNA sequencing was used to study abdominal fat tissue of four ducks each with high or low abdominal fat rates. In all, 336 upregulated and 297 downregulated mRNAs, and 95 upregulated and 119 downregulated lncRNAs were identified. Target gene prediction of differentially expressed lncRNAs identified 602 genes that were further subjected to Gene Ontology and KEGG pathway analysis. The target genes were enriched in pathways associated with fat synthesis and metabolism and participated in biological processes, including Linoleic acid metabolism, lipid storage, and fat cell differentiation, indicating that these lncRNAs play an important role in abdominal fat deposition. PPAPA, FOXO3, FASN, PNPLA2, FKBP5, TCF7L2, BMP2, FGF2, LIFR, ZBTB16, SIRT, GYG2, NCOR1, and NR3C1 were involved in the regulation of abdominal fat deposition. PNPLA2, TCF7L2, FGF2, LIFR, BMP2, FKBP5, GYG2, and ZBTB16 were regulated by the lncRNAs TCONS_00038080, TCONS_0033547, TCONS_00066773, XR_001190174.3, XR_003492471.1, XR_003493494.1, XR_001192142.3, XR_002405656.2, XR_002401822.2, XR_003497063.1, and so on. This study lays foundations for exploring molecular mechanisms underlying the regulation of abdominal fat deposition in ducks and provides a theoretical basis for breeding high-quality meat-producing ducks.
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Affiliation(s)
| | - Zhixiu Wang
- Correspondence: (Z.W.); (G.C.); Tel.: +86-514-87997206 (Z.W. & G.C.)
| | | | | | | | | | | | | | - Guohong Chen
- Correspondence: (Z.W.); (G.C.); Tel.: +86-514-87997206 (Z.W. & G.C.)
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16
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Ji C, Liu J, Luo R. Regulatory role of mitochondrial genes in the tenderisation of lamb meat during postmortem ageing. Int J Food Sci Technol 2022. [DOI: 10.1111/ijfs.15678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Chen Ji
- School of Agriculture Ningxia University Yinchuan Ningxia 750021 China
| | - Jijuan Liu
- School of Food and Wine Institute Ningxia University Yinchuan Ningxia 750021 China
| | - Ruiming Luo
- School of Agriculture Ningxia University Yinchuan Ningxia 750021 China
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17
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Shi J, Zhang Q, Song Y, Lei Z, Fu L, Cheng S. Exploring the effects of different male parent crossings on sheep muscles and related regulatory genes using mRNA-Seq. Anim Biosci 2022; 35:1129-1140. [PMID: 34991197 PMCID: PMC9262716 DOI: 10.5713/ab.21.0463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/17/2021] [Indexed: 11/27/2022] Open
Abstract
Objective With improvements in living standards and increase in population globally, the demand for meat products has been increasing; improved meat production from livestock could effectively meet this demand. In this study, we examined the differences in the muscle traits of different male crossbred sheep and attempted to identify key genes that regulate these traits. Methods Dubo sheep × Small-tailed Han sheep (DP×STH) and Suffolk × Small-tailed Han sheep (SFK×STH) were selected to determine meat quality and production performance by Masson staining. Transcriptome sequencing and bioinformatic analysis were performed to identify differentially expressed genes (DEGs) related to meat quality. The presence of DEGs was confirmed by real-time polymerase chain reaction (qPCR). Results The production performance of SFK×STH sheep was better than that of DP×STH sheep, but the meat quality of DP×STH sheep was better than that of SFK×STH sheep. The muscle fiber diameter of DP×STH sheep was smaller than that of SFK×STH sheep. Twenty-two DEGs were identified. Among them, four Gene Ontology terms were related to muscle traits, and three DEGs were related to muscle or muscle fibers. There were no significant differences in the number of single nucleotide mutations and mutation sites in the different male parent cross combinations. Conclusion This study provides genetic resources for future sheep muscle development and cross-breeding research.
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Affiliation(s)
- Jinping Shi
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Quanwei Zhang
- College of Life Science and Biotechnology, Gansu Agricultural University, Lanzhou 730070, China
| | - Yali Song
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Zhaomin Lei
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Lingjuan Fu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Shuru Cheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
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18
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Su XH, He HY, Fang C, Liu LL, Liu WJ. Transcriptome profiling of LncRNAs in sheep tail fat deposition. Anim Biotechnol 2021:1-11. [PMID: 34865605 DOI: 10.1080/10495398.2021.2002882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
LncRNAs have recently received special attention due to their critical role in many important biological processes. There are few reports on its regulatory function in sheep fat deposition. In this study, two sheep populations with different tail types in Xinjiang, Bashibai sheep (fat-tailed) and the hybrid population of Bashibai sheep and wild argali (small-tailed) were selected for whole transcriptome sequencing from their tail tissues. First, 728 differentially expressed LncRNAs of tail fat between Bashibai and F2 sheep were identified by RNA-seq. Second, the tissue expression profile and relative expression difference between Bashibai and F2 sheep of 2 of 728 DE LncRNAs were analyzed by RT-PCR. LncRNA-MSTRG.24995 was highly expressed in tail fat, while lncRNA-MSTRG.36913 was highly expressed in subcutaneous fat. In addition, the expressions of LncRNA-MSTRG.24995 and LncRNA-MSTRG.36913 in tail fat of F2 sheep were significantly lower than that of Bashibai sheep, while those patterns in longissimus dorsi, quadriceps femoris and rumen were reversed. Third, the expression pattern of target genes FASN and THRSP in each tissue was similar with that of corresponding LncRNAs. The LncRNA-MSTRG.24995 directly affects tail fat deposition by FASN gene, while the LncRNA-MSTRG.36913 indirectly affects that by THRSP gene. This will help us to understand molecular mechanism of fat tail deposition from transcriptomic perspectives.
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Affiliation(s)
- Xiao-Hui Su
- Faculty of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Hai-Ying He
- Faculty of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Chao Fang
- Faculty of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Ling-Ling Liu
- Faculty of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Wu-Jun Liu
- Faculty of Animal Science, Xinjiang Agricultural University, Urumqi, China
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19
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Li J, Yang C, Ran J, Yu C, Yin L, Li Z, Liu Y. The age-dependent variations for fatty acid composition and sensory quality of chicken meat and associations between gene expression patterns and meat quality. Livest Sci 2021. [DOI: 10.1016/j.livsci.2021.104736] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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20
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Yuan Z, Ge L, Sun J, Zhang W, Wang S, Cao X, Sun W. Integrative analysis of Iso-Seq and RNA-seq data reveals transcriptome complexity and differentially expressed transcripts in sheep tail fat. PeerJ 2021; 9:e12454. [PMID: 34760406 PMCID: PMC8571958 DOI: 10.7717/peerj.12454] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/18/2021] [Indexed: 01/22/2023] Open
Abstract
Background Nowadays, both customers and producers prefer thin-tailed fat sheep. To effectively breed for this phenotype, it is important to identify candidate genes and uncover the genetic mechanism related to tail fat deposition in sheep. Accumulating evidence suggesting that post-transcriptional modification events of precursor-messenger RNA (pre-mRNA), including alternative splicing (AS) and alternative polyadenylation (APA), may regulate tail fat deposition in sheep. Differentially expressed transcripts (DETs) analysis is a way to identify candidate genes related to tail fat deposition. However, due to the technological limitation, post-transcriptional modification events in the tail fat of sheep and DETs between thin-tailed and fat-tailed sheep remains unclear. Methods In the present study, we applied pooled PacBio isoform sequencing (Iso-Seq) to generate transcriptomic data of tail fat tissue from six sheep (three thin-tailed sheep and three fat-tailed sheep). By comparing with reference genome, potential gene loci and novel transcripts were identified. Post-transcriptional modification events, including AS and APA, and lncRNA in sheep tail fat were uncovered using pooled Iso-Seq data. Combining Iso-Seq data with six RNA-sequencing (RNA-Seq) data, DETs between thin- and fat-tailed sheep were identified. Protein protein interaction (PPI) network, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were implemented to investigate the potential functions of DETs. Results In the present study, we revealed the transcriptomic complexity of the tail fat of sheep, result in 9,001 potential novel gene loci, 17,834 AS events, 5,791 APA events, and 3,764 lncRNAs. Combining Iso-Seq data with RNA-Seq data, we identified hundreds of DETs between thin- and fat-tailed sheep. Among them, 21 differentially expressed lncRNAs, such as ENSOART00020036299, ENSOART00020033641, ENSOART00020024562, ENSOART00020003848 and 9.53.1 may regulate tail fat deposition. Many novel transcripts were identified as DETs, including 15.527.13 (DGAT2), 13.624.23 (ACSS2), 11.689.28 (ACLY), 11.689.18 (ACLY), 11.689.14 (ACLY), 11.660.12 (ACLY), 22.289.6 (SCD), 22.289.3 (SCD) and 22.289.14 (SCD). Most of the identified DETs have been enriched in GO and KEGG pathways related to extracellular matrix (ECM). Our result revealed the transcriptome complexity and identified many candidate transcripts in tail fat, which could enhance the understanding of molecular mechanisms behind tail fat deposition.
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Affiliation(s)
- Zehu Yuan
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Ling Ge
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jingyi Sun
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Weibo Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Shanhe Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Xiukai Cao
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Wei Sun
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China.,College of Animal Science and Technology, Yangzhou University, Yangzhou, China
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21
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Li J, Yang C, Ren P, Lin Z, Zhang D, Jiang X, Wang L, Liu Y. Transcriptomics analysis of Daheng broilers reveals that PLIN2 regulates chicken preadipocyte proliferation, differentiation and apoptosis. Mol Biol Rep 2021; 48:7985-7997. [PMID: 34716501 DOI: 10.1007/s11033-021-06831-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/20/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Intramuscular fat content, an important meat quality trait, strongly affects flavor, juiciness, and tenderness. Sex hormones regulate lipid metabolism, and female hormones stimulate fat deposition, thereby making the female chickens always fatter than males. In this study, the effect of sex on IMF deposition was screened following transcriptomics in chickens. METHODS AND RESULTS Results confirmed significantly higher IMF content of 150-day female chickens as compared to the male chickens. The female chickens manifested higher serum TG, LDL-C, and VLDL, and significantly lower HDL-C contents than male chickens. Moreover, differential expression of genes involved in lipid metabolism were obtained in the muscle and liver between female and male chicken, which could partly interpret the possible reasons for the sex-mediated differences of IMF content. Cellular results revealed that inhibition of PLIN2 significantly inhibited chicken preadipocyte proliferation and induces apoptosis of preadipocytes, as well as promoted adipocyte differentiation. CONCLUSIONS According to our results, PLIN2 may be considered as a molecular marker for poultry meat quality and applying this gene in early breed selection.
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Affiliation(s)
- Jingjing Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu Campus, Chengdu, 611130, China
| | - Chaowu Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan, China
| | - Peng Ren
- Faculty of Life Sciences, Southwest University of Science and Technology, Mianyang, 621010, Sichuan, China
| | - Zhongzhen Lin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu Campus, Chengdu, 611130, China
| | - Donghao Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu Campus, Chengdu, 611130, China
| | - Xiaosong Jiang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan, China
| | - Li Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu Campus, Chengdu, 611130, China
| | - Yiping Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu Campus, Chengdu, 611130, China.
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He X, Wu R, Yun Y, Qin X, Chen L, Han Y, Wu J, Sha L, Borjigin G. Transcriptome analysis of messenger RNA and long noncoding RNA related to different developmental stages of tail adipose tissues of sunite sheep. Food Sci Nutr 2021; 9:5722-5734. [PMID: 34646540 PMCID: PMC8498062 DOI: 10.1002/fsn3.2537] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 08/03/2021] [Accepted: 08/09/2021] [Indexed: 12/18/2022] Open
Abstract
The tail fat of sheep is the most typical deposited fat, and it can be widely used in human daily life, such as diet, cosmetics, and industrial raw materials. To understand the potential regulatory mechanism of different growth stages of tail fat in Sunite sheep, we performed high-throughput RNA sequencing to characterize the long noncoding RNA (lncRNA) and messenger RNA (mRNA) expression profiles of the sheep tail fat at the age of 6, 18, and 30 months. A total of 223 differentially expressed genes (DEGs) and 148 differentially expressed lncRNAs were found in the tail fat of 6-, 18-, and 30-month-old sheep. Based on functional analysis, we found that fat-related DEGs were mainly expressed at 6 months of age and gradually decreased at 18 and 30 months of age. The target gene prediction analysis shows that most of the lncRNAs target more than 20 mRNAs as their transregulators. Further, we obtained several fat-related differentially expressed target genes; these target genes interact with different differentially expressed lncRNAs at various ages and play an important role in the development of tail fat. Based on the DEGs and differentially expressed lncRNAs, we established three co-expression networks for each comparison group. Finally, we concluded that the development of the sheep tail fat is more active during the early stage of growth and gradually decreases with the increase in age. The mutual regulation of lncRNAs and mRNAs may play a key role in this complex biological process.
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Affiliation(s)
- Xige He
- College of Food Science and EngineeringInner Mongolia Agricultural UniversityHohhotChina
| | - Rihan Wu
- College of Biochemistry and EngineeringHohhot Vocational CollegeHohhotChina
| | - Yueying Yun
- College of Food Science and EngineeringInner Mongolia Agricultural UniversityHohhotChina
- School of Life Science and TechnologyInner Mongolia University of Science and TechnologyBaotouChina
| | - Xia Qin
- College of Food Science and EngineeringInner Mongolia Agricultural UniversityHohhotChina
| | - Lu Chen
- College of Food Science and EngineeringInner Mongolia Agricultural UniversityHohhotChina
| | - Yunfei Han
- College of Food Science and EngineeringInner Mongolia Agricultural UniversityHohhotChina
| | - Jindi Wu
- College of Food Science and EngineeringInner Mongolia Agricultural UniversityHohhotChina
| | - Lina Sha
- College of Food Science and EngineeringInner Mongolia Agricultural UniversityHohhotChina
| | - Gerelt Borjigin
- College of Food Science and EngineeringInner Mongolia Agricultural UniversityHohhotChina
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Shi J, Wang X, Song Y, Liu T, Cheng S, Zhang Q. Excavation of Genes Related to the Mining of Growth, Development, and Meat Quality of Two Crossbred Sheep Populations Based on Comparative Transcriptomes. Animals (Basel) 2021; 11:ani11061492. [PMID: 34064178 PMCID: PMC8224371 DOI: 10.3390/ani11061492] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/13/2021] [Accepted: 05/17/2021] [Indexed: 11/04/2022] Open
Abstract
Simple Summary In this study, we measured the performance parameters of two crossbred sheep breeds, using Masson staining of the muscle tissue, and using the Illumina high-throughput sequencing platform to determine the differentially expressed genes (DEGs) in Dorper (DP) × Small-tailed Han (STH) sheep and Mongolia (MG) × Small-tailed Han sheep (STH). New transcripts of the muscle transcriptome were examined for the first time. DP × STH sheep were superior to MG × STH sheep in terms of meat quality and muscle morphology. In addition, 13 DEGs were found to play important roles in growth, development, and meat quality. The findings of this work may provide valuable resources for future research on muscle development in sheep. Abstract Crossbreeding can improve production performance and meat quality in sheep. The objective of this study was to look for genes related to sheep growth, development, and muscle. In this study, Dorper (DP) × Small Tailed Han (STH) sheep and Mongolia (MG) × Small-tailed Han (STH) sheep were used to estimate the productive performance and meat quality in a crossbreed. Subsequently, transcriptome analysis and bioinformatic analysis were performed on the Longissimus dorsi muscles of DP × STH and MG × STH sheep to identify differentially expressed genes (DEGs) related to growth, development, and meat quality. The presence of DEGs was confirmed by real-time PCR (qPCR). Productive performance and meat quality of the DP × STH sheep were better than the MG × STH sheep. Compared to DP × STH, a total of 1445 DEGs were identified in MG × STH sheep (1026 DEG were up-regulated and 419 DEG were down-regulated). Of these, 38 DEGs were related to growth, 161 to development, and 43 to muscle. In addition, 13 co-expressed genes (FGFRL1, SIX1, PLCB1, CRYAB, MYL2, ADIPOQ, GPX1, PPARD, GPC1, CDC42, LOC101106246, IGF1, and LARGE) were identified. The expression of DEGs was consistent with the comparative transcriptome analysis. This work provides genetics resources for future research on muscle development in sheep.
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Affiliation(s)
- Jinping Shi
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (J.S.); (Y.S.); (T.L.)
| | - Xueying Wang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China;
| | - Yali Song
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (J.S.); (Y.S.); (T.L.)
| | - Ting Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (J.S.); (Y.S.); (T.L.)
| | - Shuru Cheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (J.S.); (Y.S.); (T.L.)
- Correspondence: (S.C.); (Q.Z.); Tel.: +86-931-763-2509 (S.C.)
| | - Quanwei Zhang
- College of Life Science and Biotechnology, Gansu Agricultural University, Lanzhou 730070, China
- Correspondence: (S.C.); (Q.Z.); Tel.: +86-931-763-2509 (S.C.)
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24
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Zhang W, Xu M, Wang J, Wang S, Wang X, Yang J, Gao L, Gan S. Comparative Transcriptome Analysis of Key Genes and Pathways Activated in Response to Fat Deposition in Two Sheep Breeds With Distinct Tail Phenotype. Front Genet 2021; 12:639030. [PMID: 33897762 PMCID: PMC8060577 DOI: 10.3389/fgene.2021.639030] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 03/08/2021] [Indexed: 01/21/2023] Open
Abstract
Fat tail in sheep presents a valuable energy reserve that has historically facilitated adaptation to harsh environments. However, in modern intensive and semi-intensive sheep industry systems, breeds with leaner tails are more desirable. In the present study, RNA sequencing (RNA-Seq) was applied to determine the transcriptome profiles of tail fat tissues in two Chinese sheep breeds, fat-rumped Altay sheep and thin-tailed Xinjiang fine wool (XFW) sheep, with extreme fat tail phenotype difference. Then the differentially expressed genes (DEGs) and their sequence variations were further analyzed. In total, 21,527 genes were detected, among which 3,965 displayed significant expression variations in tail fat tissues of the two sheep breeds (P < 0.05), including 707 upregulated and 3,258 downregulated genes. Gene Ontology (GO) analysis disclosed that 198 DEGs were related to fat metabolism. In Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, the majority of DEGs were significantly enriched in "adipocytokine signaling," "PPAR signaling," and "metabolic pathways" (P < 0.05); moreover, some genes were involved in multiple pathways. Among the 198 DEGs, 22 genes were markedly up- or downregulated in tail fat tissue of Altay sheep, indicating that these genes might be closely related to the fat tail trait of this breed. A total of 41,724 and 42,193 SNPs were detected in the transcriptomic data of tail fat tissues obtained from Altay and XFW sheep, respectively. The distribution of seven SNPs in the coding regions of the 22 candidate genes was further investigated in populations of three sheep breeds with distinct tail phenotypes. In particular, the g.18167532T/C (Oar_v3.1) mutation of the ATP-binding cassette transporter A1 (ABCA1) gene and g.57036072G/T (Oar_v3.1) mutation of the solute carrier family 27 member 2 (SLC27A2) gene showed significantly different distributions and were closely associated with tail phenotype (P < 0.05). The present study provides transcriptomic evidence explaining the differences in fat- and thin-tailed sheep breeds and reveals numerous DEGs and SNPs associated with tail phenotype. Our data provide a valuable theoretical basis for selection of lean-tailed sheep breeds.
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Affiliation(s)
- Wei Zhang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Agricultural Vocational Technical College, Changji, China
| | - Mengsi Xu
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Juanjuan Wang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Shiyin Wang
- Xinjiang Agricultural Vocational Technical College, Changji, China
| | - Xinhua Wang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Jingquan Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Lei Gao
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Shangquan Gan
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
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25
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Wang X, Fang C, He H, Cao H, Liu L, Jiang L, Ma Y, Liu W. Identification of key genes in sheep fat tail evolution Based on RNA-seq. Gene 2021; 781:145492. [PMID: 33631247 DOI: 10.1016/j.gene.2021.145492] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 02/01/2021] [Accepted: 02/03/2021] [Indexed: 12/21/2022]
Abstract
Fat tail is one of the most important domesticated characteristics in sheep; however its molecular mechanism is poorly understood. Here we took small-tailed F2 hybrid of wild Argali sheep and typical fat-tailed Bashby sheep as research object. First, histological analysis revealed that the mean diameter and area in tail and subcutaneous fat cells, and surface density in tail fat in Bashby sheep were significantly larger than that in F2 sheep, and surface density of fat in subcutaneous fat in Bashby sheep was significantly lower than that in F2 sheep. Second, 873 differentially expressed genes (DEGs) of tail fat between Bashby and F2 sheep were identified by RNA-seq. Third, the tissue expression profile and relative expression difference between Bashby and F2 sheep of 7 of 873 DEGs were analyzed by RT-PCR. SCD, ESR1, EMR1, PHYH, STAT3 and GPAM genes were highly expressed in fat, muscle and liver, and ALDH1A1 were highly expressed in small intestine. In addition, the expressions of SCD, PHYH and CPAM genes in tail fat of F2 sheep were lower than that of Bashby sheep, while the expression patterns of ESR1 and EMR1 were reversed. Our findings will not only help understand molecular mechanism of fat tail, but also provide theoretical material in sheep evolution.
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Affiliation(s)
- Xinyue Wang
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China.
| | - Chao Fang
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; Department of Veterinary Management of Animal Resources, Fundamental and Applied Research for Animals and Health (FARAH), University of Liège, Liège, Belgium.
| | - Haiying He
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China.
| | - Hang Cao
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China.
| | - Lingling Liu
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China.
| | - Lin Jiang
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100000, China.
| | - Yuehui Ma
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100000, China.
| | - Wujun Liu
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China.
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26
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Han J, Guo T, Yue Y, Lu Z, Liu J, Yuan C, Niu C, Yang M, Yang B. Quantitative proteomic analysis identified differentially expressed proteins with tail/rump fat deposition in Chinese thin- and fat-tailed lambs. PLoS One 2021; 16:e0246279. [PMID: 33529214 PMCID: PMC7853479 DOI: 10.1371/journal.pone.0246279] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/17/2021] [Indexed: 11/19/2022] Open
Abstract
Tail adipose as one of the important functional tissues can enhance hazardous environments tolerance for sheep. The objective of this study was to gain insight into the underlying development mechanisms of this trait. A quantitative analysis of protein abundance in ovine tail/rump adipose tissue was performed between Chinese local fat- (Kazakh, Hu and Lanzhou) and thin-tailed (Alpine Merino, Tibetan) sheep in the present study by using lable-free approach. Results showed that 3400 proteins were identified in the five breeds, and 804 were differentially expressed proteins, including 638 up regulated proteins and 83 down regulated proteins in the tail adipose tissues between fat- and thin-tailed sheep, and 8 clusters were distinguished for all the DEPs’ expression patterns. The differentially expressed proteins are mainly associated with metabolism pathways and peroxisome proliferator activated receptor signaling pathway. Furthermore, the proteomics results were validated by quantitative real-time PCR and Western Blot. Our research has also suggested that the up-regulated proteins ACSL1, HSD17β4, FABP4 in the tail adipose tissue might contribute to tail fat deposition by facilitating the proliferation of adipocytes and fat accumulation in tail/rump of sheep. Particularly, FABP4 highly expressed in the fat-tail will play an important role for tail fat deposition. Our study might provide a novel view to understanding fat accumulation in special parts of the body in sheep and other animals.
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Affiliation(s)
- Jilong Han
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
- College of Animal Science and Technology, Shihezi University, Shihezi, China
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, CAAS, Beijing, China
| | - Tingting Guo
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
- Engineering Research Center of Sheep and Goat Breeding, CAAS, Lanzhou, China
| | - Yaojing Yue
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
- Engineering Research Center of Sheep and Goat Breeding, CAAS, Lanzhou, China
| | - Zengkui Lu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
- Engineering Research Center of Sheep and Goat Breeding, CAAS, Lanzhou, China
| | - Jianbin Liu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
- Engineering Research Center of Sheep and Goat Breeding, CAAS, Lanzhou, China
| | - Chao Yuan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
- Engineering Research Center of Sheep and Goat Breeding, CAAS, Lanzhou, China
| | - Chune Niu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
- Engineering Research Center of Sheep and Goat Breeding, CAAS, Lanzhou, China
| | - Min Yang
- College of Animal Science and Technology, Shihezi University, Shihezi, China
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, CAAS, Beijing, China
- * E-mail: (MY); (BY)
| | - Bohui Yang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
- Engineering Research Center of Sheep and Goat Breeding, CAAS, Lanzhou, China
- * E-mail: (MY); (BY)
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Miao X, Luo Q, Xie L, Zhao H, Qin X. Comparative DNA methylome analysis of estrus ewes reveals the complex regulatory pathways of sheep fecundity. Reprod Biol Endocrinol 2020; 18:77. [PMID: 32753034 PMCID: PMC7401212 DOI: 10.1186/s12958-020-00633-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 07/21/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND/AIMS Sheep are important livestock with variant ovulation rate and fertility. Dorset sheep is a typical breed with low prolificacy, whereas Small Tail Han sheep with FecB mutation (HanBB) have hyperprolificacy. Our previous studies have revealed the gene expression difference between the ovaries from Dorset and HanBB sheep contributes to the difference of fecundity, however, what leads to these gene expression difference remains unclear. DNA methylation, an important epigenetic process, plays a crucial role in gene expression regulation. METHODS In the present study, we constructed a methylated DNA immunoprecipitation combined with high throughput sequencing (MeDIP-seq) strategy to investigate the differentially methylated genes between the Dorset and HanBB ovaries. RESULTS Our findings suggest the genes involved in immune response, branched-chain amino acid metabolism, cell growth and cell junction were differentially methylated in or around the gene body regions. CONCLUSIONS These findings provide prospective insights on the epigenetic basis of sheep fecundity.
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Affiliation(s)
- Xiangyang Miao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Qingmiao Luo
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Lingli Xie
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Huijing Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiaoyu Qin
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
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Cheng S, Wang X, Wang Q, Yang L, Shi J, Zhang Q. Comparative analysis of Longissimus dorsi tissue from two sheep groups identifies differentially expressed genes related to growth, development and meat quality. Genomics 2020; 112:3322-3330. [PMID: 32534014 DOI: 10.1016/j.ygeno.2020.06.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 05/23/2020] [Accepted: 06/05/2020] [Indexed: 12/25/2022]
Abstract
From a genetic perspective, the advantages of crossbreeding in sheep are unclear. In the present study, a comparative transcriptomic analysis was performed using Longissimus dorsi tissues from two sheep groups in order to identify differentially expressed genes (DEGs) related to growth, development and meat quality. Compared to Small Tail Han sheep, a total of 874 DEGs were identified in the crossbred sheep. Among these DEGs, 30, 116 and 32 DEGs were related to growth, development and meat quality, respectively. Seven DEGs highlighted by functional analysis as playing crucial roles in growth, development and meat quality were validated by the gene-act-network and co-expression-network. The expression levels of DEG mRNAs and proteins were further confirmed using RT-qPCR and western blot analyses. The results were consistent with the comparative transcriptome data. The data from this transcriptomic analysis will help to understand genetic heterosis and molecular-assisted breeding in sheep.
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Affiliation(s)
- Shuru Cheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Xueyin Wang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Qi Wang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Lei Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Jinping Shi
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Quanwei Zhang
- College of Life Science and Biotechnology, Gansu Agricultural University, Lanzhou 730070, China.
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29
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Comparison Between the Gut Microbiota in Different Gastrointestinal Segments of Large-Tailed Han and Small-Tailed Han Sheep Breeds with High-Throughput Sequencing. Indian J Microbiol 2020; 60:436-450. [PMID: 33087993 DOI: 10.1007/s12088-020-00885-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 05/11/2020] [Indexed: 12/27/2022] Open
Abstract
Commensal microorganisms are essential to the normal development and function of many aspects of animal biology. However, the dynamic shift patterns of the microbiota of different gut segments in sheep and the correlation between fat type large-tailed phenotype and microbiota remain poorly unknown. This study therefore sought to assess the composition and distribution of the intestinal microbiome, and compared the difference of gut microbiota from different gastrointestinal segments within breeds and same intestinal sections between breeds. For these analyses, 16S rRNA V4 regions from 4 gut sections prepared from each of six individuals (3 from each breed) were sequenced to detect the microbiome composition in these samples. These analyses revealed the presence of 51,173 operational taxonomic units distributed across 24 phyla and 420 genera in these samples, with Firmicutes and Bacteroidetes being the most prevalent phyla of microbes present in these samples. Moreover, the bacterial composition showed distinct microbial communities in different gastrointestinal segments within breed, but showed similar and relative fixed bacterial abundance in the same intestinal segments from individuals of different breeds. We also found that only a few bacterial species (Lachnospiraceae, Akkermansia) were needed to distinguish between Small-tailed Han sheep (STH) and Large-tailed Han sheep (LTH) and their metabolic process maybe influence the fat type large-tailed phenotype formation in sheep. The functional profile analysis revealed that the environment information processing, genetic information processing, and metabolic pathways were enriched in all samples. The main functional roles of the gut microbiota were amino acid metabolism, replication and repair, carbohydrate metabolism, and membrane transport. Finally, our findings suggested that distinguished gut species between STH and LTH have relative fixed and the potential correlation is existing between the intestinal microorganisms and the large-tailed phenotype trait formation of sheep, which may offer clues for further investigation to detect the roles of intestinal microbiota in the metabolism and fat deposition in the tail of sheep.
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30
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Cheng S, Wang X, Zhang Q, He Y, Zhang X, Yang L, Shi J. Comparative Transcriptome Analysis Identifying the Different Molecular Genetic Markers Related to Production Performance and Meat Quality in Longissimus Dorsi Tissues of MG × STH and STH Sheep. Genes (Basel) 2020; 11:E183. [PMID: 32050672 PMCID: PMC7074365 DOI: 10.3390/genes11020183] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/05/2020] [Accepted: 02/07/2020] [Indexed: 12/24/2022] Open
Abstract
Crossbred sheep have many prominent traits, such as excellent production performance and high-quality meat, when compared to local sheep breeds. However, the genetic molecular markers related to these characteristics remain unclear. The crossbred MG × STH (small-tailed Han sheep (STH) × Mongolian sheep (MG)) breed and the STH breed were selected to measure production performance and meat quality. We used 14 indexes of production performance and meat quality, which in the MG × STH population showed significant differences compared to the STH breed. Subsequently, the longissimusdorsi from the two sheep were subjected to comparative transcriptomic analyses to identify differentially expressed genes (DEGs) related to production performance and meat quality. A total of 874 DEGs were identified between the two sheep groups. A total of 110 unique DEGs related to sheep production performance and meat quality were selected as the candidate DEGs. We found 6 production-performance-related and 30 meat-quality-related DEGs through a correlation analysis, including SPARC, ACVRL1, FNDC5 and FREM1. The expression levels of 11 DEGs were validated by real-time PCR, and the results were in accordance with the results of the comparative transcriptomic and correlation analyses. These results will assist in understanding sheep heterosis and molecular marker-assisted selection.
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Affiliation(s)
- Shuru Cheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (L.Y.); (J.S.)
| | - Xueying Wang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China;
| | - Quanwei Zhang
- College of Life Science and Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (Y.H.); (X.Z.)
| | - Yuqin He
- College of Life Science and Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (Y.H.); (X.Z.)
| | - Xia Zhang
- College of Life Science and Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (Y.H.); (X.Z.)
| | - Lei Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (L.Y.); (J.S.)
| | - Jinping Shi
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (L.Y.); (J.S.)
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31
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Fan H, Hou Y, Sahana G, Gao H, Zhu C, Du L, Zhao F, Wang L. A Transcriptomic Study of the Tail Fat Deposition in Two Types of Hulun Buir Sheep According to Tail Size and Sex. Animals (Basel) 2019; 9:ani9090655. [PMID: 31491862 PMCID: PMC6770480 DOI: 10.3390/ani9090655] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/28/2019] [Accepted: 08/30/2019] [Indexed: 01/19/2023] Open
Abstract
Simple Summary Based on tail types, Hulun Buir sheep were divided into two lines including small and big fat-tailed, but these two lines have similar genetic background. In this study, we investigated the morphology and transcription level differences of tail fat between these two lines. The RNA-seq analyses indicated several differentially expressed genes when compared between sexes or two tail sizes. Interestingly, we also found an obvious sex difference in the fat metabolism in Hulun Buir sheep. Two different co-expression networks were only shown either in male or in female sheep. Our findings will provide theoretical background in understanding the genetic mechanism of fat deposition in sheep. Abstract Hulun Buir sheep of similar genetic background were divided into two lines based on tail types: Small- and big fat-tailed. To explore the molecular mechanism of fat deposition in sheep tails, we firstly evaluated the morphology and transcription level differences of tail fat between these two lines. RNA-Seq technology was used to identify differentially expressed genes (DEGs) in phenotypic extremes of tail sizes. Five comparisons were performed taking into account two factors, sex and tail type. We screened out 373 DEGs between big-tailed and small-tailed Hulun Buir sheep, and 775 and 578 DEGs between two types of tails in male and female sheep, respectively. The results showed an obvious sex difference in the fat metabolism in sheep based on gene ontology (GO), pathway, and network analyses. Intriguingly, there were two different co-expression networks only respectively shown in male and female sheep, which were insulin-related network acting on upstream pathways and PPARG-related network effect in downstream pathways. Furthermore, these two networks were linked by a classic pathway of regulating adipogenesis. This is the first study to investigate the sex differences of fat metabolism in domestic animals, and it demonstrates a new experimental way to study fat metabolism. Our findings will provide theoretical background in understanding the tail-size phenotype in sheep and can be exploited in breeding small-tailed sheep.
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Affiliation(s)
- Hongying Fan
- Key Laborary of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Key Laboratory of Mariculture, Ocean University of China, Qingdao 266000, China
| | - Yali Hou
- Beijing Institute of Genomics, Chinese Academy of Sciences and University of Chinese Academy of Sciences, Beijing 100101, China
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
| | - Hongding Gao
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
| | - Caiye Zhu
- Key Laborary of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lixin Du
- Key Laborary of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fuping Zhao
- Key Laborary of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Lixian Wang
- Key Laborary of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Bakhtiarizadeh MR, Salehi A, Alamouti AA, Abdollahi-Arpanahi R, Salami SA. Deep transcriptome analysis using RNA-Seq suggests novel insights into molecular aspects of fat-tail metabolism in sheep. Sci Rep 2019; 9:9203. [PMID: 31235755 PMCID: PMC6591244 DOI: 10.1038/s41598-019-45665-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 06/12/2019] [Indexed: 12/11/2022] Open
Abstract
Fat-tail content of sheep breeds is varied and the molecular mechanisms regulating fat-tail development have not been well characterized. Aiming at better identifying the important candidate genes and their functional pathways contributing to fat deposition in the tail, a comparative transcriptome analysis was performed between fat- (Lori-Bakhtiari) and thin-tailed (Zel) Iranian sheep breeds using RNA-seq. The experiment was conducted on six male lambs (three lambs per each breed) at seven months of age. Four different combinations of aligners and statistical methods including Hisat2 + edgeR, Hisat2 + DESeq2, STAR + edgeR and STAR + DESeq2 were used to identify the differentially expressed genes (DEGs). The DEGs were selected for functional enrichment analysis and protein-protein interaction (PPI) network construction. Module analysis was also conducted to mine the functional sub-networks from the PPI network. In total, 264 genes including 80 up- and 184 down-regulated genes were identified as DEGs. The RNA-Seq results were validated by Q-RT-PCR. Functional analysis of DEGs and the module analysis of PPI network demonstrated that in addition to pathways affecting lipid metabolism, a series of enriched functional terms related to "response to interleukin", "MAPK signaling pathways", "Wnt signaling pathway", "ECM-receptor interaction", "regulation of actin cytoskeleton", and "response to cAMP" might contribute to the deposition of fat in tails of sheep. Overall results using RNA-Seq analysis characterized important candidate genes involved in the fatty acid metabolism and regulation of fat deposition, suggesting novel insights into molecular aspects of fat-tail metabolism in sheep. Selected DEGs should be further investigated as potential markers associated with the fat-tail development in sheep breeds.
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Affiliation(s)
| | - Abdolreza Salehi
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
| | - Ali A Alamouti
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
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Identification and Expression Analysis of Long Noncoding RNAs in Fat-Tail of Sheep Breeds. G3-GENES GENOMES GENETICS 2019; 9:1263-1276. [PMID: 30787031 PMCID: PMC6469412 DOI: 10.1534/g3.118.201014] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Emerging evidence suggests that long non-coding RNAs (lncRNAs) participate in the regulation of a diverse range of biological processes. However, most studies have been focused on a few established model organisms and little is known about lncRNAs in fat-tail development in sheep. Here, the first profile of lncRNA in sheep fat-tail along with their possible roles in fat deposition were investigated, based on a comparative transcriptome analysis between fat-tailed (Lori-Bakhtiari) and thin-tailed (Zel) Iranian sheep breeds. Among all identified lncRNAs candidates, 358 and 66 transcripts were considered novel intergenic (lincRNAs) and novel intronic (ilncRNAs) corresponding to 302 and 58 gene loci, respectively. Our results indicated that a low percentage of the novel lncRNAs were conserved. Also, synteny analysis identified 168 novel lincRNAs with the same syntenic region in human, bovine and chicken. Only seven lncRNAs were identified as differentially expressed genes between fat and thin tailed breeds. Q-RT-PCR results were consistent with the RNA-Seq data and validated the findings. Target prediction analysis revealed that the novel lncRNAs may act in cis or trans and regulate the expression of genes that are involved in the lipid metabolism. A gene regulatory network including lncRNA-mRNA interactions were constructed and three significant modules were found, with genes relevant to lipid metabolism, insulin and calcium signaling pathway. Moreover, integrated analysis with AnimalQTLdb database further suggested six lincRNAs and one ilncRNAs as candidates of sheep fat-tail development. Our results highlighted the putative contributions of lncRNAs in regulating expression of genes associated with fat-tail development in sheep.
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Suárez-Vega A, Arranz JJ, Pérez V, de la Fuente LF, Mateo J, Gutiérrez-Gil B. Early adipose deposits in sheep: comparative analysis of the perirenal fat transcriptome of Assaf and Churra suckling lambs. Anim Genet 2018; 49:605-617. [PMID: 30311245 DOI: 10.1111/age.12725] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2018] [Indexed: 11/28/2022]
Abstract
Adipose deposits influence the quality of ruminant carcasses, and in suckling lambs, internal types of adipose deposits represent a notable proportion of total fat. The aim of this study was to perform a comparative analysis of the perirenal fat transcriptomes of suckling lambs from two breeds with different growth and carcass characteristics. The perirenal fat tissue from 14 suckling lambs (Assaf, n = 8; Churra, n = 6) was used for the RNA-seq analysis. The functional enrichment analysis of the 670 highly expressed genes (>150 fragments per kilobase of exon per million fragments mapped) in the perirenal fat transcriptome of both breeds revealed that the majority of these genes were involved in energy processes. The expression of the UCP1 gene, a classical biomarker of brown fat, and the presence of multilocular adipocytes in the two breeds supported the presence of brown fat at the transition stage towards white fat tissue. The differential expression analysis performed identified 373 differentially expressed genes (DEGs) between the two compared breeds. Brown/white fat gene biomarkers were not included in the list of DEGs. In Assaf lambs, DEGs were enriched in Gene Ontology (GO) biological processes related to fatty-acid oxidation, whereas in Churra lambs, the majority of the significantly enriched GO terms were related to cholesterol synthesis, which suggests that upregulated DEGs in Assaf lambs are implicated in fat burning, whereas the Churra upregulated DEGs are linked to fat accumulation. These results can help to increase knowledge of the genes controlling early fat deposition in ruminants and shed light on fundamental aspects of adipose tissue growth.
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Affiliation(s)
- A Suárez-Vega
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071, Spain
| | - J J Arranz
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071, Spain
| | - V Pérez
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071, Spain
| | - L F de la Fuente
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071, Spain
| | - J Mateo
- Departamento de Higiene y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071, Spain
| | - B Gutiérrez-Gil
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071, Spain
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35
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Ovarian transcriptomic analysis reveals the alternative splicing events associated with fecundity in different sheep breeds. Anim Reprod Sci 2018; 198:177-183. [PMID: 30318312 DOI: 10.1016/j.anireprosci.2018.09.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 09/18/2018] [Accepted: 09/27/2018] [Indexed: 12/11/2022]
Abstract
Alternative splicing (AS) is one of the most common mechanisms that accounts for the greater macromolecular and cellular complexity of higher eukaryotic organisms. This study focused on the splicing events in the ovaries of different sheep breeds, namely the Han and Dorset breeds. Of the groups studied, cassette splicing events accounted for the maximum number of the AS events with significant differences, whereas the splicing events that were mutually exclusive with introns accounted for the smallest proportion of splicing events. Greater than 1000 AS events with significant differences were identified between the Han BB and Dorset sheep. The number of AS events with significant differences between Han ++ and Dorset sheep, however, was fewer than that of the comparison of Han BB and Dorset sheep. Seven randomly selected genes with AS events were detected in this study and were validated by reverse transcription-polymerase chain reaction (RT-PCR). Furthermore, there are many genes which were common to the two genotype groups (Han BB and Dorset sheep, as well as the Han ++ and Dorset sheep). In addition, genes detected in the present study were involved in different pathways, including the pathways related with fertility or fecundity. The present study could provide the detailed understanding on the mechanisms of alternative splicing events associated with fecundity in different sheep breeds.
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Ma L, Zhang M, Jin Y, Erdenee S, Hu L, Chen H, Cai Y, Lan X. Comparative Transcriptome Profiling of mRNA and lncRNA Related to Tail Adipose Tissues of Sheep. Front Genet 2018; 9:365. [PMID: 30250481 PMCID: PMC6139350 DOI: 10.3389/fgene.2018.00365] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 08/21/2018] [Indexed: 01/05/2023] Open
Abstract
The Lanzhou Fat-Tail sheep (LFTS, long fat-tailed sheep) is an endangered sheep breed in China with a fat tail compared to the traditional local varieties, Small Tail Han sheep (STHS, thin-tailed sheep) with a small tail, and Tibetan sheep (TS, short thin-tailed sheep) with a little tail. However, little is known regarding how tail fat deposition is regulated by long noncoding RNA (lncRNA). To evaluate the lncRNA and mRNA associated with tail fat deposition and development among these breeds, high-throughput RNA sequencing of three individuals each of LFTS, STHS, and TS were performed and analyzed in this study. RNA sequencing data from these three groups revealed 10 differentially expressed genes (DEGs) and 37 differentially expressed lncRNAs between the LFTS and STHS groups, 390 DEGs and 59 differentially expressed lncRNAs between the LFTS and TS groups, and 80 DEGs and 16 differentially expressed lncRNAs between the STHS and TS groups (p-value < 0.05 and fold change ≥ 2), respectively. Gene Ontology and pathway analysis of DEGs and target genes of differentially expressed lncRNAs revealed enrichment in fatty acid metabolism and fatty acid elongation-related pathways that contribute to fat deposition. Subsequently, the expression of 14 DEGs and 6 differentially expressed lncRNAs was validated by quantitative real-time PCR. Finally, two co-expression networks of differentially expressed mRNA and lncRNAs were constructed. The results suggested that some differentially expressed lncRNAs (TCONS_00372767, TCONS_00171926, TCONS_00054953, and TCONS_00373007) may play crucial roles as core lncRNAs in tail fat deposition processes. In summary, the present study extends the sheep tail fat lncRNA database and these differentially expressed mRNA and lncRNAs may provide novel candidate regulators for future genetic and molecular studies on tail fat deposition of sheep.
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Affiliation(s)
- Lin Ma
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Meng Zhang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yunyun Jin
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Sarantsetseg Erdenee
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Linyong Hu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Hong Chen
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yong Cai
- Science Experimental Center, Northwest University for Nationalities, Lanzhou, China.,College of Life Science and Engineering, Northwest University for Nationalities, Lanzhou, China
| | - Xianyong Lan
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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Li B, Qiao L, An L, Wang W, Liu J, Ren Y, Pan Y, Jing J, Liu W. Transcriptome analysis of adipose tissues from two fat-tailed sheep breeds reveals key genes involved in fat deposition. BMC Genomics 2018; 19:338. [PMID: 29739312 PMCID: PMC5941690 DOI: 10.1186/s12864-018-4747-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 04/30/2018] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND The level of fat deposition in carcass is a crucial factor influencing meat quality. Guangling Large-Tailed (GLT) and Small-Tailed Han (STH) sheep are important local Chinese fat-tailed breeds that show distinct patterns of fat depots. To gain a better understanding of fat deposition, transcriptome profiles were determined by RNA-sequencing of perirenal, subcutaneous, and tail fat tissues from both the sheep breeds. The common highly expressed genes (co-genes) in all the six tissues, and the genes that were differentially expressed (DE genes) between these two breeds in the corresponding tissues were analyzed. RESULTS Approximately 47 million clean reads were obtained for each sample, and a total of 17,267 genes were annotated. Of the 47 highly expressed co-genes, FABP4, ADIPOQ, FABP5, and CD36 were the four most highly transcribed genes among all the known genes related to adipose deposition. FHC, FHC-pseudogene, and ZC3H10 were also highly expressed genes and could, thus, have roles in fat deposition. A total of 2091, 4233, and 4131 DE genes were identified in the perirenal, subcutaneous, and tail fat tissues between the GLT and STH breeds, respectively. Gene Ontology (GO) analysis showed that some DE genes were associated with adipose metabolism. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that PPAR signaling pathway and ECM-receptor interaction were specifically enriched. Four genes, namely LOC101102230, PLTP, C1QTNF7, and OLR1 were up-regulated and two genes, SCD and UCP-1, were down-regulated in all the tested tissues of STH. Among the genes involved in ECM-receptor interaction, the genes encoding collagens, laminins, and integrins were quite different depending on the depots or the breeds. In STH, genes such as LAMB3, RELN, TNXB, and ITGA8, were identified to be up regulated and LAMB4 was observed to be down regulated. CONCLUSIONS This study unravels the complex transcriptome profiles in sheep fat tissues, highlighting the candidate genes involved in fat deposition. Further studies are needed to investigate the roles of the candidate genes in fat deposition and in determining the meat quality of sheep.
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Affiliation(s)
- Baojun Li
- Shanxi Agricultural University, College of Veterinary and Animal Science, Taigu, 030801, China
| | - Liying Qiao
- Shanxi Agricultural University, College of Veterinary and Animal Science, Taigu, 030801, China
| | - Lixia An
- Shanxi Agricultural University, College of Information, Taigu, 030800, China
| | - Weiwei Wang
- Shanxi Agricultural University, College of Veterinary and Animal Science, Taigu, 030801, China
| | - Jianhua Liu
- Shanxi Agricultural University, College of Veterinary and Animal Science, Taigu, 030801, China
| | - Youshe Ren
- Shanxi Agricultural University, College of Veterinary and Animal Science, Taigu, 030801, China
| | - Yangyang Pan
- Shanxi Agricultural University, College of Veterinary and Animal Science, Taigu, 030801, China
| | - Jiongjie Jing
- Shanxi Agricultural University, College of Veterinary and Animal Science, Taigu, 030801, China
| | - Wenzhong Liu
- Shanxi Agricultural University, College of Veterinary and Animal Science, Taigu, 030801, China.
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38
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Yang S, Wang Y, Wang L, Shi Z, Ou X, Wu D, Zhang X, Hu H, Yuan J, Wang W, Cao F, Liu G. RNA-Seq reveals differentially expressed genes affecting polyunsaturated fatty acids percentage in the Huangshan Black chicken population. PLoS One 2018; 13:e0195132. [PMID: 29672513 PMCID: PMC5908183 DOI: 10.1371/journal.pone.0195132] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 03/16/2018] [Indexed: 12/16/2022] Open
Abstract
Fatty acids metabolic products determine meat quality in chickens. Identifying genes associated with fatty acids composition could provide valuable information for the complex genetic networks of genes with underlying variations in fatty acids synthesis. RNA sequencing (RNA-Seq) was conducted to explore the chicken transcriptome from the thigh muscle tissue of 6 Huangshan Black Chickens with 3 extremely high and low phenotypic values for percentage of polyunsaturated fatty acids (PUFAs). In total, we obtained 41,139,108–44,901,729 uniquely mapped reads, which covered 74.15% of the current annotated transcripts including 18964 mRNA transcripts, across all the six thigh muscle tissue samples. Of these, we revealed 274 differentially expressed genes (DEGs) with a highly significant correlation with polyunsaturated fatty acids percentage between the comparison groups based on the ratio of PUFA/SFA. Gene ontology and pathway analysis indicated that the DEGs were enriched in particular biological processes affecting fatty acids metabolism, biosynthesis of unsaturated fatty acids (USFAs), and cell junction-related pathways. Integrated interpretation of differential gene expression and formerly reported quantitative trait loci (QTL) demonstrated that FADS2, DCN, FRZB, OGN, PRKAG3, LHFP, CHCHD10, CYTL1, FBLN5, and ADGRD1 are the most promising candidate genes affecting polyunsaturated fatty acids percentage.
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Affiliation(s)
- Shaohua Yang
- College of Food Science and Engineering, Hefei University of Technology, Hefei, Anhui, P. R. China
| | - Ying Wang
- College of Food Science and Engineering, Hefei University of Technology, Hefei, Anhui, P. R. China
| | - Lulu Wang
- College of Food Science and Engineering, Hefei University of Technology, Hefei, Anhui, P. R. China
| | - Zhaoyuan Shi
- College of Food Science and Engineering, Hefei University of Technology, Hefei, Anhui, P. R. China
| | - Xiaoqian Ou
- College of Food Science and Engineering, Hefei University of Technology, Hefei, Anhui, P. R. China
| | - Dan Wu
- College of Food Science and Engineering, Hefei University of Technology, Hefei, Anhui, P. R. China
| | - Xinmiao Zhang
- College of Food Science and Engineering, Hefei University of Technology, Hefei, Anhui, P. R. China
| | - Hao Hu
- College of Food Science and Engineering, Hefei University of Technology, Hefei, Anhui, P. R. China
| | - Jia Yuan
- College of Food Science and Engineering, Hefei University of Technology, Hefei, Anhui, P. R. China
| | - Wei Wang
- Agricultural Products Quality and Safety Supervision and Management Bureau, Xuancheng, Anhui, P. R. China
| | - Fuhu Cao
- College of Food Science and Engineering, Hefei University of Technology, Hefei, Anhui, P. R. China
- * E-mail: (FC); (GL)
| | - Guoqing Liu
- College of Food Science and Engineering, Hefei University of Technology, Hefei, Anhui, P. R. China
- * E-mail: (FC); (GL)
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Miao X, Luo Q, Zhao H, Qin X. An Integrated Analysis of miRNAs and Methylated Genes Encoding mRNAs and lncRNAs in Sheep Breeds with Different Fecundity. Front Physiol 2017; 8:1049. [PMID: 29326596 PMCID: PMC5736872 DOI: 10.3389/fphys.2017.01049] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 11/30/2017] [Indexed: 01/12/2023] Open
Abstract
In our previous study, we investigated the regulatory relationship between lncRNAs, miRNA, and mRNAs in an effort to shed light onto the regulatory mechanisms involved in sheep fecundity. As an extension of this study, here, we aimed to identify potential regulators of sheep fecundity using a genome-wide analysis of miRNAs and the methylated genes encoding mRNAs and lncRNAs in the ovaries of Dorset sheep (low fecundity) and Small Tail Han ewes (high fecundity) with the genotype BB (Han BB) and the genotype ++ (Han ++) by performing RNA-Seq and MeDIP-Seq analyses. Methylated coding-non-coding gene co-expression networks for Han and Dorset sheep were constructed using the methylated genes encoding the differentially expressed mRNAs and lncRNAs identified in this study. In the Han BB vs. Dorset comparison, the lncRNAs TTC26 and MYH15 had the largest degree. Similarly, the lncRNA NYAP1 had the largest degree in the Han ++ vs. Dorset comparison. None of the methylated genes encoding lncRNAs were co-expressed with the methylated genes encoding mRNAs in the Han BB vs. Han ++ comparison. The methylated genes encoding lncRNAs identified here may play a vital regulatory role in sheep breeding. Our results suggest that miRNAs might play a key role in sheep prolificacy by regulating target genes related to thyroid hormone synthesis, and methylated genes encoding lncRNAs associated with tight junctions might contribute to the high breeding rate in Han sheep. These findings may contribute to a deeper understanding of sheep prolificacy.
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Affiliation(s)
- Xiangyang Miao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qingmiao Luo
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huijing Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoyu Qin
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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40
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Comparative transcriptome analysis reveals potentially novel roles of Homeobox genes in adipose deposition in fat-tailed sheep. Sci Rep 2017; 7:14491. [PMID: 29101335 PMCID: PMC5670210 DOI: 10.1038/s41598-017-14967-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 10/18/2017] [Indexed: 12/12/2022] Open
Abstract
Adipose tissues are phenotypically, metabolically and functionally heterogeneous based on the sites of their deposition. Undesirable fat deposits in the body are often detrimental to animal and human health. To unravel the potential underlying mechanisms governing accumulation of adipose tissues in various regions of the body, i.e., subcutaneous (SAT), visceral (VAT) and tail (TAT), we profiled transcriptomes from Tan sheep, a Chinese indigenous breed with notable fat tail using RNA-seq. Upon comparison, we identified a total of 1,058 differentially expressed genes (DEGs) between the three adipose types (218, 324, and 795 in SAT/VAT, SAT/TAT, and VAT/TAT, respectively), from which several known key players were identified that are involved in lipid metabolic process, Wnt signals, Vitamin A metabolism, and transcriptional regulation of adipocyte differentiation. We also found that many elevated genes in VAT were notably enriched for key biological processes such as cytokine secretion, signaling molecule interaction and immune systems. Several developmental genes including HOXC11, HOXC12 and HOXC13, and adipose-expressed genes in the tail region, such as HOTAIR_2, HOTAIR_3 and SP9 were specially highlighted, indicating their strong associations with tail fat development in fat-tailed sheep. Our results provide new insight into exploring the specific fat deposition in tail, also contribute to the understanding of differences between adipose depots.
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41
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Huang W, Zhang X, Li A, Xie L, Miao X. Differential regulation of mRNAs and lncRNAs related to lipid metabolism in two pig breeds. Oncotarget 2017; 8:87539-87553. [PMID: 29152100 PMCID: PMC5675652 DOI: 10.18632/oncotarget.20978] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 08/27/2017] [Indexed: 01/02/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) can regulate lipid metabolism and adipogenesis. However, there is little research on the role of lncRNAs in fat deposition in pig. In this study, RNA-seq technology was used to analyze the gene expression profiles of subcutaneous adipose tissue in Laiwu (LW) and Large White (LY) pigs. Then, key lncRNAs and genes associated with lipid metabolism and adipogenic differentiation were identified. Fifty four lncRNAs and 482 known mRNAs were differentially expressed in the two pig breeds. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analyses revealed that differentially expressed genes and the target genes of differentially expressed lncRNAs were significantly enriched in PPAR signaling pathway and biological processes including fat cell differentiation and fatty acid metabolism. Key lncRNAs might regulate adipogenic differentiation and fatty acid metabolism by regulating genes involved in above signaling pathway and biological processes. Specifically, XLOC_014379, XLOC_011279, XLOC_064871, XLOC_019518 and XLOC_013639 might target SCD, LPIN1, TRIB3, EGR2 and FABP3, respectively, and then play critical regulatory role. These results are useful for understanding fat deposition in pig, breeding livestock with high quality meat, and preventing and treating lipid metabolic disease.
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Affiliation(s)
- Wanlong Huang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiuxiu Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ai Li
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lingli Xie
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiangyang Miao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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42
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Global transcriptome analysis identifies differentially expressed genes related to lipid metabolism in Wagyu and Holstein cattle. Sci Rep 2017; 7:5278. [PMID: 28706200 PMCID: PMC5509646 DOI: 10.1038/s41598-017-05702-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 06/01/2017] [Indexed: 11/22/2022] Open
Abstract
Fat deposition of beef cattle varies between breeds. However, the regulation mechanism is still not elucidated completely at molecular level. In the present study, we comparatively analyzed transcriptome of subcutaneous adipose tissue between Wagyu and Holstein cattle with a significant difference in fat deposition to identify key genes associated with fat metabolism and adipogenesis by high-throughput RNA-seq technology. A total of 59,149,852 and 69,947,982 high quality reads were generated, respectively. With further analysis, 662 differentially expressed genes were identified. Gene Ontology and KEGG pathway analysis revealed that many differentially expressed genes were enriched in several biological processes and pathways relevant to adipogenesis and lipid metabolism, in which PPAR and fatty acid metabolism signaling pathways with related genes such as PPARγ, PLIN2 and ELOVL6 et al. play a critical role. Protein-protein interaction network analysis showed EGR1, FOS, SERPINE1, AGT, MMP2 may have great impact on adipocyte differentiation and adipogenesis. Moreover, potential alternative splicing events and single nucleotide polymorphisms (SNPs) were also identified. In summary, we comprehensively analyzed and discussed the transcriptome of subcutaneous adipose tissue of Wagyu and Holstein cattle, which might provide a theoretical basis for better understanding molecular mechanism of fat metabolism and deposition in beef cattle.
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43
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Overexpression of placenta specific 8 is associated with malignant progression and poor prognosis of clear cell renal cell carcinoma. Int Urol Nephrol 2017; 49:1165-1176. [PMID: 28349447 DOI: 10.1007/s11255-017-1578-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 03/21/2017] [Indexed: 12/14/2022]
Abstract
BACKGROUND Placenta specific 8 (PLAC8) plays an important role in many different cellular processes and human diseases, including multiple types of cancer. However, the functional role of PLAC8 in clear cell renal cell carcinoma (ccRCC) has never been elucidated. METHODS PLAC8 mRNA expression was investigated in 31 pairs of fresh ccRCC tumor tissues and matched adjacent non-tumor tissues by RT-qPCR and confirmed by analyzing the TCGA KRCC dataset which contains RNA-seq data of 534 ccRCC and 72 solid normal tissues. Protein level of PLAC8 expression was also investigated using immunohistochemistry in 129 ccRCC samples. Correlations with clinicopathological factors and overall survival were analyzed. To examine its effect on the biological activity, PLAC8 siRNAs were transfected into ccRCC cells. Cell proliferation was assessed by CCK8 cell viability assays, clone formation assays, and EdU incorporation assays. Cell invasion was examined using transwell assays. RNA sequencing was then performed to further elucidate the mechanisms by which PLAC8 regulates the cancer. RESULTS PLAC8 expression was positively correlated with tumor size, metastasis, and clinical stage of ccRCC. Additionally, high PLAC8 expression was closely associated with a shorter overall survival time. Knockdown of PLAC8 with siRNAs significantly reduced the proliferation and invasion of RCC cells and increased the sensitivity of RCC cells to cisplatin. RNA-seq analysis revealed that knockdown of PLAC8 down-regulated the expression of a panel of inflammatory mediators, which suggested that PLAC8 is associated with the ccRCC inflammatory microenvironment. Patients with high expression of PLAC8 had a significantly higher number of infiltrative lymphocytes than patients with low expression of PLAC8. CONCLUSION Our findings suggest that PLAC8 may be a potential prognostic indicator and therapeutic target for ccRCC.
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Guo Y, Zhang X, Huang W, Miao X. Identification and characterization of differentially expressed miRNAs in subcutaneous adipose between Wagyu and Holstein cattle. Sci Rep 2017; 7:44026. [PMID: 28272430 PMCID: PMC5341059 DOI: 10.1038/srep44026] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 02/02/2017] [Indexed: 12/22/2022] Open
Abstract
MicroRNAs (miRNAs) are important post-transcriptional regulators involved in animal adipogenesis, however, their roles in bovine fat deposition remain poorly understood. In the present study, we conducted a comparative RNA sequencing to identify the key miRNAs involved in beef lipid accumulation by comparing the backfat small RNA samples between Wagyu (high intramuscular fat) and Holstein (moderate intramuscular fat) cattle. Fifteen miRNAs such as bta-miR-142-3p, bta-miR-379, bta-miR-196a, bta-miR-196b, bta-miR-30f and bta-miR-2887 were identified to have a higher expression level in Wagyu cattle compared with Holstein, whereas bta-miR-320a, bta-miR-874 and bta-miR-1247-3p had a lower expression level in Wagyu. Furthermore, a total of 1345 potential target genes of differentially expressed miRNAs were predicted using bioinformatics tools, in which PPARα and RXRα were known to play a critical role in adipocyte differentiation and lipid metabolism. In conclusion, the present study constructed a high-throughput RNA sequencing screen and successfully identified miRNAs such as bta-miR-874, bta-miR-320a and bta-miR-196b which may affect beef fat deposition. The present findings may provide a theoretical foundation for the utilization of beef cattle germplasm resources.
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Affiliation(s)
- Yuntao Guo
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiuxiu Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wanlong Huang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiangyang Miao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
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Yang J, Liu AY, Tang B, Luo D, Lai YJ, Zhu BL, Wang XF, Yan Z, Chen GJ. Chronic nicotine differentially affects murine transcriptome profiling in isolated cortical interneurons and pyramidal neurons. BMC Genomics 2017; 18:194. [PMID: 28219337 PMCID: PMC5319194 DOI: 10.1186/s12864-017-3593-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 02/14/2017] [Indexed: 12/18/2022] Open
Abstract
Background Nicotine is known to differentially regulate cortical interneuron and pyramidal neuron activities in the neocortex, while the underlying molecular mechanisms have not been well studied. In this study, RNA-sequencing was performed in acutely isolated cortical somatostatin (Sst)- positive interneurons and pyramidal neurons (Thy1) from mice treated with systemic nicotine for 14 days. We assessed the differentially expressed genes (DEGs) by nicotine in Sst- or Thy1- neurons, respectively, and then compared DEGs between Sst- and Thy1- neurons in the absence and presence of nicotine. Results In Sst-neurons, the DEGs by nicotine were associated with glycerophospholipid and nicotinate and nicotinamide metabolism; while in Thy1-neurons those related to immune response and purine and pyrimidine metabolisms were affected. Under basal condition, the DEGs between Sst- and Thy1- neurons were frequently associated with signal transduction, phosphorylation and potassium channel regulation. However, some new DEGs between Sst- and Thy1- neurons were found after nicotine, the majority of which belong to mitochondrial respiratory chain complex. Conclusions Nicotine differentially affected subset of genes in Sst- and Thy1- neurons, which might contribute to the distinct effect of nicotine on interneuron and pyramidal neuron activities. Meanwhile, the altered transcripts associated with mitochondrial activity were found between interneurons and pyramidal neurons after chronic nicotine. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3593-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jie Yang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, 1 Youyi Road, Chongqing, 400016, China
| | - Ai-Yi Liu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, 1 Youyi Road, Chongqing, 400016, China
| | - Bo Tang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, 1 Youyi Road, Chongqing, 400016, China
| | - Dong Luo
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, 1 Youyi Road, Chongqing, 400016, China
| | - Yu-Jie Lai
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, 1 Youyi Road, Chongqing, 400016, China
| | - Bing-Lin Zhu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, 1 Youyi Road, Chongqing, 400016, China
| | - Xue-Feng Wang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, 1 Youyi Road, Chongqing, 400016, China
| | - Zhen Yan
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY, 14214, USA
| | - Guo-Jun Chen
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, 1 Youyi Road, Chongqing, 400016, China.
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Co-expression analysis and identification of fecundity-related long non-coding RNAs in sheep ovaries. Sci Rep 2016; 6:39398. [PMID: 27982099 PMCID: PMC5159859 DOI: 10.1038/srep39398] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 11/23/2016] [Indexed: 11/08/2022] Open
Abstract
Small Tail Han sheep, including the FecBBFecBB (Han BB) and FecB+ FecB+ (Han++) genotypes, and Dorset sheep exhibit different fecundities. To identify novel long non-coding RNAs (lncRNAs) associated with sheep fecundity to better understand their molecular mechanisms, a genome-wide analysis of mRNAs and lncRNAs from Han BB, Han++ and Dorset sheep was performed. After the identification of differentially expressed mRNAs and lncRNAs, 16 significant modules were explored by using weighted gene coexpression network analysis (WGCNA) followed by functional enrichment analysis of the genes and lncRNAs in significant modules. Among these selected modules, the yellow and brown modules were significantly related to sheep fecundity. lncRNAs (e.g., NR0B1, XLOC_041882, and MYH15) in the yellow module were mainly involved in the TGF-β signalling pathway, and NYAP1 and BCORL1 were significantly associated with the oxytocin signalling pathway, which regulates several genes in the coexpression network of the brown module. Overall, we identified several gene modules associated with sheep fecundity, as well as networks consisting of hub genes and lncRNAs that may contribute to sheep prolificacy by regulating the target mRNAs related to the TGF-β and oxytocin signalling pathways. This study provides an alternative strategy for the identification of potential candidate regulatory lncRNAs.
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Miao X, Luo Q, Zhao H, Qin X. Genome-wide analysis of miRNAs in the ovaries of Jining Grey and Laiwu Black goats to explore the regulation of fecundity. Sci Rep 2016; 6:37983. [PMID: 27897262 PMCID: PMC5126701 DOI: 10.1038/srep37983] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 11/02/2016] [Indexed: 11/09/2022] Open
Abstract
Goat fecundity is important for agriculture and varies depending on the genetic background of the goat. Two excellent domestic breeds in China, the Jining Grey and Laiwu Black goats, have different fecundity and prolificacies. To explore the potential miRNAs that regulate the expression of the genes involved in these prolific differences and to potentially discover new miRNAs, we performed a genome-wide analysis of the miRNAs in the ovaries from these two goats using RNA-Seq technology. Thirty miRNAs were differentially expressed between the Jining Grey and Laiwu Black goats. Gene Ontology and KEGG pathway analyses revealed that the target genes of the differentially expressed miRNAs were significantly enriched in several biological processes and pathways. A protein-protein interaction analysis indicated that the miRNAs and their target genes were related to the reproduction complex regulation network. The differential miRNA expression profiles found in the ovaries between the two distinctive breeds of goats studied here provide a unique resource for addressing fecundity differences in goats.
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Affiliation(s)
- Xiangyang Miao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Qingmiao Luo
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huijing Zhao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaoyu Qin
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Ovarian transcriptomic study reveals the differential regulation of miRNAs and lncRNAs related to fecundity in different sheep. Sci Rep 2016; 6:35299. [PMID: 27731399 PMCID: PMC5059661 DOI: 10.1038/srep35299] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 09/27/2016] [Indexed: 01/18/2023] Open
Abstract
miRNAs and lncRNAs, which represent one of the most highly expressed classes of ncRNAs in development, are attracting increasing interest. A variety of regulators is considered to be implicated in sheep species with different fecundity. However, interactions between miRNAs and lncRNAs and changes in the expression of regulatory lncRNAs in sheep fecundity have not yet been reported. To characterize the important roles of miRNAs and lncRNAs and elucidate their regulating networks in sheep prolificacy, a genome-wide analysis of miRNAs and lncRNAs from Small Tail Han sheep of genotypes FecBBFecBB (Han BB) and FecB+ FecB+ (Han++) and from Dorset sheep (Dorset) was performed. An integrated analysis of miRNAs and lncRNAs was performed to study the regulatory function of miRNAs and lncRNAs in fecundity, revealing significantly correlated patterns of expression. Dramatic changes of miRNAs and lncRNAs suggest their critical roles in sheep fecundity. In conclusion, this is the first study performing thorough investigations of regulatory relationships among lncRNAs, miRNA and mRNAs, which will provide a novel view of the regulatory mechanisms involved in sheep fecundity. These results may provide further insight into sheep fecundity and help us to improve sheep prolificacy.
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Transcriptomic Analysis Identifies Candidate Genes Related to Intramuscular Fat Deposition and Fatty Acid Composition in the Breast Muscle of Squabs (Columba). G3-GENES GENOMES GENETICS 2016; 6:2081-90. [PMID: 27175015 PMCID: PMC4938661 DOI: 10.1534/g3.116.029793] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Despite the fact that squab is consumed throughout the world because of its high nutritional value and appreciated sensory attributes, aspects related to its characterization, and in particular genetic issues, have rarely been studied. In this study, meat traits in terms of pH, water-holding capacity, intramuscular fat content, and fatty acid profile of the breast muscle of squabs from two meat pigeon breeds were determined. Breed-specific differences were detected in fat-related traits of intramuscular fat content and fatty acid composition. RNA-Sequencing was applied to compare the transcriptomes of muscle and liver tissues between squabs of two breeds to identify candidate genes associated with the differences in the capacity of fat deposition. A total of 27 differentially expressed genes assigned to pathways of lipid metabolism were identified, of which, six genes belonged to the peroxisome proliferator-activated receptor signaling pathway along with four other genes. Our results confirmed in part previous reports in livestock and provided also a number of genes which had not been related to fat deposition so far. These genes can serve as a basis for further investigations to screen markers closely associated with intramuscular fat content and fatty acid composition in squabs. The data from this study were deposited in the National Center for Biotechnology Information (NCBI)’s Sequence Read Archive under the accession numbers SRX1680021 and SRX1680022. This is the first transcriptome analysis of the muscle and liver tissue in Columba using next generation sequencing technology. Data provided here are of potential value to dissect functional genes influencing fat deposition in squabs.
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Ovarian proteomic study reveals the possible molecular mechanism for hyperprolificacy of Small Tail Han sheep. Sci Rep 2016; 6:27606. [PMID: 27271055 PMCID: PMC4897777 DOI: 10.1038/srep27606] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 05/17/2016] [Indexed: 11/27/2022] Open
Abstract
Small Tail Han sheep is a widely bred farm animal in China which has attracted lots of attention due to their high prolificacy and year-round estrus. However, the molecular mechanism of its fecundity remains unrevealed. The FecB gene polymorphism has been found to be associated with the ovulation rate and litter size of sheep. In the present study, we constructed an iTRAQ-based quantitative proteomics analysis to compare the ovarian proteomes of FecB+FecB+ genotype Small Tail Han sheep ewes (Han ++), FecBBFecBB Han ewes (Han BB) and Dorset ewes (Dorset). Hundreds of differentially expressed proteins between each two groups were identified; GO and KEGG pathway analysis indicated that the expressions of those proteins involved in ribosome assembly, protein translation and mTOR pathway between Dorset and both Han groups were highly different. Between Han ++ and Han BB groups, higher level of protein expressions were related to mitochondrial oxidation functions such as oxidoreductase activity, cytochrome-c oxidase activity and electron carrier activity. This was identified in Han BB group, which may contribute to the elevated ovulation rate of Han BB ewes. In conclusion, our work provided a prospective understanding of the molecular mechanism for high prolificacy of Small Tail Han sheep.
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