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M. Abdelsattar M, Vargas-Bello-Pérez E, Zhang N. Age-related changes in blood biochemical composition of Hu sheep. ITALIAN JOURNAL OF ANIMAL SCIENCE 2022. [DOI: 10.1080/1828051x.2022.2108730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
- Mahmoud M. Abdelsattar
- Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research of Chinese Academy of Agricultural Sciences, Beijing, China
- Department of Animal and Poultry Production, Faculty of Agriculture, South Valley University, Qena, Egypt
| | - Einar Vargas-Bello-Pérez
- Department of Animal Sciences, School of Agriculture, Policy and Development, University of Reading, Reading, UK
| | - Naifeng Zhang
- Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research of Chinese Academy of Agricultural Sciences, Beijing, China
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Hodge MJ, de las Heras-Saldana S, Rindfleish SJ, Stephen CP, Pant SD. Characterization of Breed Specific Differences in Spermatozoal Transcriptomes of Sheep in Australia. Genes (Basel) 2021; 12:genes12020203. [PMID: 33573244 PMCID: PMC7912062 DOI: 10.3390/genes12020203] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/10/2021] [Accepted: 01/22/2021] [Indexed: 01/27/2023] Open
Abstract
Reduced reproductive efficiency results in economic losses to the Australian sheep industry. Reproductive success, particularly after artificial insemination, is dependent on a number of contributing factors on both ewe and ram sides. Despite considerable emphasis placed on characterising ewe side contributions, little emphasis has been placed on characterising ram side contributions to conception success. Over 14,000 transcripts are in spermatozoa of other species, which are transferred to the ova on fertilisation. These transcripts conceivably influence early embryonic development and whether conception is successful. Semen was collected (n = 45) across three breeds; Merino, Dohne, and Poll Dorset. Following collection, each ejaculate was split in two; an aliquot was assessed utilising Computer Assisted Semen Analysis (CASA) and the remaining was utilised for RNA extraction and subsequent next-generation sequencing. Overall, 754 differentially expressed genes were identified in breed contrasts and contrast between ejaculates of different quality. Downstream analysis indicated that these genes could play significant roles in a broad range of physiological functions, including maintenance of spermatogenesis, fertilisation, conception, embryonic development, and offspring production performance. Overall results provide evidence that the spermatozoal transcriptome could be a crucial contributing factor in improving reproductive performance as well as in the overall productivity and profitability of sheep industries.
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Affiliation(s)
- Marnie J. Hodge
- Graham Centre for Agricultural Innovation (Charles Sturt University and NSW Department of Primary Industries), Charles Sturt University, Wagga Wagga, NSW 2678, Australia; (M.J.H.); (C.P.S.)
- Apiam Animal Health, Apiam Genetic Services, Dubbo, NSW 2830, Australia;
| | - Sara de las Heras-Saldana
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia;
| | | | - Cyril P. Stephen
- Graham Centre for Agricultural Innovation (Charles Sturt University and NSW Department of Primary Industries), Charles Sturt University, Wagga Wagga, NSW 2678, Australia; (M.J.H.); (C.P.S.)
| | - Sameer D. Pant
- Graham Centre for Agricultural Innovation (Charles Sturt University and NSW Department of Primary Industries), Charles Sturt University, Wagga Wagga, NSW 2678, Australia; (M.J.H.); (C.P.S.)
- Correspondence:
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Esmaeili-Fard SM, Gholizadeh M, Hafezian SH, Abdollahi-Arpanahi R. Genome-wide association study and pathway analysis identify NTRK2 as a novel candidate gene for litter size in sheep. PLoS One 2021; 16:e0244408. [PMID: 33481819 PMCID: PMC7822323 DOI: 10.1371/journal.pone.0244408] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/08/2020] [Indexed: 12/14/2022] Open
Abstract
Litter size is one of the most important economic traits in sheep. Identification of gene variants that are associated with the prolificacy rate is an important step in breeding program success and profitability of the farm. So, to identify genetic mechanisms underlying the variation in litter size in Iranian Baluchi sheep, a two-step genome-wide association study (GWAS) was performed. GWAS was conducted using genotype data from 91 Baluchi sheep. Estimated breeding values (EBVs) for litter size calculated for 3848 ewes and then used as the response variable. Besides, a pathway analysis using GO and KEGG databases were applied as a complementary approach. A total of three single nucleotide polymorphisms (SNPs) associated with litter size were identified, one each on OAR2, OAR10, and OAR25. The SNP on OAR2 is located within a novel putative candidate gene, Neurotrophic receptor tyrosine kinase 2. This gene product works as a receptor which is essential for follicular assembly, early follicular growth, and oocyte survival. The SNP on OAR25 is located within RAB4A which is involved in blood vessel formation and proliferation through angiogenesis. The SNP on OAR10 was not associated with any gene in the 1Mb span. Moreover, gene-set analysis using the KEGG database identified several pathways, such as Ovarian steroidogenesis, Steroid hormone biosynthesis, Calcium signaling pathway, and Chemokine signaling. Also, pathway analysis using the GO database revealed several functional terms, such as cellular carbohydrate metabolic, biological adhesion, cell adhesion, cell junction, and cell-cell adherens junction, among others. This is the first study that reports the NTRK2 gene affecting litter size in sheep and our study of this gene functions showed that this gene could be a good candidate for further analysis.
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Affiliation(s)
- Seyed Mehdi Esmaeili-Fard
- Department of Animal Sciences and Fisheries, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran
- * E-mail:
| | - Mohsen Gholizadeh
- Department of Animal Sciences and Fisheries, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran
| | - Seyed Hasan Hafezian
- Department of Animal Sciences and Fisheries, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran
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Tao L, He XY, Jiang YT, Lan R, Li M, Li ZM, Yang WF, Hong QH, Chu MX. Combined approaches to reveal genes associated with litter size in Yunshang black goats. Anim Genet 2020; 51:924-934. [PMID: 32986880 DOI: 10.1111/age.12999] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2020] [Indexed: 01/25/2023]
Abstract
Intensive artificial selection has been imposed in Yunshang black goats, the first black specialist mutton goat breed in China, with a breeding object of improving reproductive performance, which has contributed to reshaping of the genome including the characterization of SNP, ROH and haplotype. However, variation in reproductive ability exists in the present population. A WGS was implemented in two subpopulations (polytocous group, PG, and monotocous group, MG) with evident differences of litter size. Following the mapping to reference genome, and SNP calling and pruning, three approaches - GWAS, ROH analysis and detection of signatures of selection - were employed to unveil candidate genes responsible for litter size. Consequently, 12 candidate genes containing OSBPL8 with the minimum P-value were uncovered by GWAS. Differences were observed in the pattern of ROH between two subpopulations that shared similar low inbreeding coefficients. Two ROH hotspots and 12 corresponding genes emerged from ROH pool association analysis. Based on the nSL statistic, 15 and 61 promising genes were disclosed under selection for MG and PG respectively. Of them, some promising genes participate in ovarian function (PPP2R5C, CDC25A, ESR1, RPS26 and SERPINBs), seasonal reproduction (DIO3, BTG1 and CRYM) and metabolism (OSBPL8, SLC39A5 and SERPINBs). Our study pinpointed some novel promising genes influencing litter size, provided a comprehensive insight into genetic makeup of litter size and might facilitate selective breeding in goats.
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Affiliation(s)
- L Tao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - X Y He
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Y T Jiang
- Yunnan Animal Science and Veterinary Institute, Kunming, 650224, China
| | - R Lan
- Yunnan Animal Science and Veterinary Institute, Kunming, 650224, China
| | - M Li
- Annoroad Gene Technology Co. Ltd, Beijing, 100176, China
| | - Z M Li
- Annoroad Gene Technology Co. Ltd, Beijing, 100176, China
| | - W F Yang
- Annoroad Gene Technology Co. Ltd, Beijing, 100176, China
| | - Q H Hong
- Yunnan Animal Science and Veterinary Institute, Kunming, 650224, China
| | - M X Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
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Seasonal effects on miRNA and transcriptomic profile of oocytes and follicular cells in buffalo (Bubalus bubalis). Sci Rep 2020; 10:13557. [PMID: 32782284 PMCID: PMC7419291 DOI: 10.1038/s41598-020-70546-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 07/28/2020] [Indexed: 12/19/2022] Open
Abstract
Season clearly influences oocyte competence in buffalo (Bubalus bubalis); however, changes in the oocyte molecular status in relation to season are poorly understood. This study characterizes the microRNA (miRNA) and transcriptomic profiles of oocytes (OOs) and corresponding follicular cells (FCs) from buffalo ovaries collected in the breeding (BS) and non-breeding (NBS) seasons. In the BS, cleavage and blastocyst rates are significantly higher compared to NBS. Thirteen miRNAs and two mRNAs showed differential expression (DE) in FCs between BS and NBS. DE-miRNAs target gene analysis uncovered pathways associated with transforming growth factor β (TGFβ) and circadian clock photoperiod. Oocytes cluster in function of season for their miRNA content, showing 13 DE-miRNAs between BS and NBS. Between the two seasons, 22 differentially expressed genes were also observed. Gene Ontology (GO) analysis of miRNA target genes and differentially expressed genes (DEGs) in OOs highlights pathways related to triglyceride and sterol biosynthesis and storage. Co-expression analysis of miRNAs and mRNAs revealed a positive correlation between miR-296-3p and genes related to metabolism and hormone regulation. In conclusion, season significantly affects female fertility in buffalo and impacts on oocyte transcriptomic of genes related to folliculogenesis and acquisition of oocyte competence.
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Xia Q, Li Q, Gan S, Guo X, Zhang X, Zhang J, Chu M. Exploring the roles of fecundity-related long non-coding RNAs and mRNAs in the adrenal glands of small-tailed Han Sheep. BMC Genet 2020; 21:39. [PMID: 32252625 PMCID: PMC7137433 DOI: 10.1186/s12863-020-00850-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 03/30/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) can play important roles in uterine and ovarian functions. However, little researches have been done on the role of lncRNAs in the adrenal gland of sheep. Herein, RNA sequencing was used to compare and analyze gene expressions in adrenal tissues between follicular phases and luteal phases in FecBBB (MM) and FecB++ (WW) sheep, respectively, and differentially expressed lncRNAs and genes associated with reproduction were identified. RESULTS In MM sheep, 38 lncRNAs and 545 mRNAs were differentially expressed in the adrenal gland between the luteal and follicular phases; In WW sheep, 513 differentially expressed lncRNAs and 2481 mRNAs were identified. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses indicated that differentially expressed lncRNAs and their target genes are mainly involved in the circadian rhythm, the mitogen activated protein kinase, thyroid, ovarian steroidogenesis and transforming growth factor beta signaling pathways. Differentially expressed lncRNAs can regulate reproduction by modulating genes involved in these signaling pathways and biological processes. Specifically, XLOC_254761, XLOC_357966, 105,614,839 and XLOC_212877 targeting CREB1, PER3, SMAD1 and TGFBR2, respectively, appear to play key regulatory roles. CONCLUSION These results broaden our understanding of lncRNAs in adrenal gland of sheep and provide new insights into the molecular mechanisms underlying sheep reproduction.
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Affiliation(s)
- Qing Xia
- Key Laboratory of Animal Genetics and Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, P. R. China
| | - Qiuling Li
- College of Life Sciences, Langfang Normal University, Langfang, 065000, P.R. China
| | - Shangquan Gan
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, P. R. China
| | - Xiaofei Guo
- Tianjin Institute of Animal Sciences, Tianjin, 300381, P. R. China
| | - Xiaosheng Zhang
- Tianjin Institute of Animal Sciences, Tianjin, 300381, P. R. China
| | - Jinlong Zhang
- Tianjin Institute of Animal Sciences, Tianjin, 300381, P. R. China
| | - Mingxing Chu
- Key Laboratory of Animal Genetics and Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, P. R. China.
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Yang H, Lin S, Lei X, Yuan C, Yu Y, Zhao Z, Chen J. Nutritional status affects the microRNA profile of the hypothalamus of female sheep. Reprod Fertil Dev 2019; 30:946-957. [PMID: 29366447 DOI: 10.1071/rd17179] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 10/21/2017] [Indexed: 12/19/2022] Open
Abstract
Recent studies on the seasonal regulation of the oestrous cycle in sheep have focussed mainly on the responses to photoperiod. However, the brain systems that control reproductive activity also respond to nutritional inputs, although the molecular mechanisms involved are not completely understood. One possibility is that small, non-coding RNAs, such as micro-RNAs (miRNAs), have significant influence. In the present study, the amounts and characteristics of miRNAs in hypothalamus from oestrous and anestrous ewes, fed low- or high-nutrient diets, were compared using Illumina HiSeq sequencing technology. In total, 398 miRNAs, including 261 novel miRNAs, were identified in ewes with an enhanced nutritional status (HEN), whereas 384 miRNAs, including 247 novel miRNAs, were identified in the ewes with a lesser nutritional status (HAN). There were eight conserved and 140 novel miRNAs expressed differentially between the two libraries. Based on quantitative real-time polymerase chain reaction, six miRNAs were assessed to verify the accuracy of the library database. Moreover, the correlation between the miRNA target and several upstream and downstream genes in the oestrus-related pathways were also verified in hypothalamus nerve cells. According to the results, nutritional status plays an important role in oestrous regulation in sheep, and the hypothalamic processes and pathways induced by nutritional signals (folic acid and tyrosine) are different from those induced by photoperiodic regulation of oestrus. We have expanded the repertoire of sheep miRNAs that could contribute to the molecular mechanisms that regulate the initiation of oestrous cycles in anestrous ewes in response to the influence of nutritional status.
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Affiliation(s)
- Heng Yang
- College of Animal Science and Technology, Shihezi University, North Fourth Road, Shihezi 832003, China
| | - Shan Lin
- College of Life Sciences, Shihezi University, North Fourth Road, Shihezi 832003, China
| | - Xiaoping Lei
- College of Animal Science and Technology, Shihezi University, North Fourth Road, Shihezi 832003, China
| | - Cong Yuan
- College of Animal Science and Technology, Shihezi University, North Fourth Road, Shihezi 832003, China
| | - Yaosheng Yu
- College of Animal Science and Technology, Shihezi University, North Fourth Road, Shihezi 832003, China
| | - Zongsheng Zhao
- College of Animal Science and Technology, Shihezi University, North Fourth Road, Shihezi 832003, China
| | - Jingbo Chen
- College of Animal Science and Technology, Shihezi University, North Fourth Road, Shihezi 832003, China
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Yurchenko AA, Deniskova TE, Yudin NS, Dotsev AV, Khamiruev TN, Selionova MI, Egorov SV, Reyer H, Wimmers K, Brem G, Zinovieva NA, Larkin DM. High-density genotyping reveals signatures of selection related to acclimation and economically important traits in 15 local sheep breeds from Russia. BMC Genomics 2019; 20:294. [PMID: 32039702 PMCID: PMC7227232 DOI: 10.1186/s12864-019-5537-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background Domestication and centuries of selective breeding have changed genomes of sheep breeds to respond to environmental challenges and human needs. The genomes of local breeds, therefore, are valuable sources of genomic variants to be used to understand mechanisms of response to adaptation and artificial selection. As a step toward this we performed a high-density genotyping and comprehensive scans for signatures of selection in the genomes from 15 local sheep breeds reared across Russia. Results Results demonstrated that the genomes of Russian sheep breeds contain multiple regions under putative selection. More than 50% of these regions matched with intervals identified in previous scans for selective sweeps in sheep genomes. These regions contain well-known candidate genes related to morphology, adaptation, and domestication (e.g., KITLG, KIT, MITF, and MC1R), wool quality and quantity (e.g., DSG@, DSC@, and KRT@), growth and feed intake (e.g., HOXA@, HOXC@, LCORL, NCAPG, LAP3, and CCSER1), reproduction (e.g., CMTM6, HTRA1, GNAQ, UBQLN1, and IFT88), and milk-related traits (e.g., ABCG2, SPP1, ACSS1, and ACSS2). In addition, multiple genes that are putatively related to environmental adaptations were top-ranked in selected intervals (e.g., EGFR, HSPH1, NMUR1, EDNRB, PRL, TSHR, and ADAMTS5). Moreover, we observed that multiple key genes involved in human hereditary sensory and autonomic neuropathies, and genetic disorders accompanied with an inability to feel pain and environmental temperatures, were top-ranked in multiple or individual sheep breeds from Russia pointing to a possible mechanism of adaptation to harsh climatic conditions. Conclusions Our work represents the first comprehensive scan for signatures of selection in genomes of local sheep breeds from the Russian Federation of both European and Asian origins. We confirmed that the genomes of Russian sheep contain previously identified signatures of selection, demonstrating the robustness of our integrative approach. Multiple novel signatures of selection were found near genes which could be related to adaptation to the harsh environments of Russia. Our study forms a basis for future work on using Russian sheep genomes to spot specific genetic variants or haplotypes to be used in efforts on developing next-generation highly productive breeds, better suited to diverse Eurasian environments. Electronic supplementary material The online version of this article (10.1186/s12864-019-5537-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrey A Yurchenko
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
| | - Tatiana E Deniskova
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, Russia
| | - Nikolay S Yudin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Arsen V Dotsev
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, Russia
| | - Timur N Khamiruev
- Research Institute of Veterinary Medicine of Eastern Siberia, The Branch of the Siberian Federal Scientific Center for Agrobiotechnologies of the Russian Academy of Sciences, Chita, Russia
| | - Marina I Selionova
- All-Russian Research Institute of Sheep and Goat Breeding - branch of the Federal State Budgetary Scientific Institution North Caucasian Agrarian Center, Stavropol, 355017, Russia
| | - Sergey V Egorov
- Siberian Research Institute of Animal Husbandry, Krasnoobsk, Russia
| | - Henry Reyer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Klaus Wimmers
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Gottfried Brem
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, Russia.,Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria
| | - Natalia A Zinovieva
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, Russia.
| | - Denis M Larkin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia. .,Royal Veterinary College, University of London, London, UK.
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Li X, Li C, Wei J, Ni W, Xu Y, Yao R, Zhang M, Li H, Liu L, Dang H, Hazi W, Hu S. Comprehensive Expression Profiling Analysis of Pituitary Indicates that circRNA Participates in the Regulation of Sheep Estrus. Genes (Basel) 2019; 10:genes10020090. [PMID: 30696117 PMCID: PMC6409929 DOI: 10.3390/genes10020090] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 01/23/2019] [Accepted: 01/23/2019] [Indexed: 01/01/2023] Open
Abstract
The pituitary gland is the most important endocrine organ that mainly regulates animal estrus by controlling the hormones synthesis. There is a significant difference between the estrus state and anestrus state of sheep pituitary system. Here, we studied the circular RNA (circRNA) expression profiles of the anterior pituitary of estrus and anestrus sheep using RNA-seq technology. Through this study, we identified a total of 12,468 circRNAs and 9231 differentially expressed circRNAs in the estrus and anestrus pituitary system of sheep. We analyzed some differentially expressed circRNAs by reverse transcription quantitative-PCR (RT-qPCR), and some circRNAs were demonstrated using RNase-R+ resistance experiments. CircRNAs involving the regulation of estrus-related terms and pathways are enriched by using gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. In addition, we also predicted partial microRNA-circRNA interaction network for circRNAs that regulate sheep estrus. Overall, this study explored a potential substantial role played by circRNAs involved in pituitary regulation on sheep estrus and proposed new questions for further study.
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Affiliation(s)
- Xiaoyue Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China.
| | - Cunyuan Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China.
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, 832003, China.
| | - Junchang Wei
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China.
| | - Wei Ni
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China.
| | - Yueren Xu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China.
| | - Rui Yao
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China.
| | - Mengdan Zhang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China.
| | - Huixiang Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China.
| | - Li Liu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China.
| | - Hanli Dang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China.
| | - Wureli Hazi
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, 832003, China.
| | - Shengwei Hu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China.
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He B, Jin S, Cao J, Mi L, Wang J. Metatranscriptomics of the Hu sheep rumen microbiome reveals novel cellulases. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:153. [PMID: 31249617 PMCID: PMC6587244 DOI: 10.1186/s13068-019-1498-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/14/2019] [Indexed: 05/11/2023]
Abstract
BACKGROUND Cellulosic biomass has great potential as a renewable biofuel resource. Robust, high-performance enzymes are needed to effectively utilize this valuable resource. In this study, metatranscriptomics was used to explore the carbohydrate-active enzymes (CAZymes), especially glycoside hydrolases (GHs), present in the rumen microbiome of Hu sheep. Select CAZymes were experimentally verified and characterized after cloning and expression in E. coli. RESULTS The metatranscriptomes of six Hu sheep rumen microbiomes yielded 42.3 Gbp of quality-checked sequence data that represented in total 2,380,783 unigenes after de novo assembling using Trinity and clustered with CD-HIT-EST. Annotation using the CAZy database revealed that 2.65% of the unigenes encoded GHs, which were assigned to 111 different CAZymes families. Firmicutes (18.7%) and Bacteroidetes (13.8%) were the major phyla to which the unigenes were taxonomically assigned. In total, 14,489 unigenes were annotated to 15 cellulase-containing GH families, with GH3, GH5 and GH9 being the predominant. From these putative cellulase-encoding unigenes, 4225 open reading frames (ORFs) were predicted to contain 2151 potential cellulase catalytic modules. Additionally, 147 ORFs were found to encode proteins that contain carbohydrate-binding modules (CBMs). Heterogeneous expression of 30 candidate cDNAs from the GH5 family in E. coli BL21 showed that 17 of the tested proteins had endoglucanase activity, while 7 exhibited exoglucanase activity. Interestingly, two of the GH5 proteins (Cel5A-h28 and Cel5A-h11) showed high specific activity against carboxymethylcellulose (CMC) and p-nitrophenyl-β-d-cellobioside (pNPC) (222.2 and 142.8 U/mg), respectively. The optimal pH value for activity of Cel5A-h11 and Cel5A-h28 was 6.0 for both enzymes, and optimal temperatures were 40 and 50 °C, respectively. Both enzymes retained over 70 and 60%, respectively, of their original activities after incubation at 40 °C for 60 min. However, their activities were rapidly diminished upon exposure to higher temperatures. Cel5A-h11 and Cel5A-h28 retained more than 80 and 60% of their maximal enzymatic activities after incubation for 16 h in buffered solutions in the pH range from 4.0 to 9.0. CONCLUSION The metatranscriptomic results revealed that the rumen microbiome of Hu sheep encoded a repertoire of new enzymes capable of cellulose degradation and metatranscriptomics was an effective method to discover novel cellulases for biotechnological applications.
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Affiliation(s)
- Bo He
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Shuwen Jin
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Jiawen Cao
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Lan Mi
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Jiakun Wang
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058 China
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Chai JM, Ma T, Wang HC, Qi ML, Tu Y, Diao QY, Zhang NF. Effect of early weaning age on growth performance, nutrient digestibility, and serum parameters of lambs. ANIMAL PRODUCTION SCIENCE 2017. [DOI: 10.1071/an15079] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
To determine the effect of a weaning program on growth performance, nutrient digestibility, and serum parameters in Hu lambs, 48 newly born twin lambs (2.53 ± 0.13 kg; 24 male and 24 female) were randomly divided into four treatments: ewe reared (ER) or weaned at 10, 20, or 30 days post birth (EW10, EW20, and EW30) and fed milk replacer (MR). All liquid feed were eliminated at 60 days of age. Creep feed was offered ad libitum to all lambs from 15 to 90 days of age. The results indicated that lambs fed MR had higher liveweight, average daily gain, and creep feed intake (P < 0.001) than those in the ER group. There were no differences between treatments in the apparent digestibility of dry matter, organic matter, nitrogen or phosphorus (P > 0.05) from 50 to 60 days of age. The apparent digestibility of dry matter, organic matter, nitrogen and phosphorus of EW20 and EW30 groups were significantly higher (P < 0.05) than that of EW10 and ER groups from 80 to 90 days of age. Lambs in the EW10 group had higher concentration of albumin, serum urea nitrogen, and immunoglobulin G levels than those of other groups (P < 0.05). In conclusion, early weaning could improve creep intake, growth performance, and nutrient utilisation of Hu lambs. Early weaning age had a significant effect on the growth of lambs.
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Yang H, Lin S, Lei X, Yuan C, Tian Z, Yu Y, Zhao Z, Chen J. Identification and profiling of microRNAs from ovary of estrous Kazakh sheep induced by nutritional status in the anestrous season. Anim Reprod Sci 2016; 175:18-26. [PMID: 27773477 DOI: 10.1016/j.anireprosci.2016.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Revised: 10/10/2016] [Accepted: 10/14/2016] [Indexed: 10/20/2022]
Abstract
Estrous regulation in sheep has an important role in the sheep industry in improving production of meat and wool. It has been reported that an enhanced nutritional status can induce estrus resulting in an end of the anestrous season earlier than occurs in ewes with a lesser nutritional status. However, the endocrine and physiological mechanisms that induce the increased incidence of estrus remains unclear. In the present study, the differences in amounts and characteristics of miRNAs in ewes at estrus or during the anestrous season were screened by using the Illumina HiSeq sequencing technology. In total, 294 miRNAs, including 174 novel miRNA candidates, were identified in ewes with an enhanced nutritional status (OEN) through assessment of the OEN library for this group and 307 miRNAs including 186 novel miRNA candidates were identified in the ewes with a lesser nutritional status (OAN) through assessing the OAN library, among which there were nine conserved and 104 novel miRNAs in differential amounts between the two libraries. Based on poly (A) q-PCR, six miRNAs were assessed to verify the accuracy of the library database. Furthermore, the family of the known miRNAs, the target genes and related pathways were also analyzed. The results indicated that the nutritional status had important roles in estrous regulation in sheep. The PLA2G4D can directly regulate ovarian follicle development, or indirectly influence leptin secretion involved in the regulation of the reproductive endocrine and physiological systems during the anestrous season. The identification of significantly different miRNAs expanded the repertoire of sheep miRNAs that have been examined and could contribute to further studies on the molecular mechanism of regulation of initiation of estrous cycles in previously anestrous ewes as influenced by different nutritional status.
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Affiliation(s)
- Heng Yang
- College of Animal Science and Technology, Shihezi University, Shihezi 832003, China
| | - Shan Lin
- College of Life Sciences, Shihezi University, Shihezi 832003, China
| | - Xiaoping Lei
- College of Animal Science and Technology, Shihezi University, Shihezi 832003, China
| | - Cong Yuan
- College of Animal Science and Technology, Shihezi University, Shihezi 832003, China
| | - Zhanwei Tian
- College of Animal Science and Technology, Shihezi University, Shihezi 832003, China
| | - Yaosheng Yu
- College of Animal Science and Technology, Shihezi University, Shihezi 832003, China
| | - Zongsheng Zhao
- College of Animal Science and Technology, Shihezi University, Shihezi 832003, China.
| | - Jingbo Chen
- College of Animal Science and Technology, Shihezi University, Shihezi 832003, China; Xinjiang Academy of Animal Sciences, Urumqi 830011, China.
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Chai J, Diao Q, Wang H, Tu Y, Tao X, Zhang N. Effects of weaning age on growth, nutrient digestibility and metabolism, and serum parameters in Hu lambs. ACTA ACUST UNITED AC 2015; 1:344-348. [PMID: 29767014 PMCID: PMC5941006 DOI: 10.1016/j.aninu.2015.11.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 11/10/2015] [Accepted: 11/12/2015] [Indexed: 11/27/2022]
Abstract
This study was conducted to investigate the effect of weaning age on growth performance, nutrient digestion and metabolism, and serological indicators, and to obtain an optimal weaning age in Hu lambs. Forty-eight newborn Hu lambs (birth weight, 2.53 ± 0.14 kg) were randomly divided into 4 groups. The lambs in control group (ER) suckled their dams. The lambs in other three experimental groups were weaned on milk replacer at 10, 20, and 30 days of age (EW10, EW20, and EW30 groups), respectively. The results were as follows: 1) lambs in EW10 and EW30 groups had a lower (P < 0.05) ADG than those in ER group within 10 days post-weaning; the weaned lambs began to show a higher (P < 0.05) ADG than those in ER group after 20 days post-weaning. 2) EW10 and EW20 groups had a higher (P < 0.05) creep feed intake than EW30 and ER groups from 15 to 60 days of age. 3) The apparent digestibility of dry matter, organic matter, gross energy, nitrogen, ether extract and phosphorus, and the deposition of nitrogen and phosphorus did not differ (P > 0.05) among groups; however, the apparent digestibility and deposition of calcium in early weaned lambs were lower (P < 0.05) than those in ewe-reared lambs. 4) The albumin content in EW30 group was lower (P < 0.05) than that in ER group; the globulin content in EW30 group was higher (P < 0.05) than that in other groups; the content of serum insulin-like growth factor-Ⅰ in weaned lambs tended to increase compared with lambs in ER group. Finally, the growth rate of lambs decreased within 10 days post-weaning, but early weaning boosted creep feed intake, leading to better growth and health later in life. The Hu lambs can be weaned on milk replacer and creep feed at 10 days of age.
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Affiliation(s)
- Jianmin Chai
- Feed Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture, Beijing 100081, China
| | - Qiyu Diao
- Feed Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture, Beijing 100081, China
| | - Haichao Wang
- Feed Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture, Beijing 100081, China
| | - Yan Tu
- Feed Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture, Beijing 100081, China
| | - Xiaojing Tao
- Jiangsu Taizhou Helen Sheep Ltd. Taizhou 225300, China
| | - Naifeng Zhang
- Feed Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture, Beijing 100081, China
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Hu X, Pokharel K, Peippo J, Ghanem N, Zhaboyev I, Kantanen J, Li MH. Identification and characterization of miRNAs in the ovaries of a highly prolific sheep breed. Anim Genet 2015; 47:234-9. [PMID: 26582387 DOI: 10.1111/age.12385] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2015] [Indexed: 12/22/2022]
Abstract
Until recently, there have been few studies concerning miRNAs or miRNA-mediated biological processes in sheep (Ovis aries). In the present study, we used a deep-sequencing approach to examine ovarian miRNAs and the mRNA transcriptomes in two ewes of a highly prolific breed, Finnsheep. We identified 113 known sheep miRNAs, 131 miRNAs conserved in other mammals and 60 novel miRNAs, the expression levels of which accounted for 78.22%, 21.73% and 0.05% of the total respectively. Furthermore, the 10 most abundantly expressed miRNAs in the two libraries were characterized in detail, and the putative target genes of these miRNAs were annotated using GO annotation and KEGG pathway enrichment analyses. Among the target genes, intracellular transducers (SMAD1, SMAD4, SMAD5 and SMAD9) and bone morphogenetic protein (BMP) receptors (BMPR1B and BMPR2) were involved in the transforming growth factor β (TGFβ) signaling pathway in the reproductive axis, and the most significant GO terms were intracellular part (GO:0044424), binding (GO:0005488) and biological_process (GO:0008150) for cellular component, molecular function and biological process respectively. Thus, these results expanded the sheep miRNA database and provided additional information on the prolificacy trait regulated through specific miRNAs in sheep and other mammals.
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Affiliation(s)
- Xiaoju Hu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China.,University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Kisun Pokharel
- Green Technology, Natural Resources Institute Finland (Luke), Jokioinen, 31600, Finland.,Department of Biology, University of Eastern Finland, Kuopio, 70211, Finland
| | - Jaana Peippo
- Green Technology, Natural Resources Institute Finland (Luke), Jokioinen, 31600, Finland
| | - Nasser Ghanem
- Green Technology, Natural Resources Institute Finland (Luke), Jokioinen, 31600, Finland.,Animal Production Department, Faculty of Agriculture, Cairo University, Cairo, Giza, 12613
| | - Ismail Zhaboyev
- Department of Biology, University of Eastern Finland, Kuopio, 70211, Finland.,Faculty of Veterinary Medicine, Kazakh National Agrarian University, Almaty, 050010, Kazakhstan
| | - Juha Kantanen
- Green Technology, Natural Resources Institute Finland (Luke), Jokioinen, 31600, Finland.,Department of Biology, University of Eastern Finland, Kuopio, 70211, Finland
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
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15
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Zhang X, Huang L, Wu T, Feng Y, Ding Y, Ye P, Yin Z. Transcriptomic Analysis of Ovaries from Pigs with High And Low Litter Size. PLoS One 2015; 10:e0139514. [PMID: 26426260 PMCID: PMC4591126 DOI: 10.1371/journal.pone.0139514] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 09/13/2015] [Indexed: 01/03/2023] Open
Abstract
Litter size is one of the most important economic traits for pig production as it is directly related to the production efficiency. Litter size is affected by interactions between multiple genes and the environment. While recent studies have identified some genes associated with prolificacy in pigs, transcriptomic studies of specific genes affecting litter size in porcine ovaries are rare. In order to identify candidate genes associated with litter size in swine, we assessed gene expression differences between the ovaries of Yorkshire pigs with extremely high and low litter sizes using the RNA-Seq method. A total of 1 243 differentially expressed genes were identified: 897 genes were upregulated and 346 genes were downregulated in high litter size ovary samples compared with low litter size ovary samples. A large number of these genes related to steroid hormone regulation in animal ovaries, including 59 Gene Ontology terms and 27 Kyoto Encyclopedia of Genes and Genomes pathways involved in steroid biosynthesis and ovarian steroidogenesis. From these differentially expressed genes, we identified a total of 11 genes using a bioinformatics screen that may be associated with high litter size in Yorkshire pigs. These results provide a list of new candidate genes for porcine litter size and prolificacy to be further investigated.
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Affiliation(s)
- Xiaodong Zhang
- Key Laboratory of Local Animal Genetic Resources Conservation and Bio-breeding of Anhui province, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui Province, People’s Republic of China
| | - Long Huang
- Key Laboratory of Local Animal Genetic Resources Conservation and Bio-breeding of Anhui province, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui Province, People’s Republic of China
| | - Tao Wu
- Key Laboratory of Local Animal Genetic Resources Conservation and Bio-breeding of Anhui province, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui Province, People’s Republic of China
| | - Yifang Feng
- Key Laboratory of Local Animal Genetic Resources Conservation and Bio-breeding of Anhui province, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui Province, People’s Republic of China
| | - Yueyun Ding
- Key Laboratory of Local Animal Genetic Resources Conservation and Bio-breeding of Anhui province, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui Province, People’s Republic of China
| | - Pengfei Ye
- Key Laboratory of Local Animal Genetic Resources Conservation and Bio-breeding of Anhui province, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui Province, People’s Republic of China
| | - Zongjun Yin
- Key Laboratory of Local Animal Genetic Resources Conservation and Bio-breeding of Anhui province, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui Province, People’s Republic of China
- * E-mail:
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Feng T, Cao GL, Chu MX, Di R, Huang DW, Liu QY, Pan ZY, Jin M, Zhang YJ, Li N. Identification and verification of differentially expressed genes in the caprine hypothalamic-pituitary-gonadal axis that are associated with litter size. Mol Reprod Dev 2015; 82:132-8. [PMID: 25651825 DOI: 10.1002/mrd.22451] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 12/03/2014] [Indexed: 11/11/2022]
Abstract
Litter size is a favorable economic trait for the goat industry, but remains a complex trait controlled by multiple genes in multiple organs. Several genes have been identified that may affect embryo survival, follicular development, and the health of fetuses during pregnancy. Jining Grey goats demonstrate the largest litter size among goat breeds indigenous to China. In order to better understand the genetic basis of this trait, six suppression subtractive hybridization (SSH) cDNA libraries were constructed using pooled mRNAs from hypothalamuses, pituitaries, and ovaries of sexually mature and adult polytocous Jining Grey goats, as testers, versus the pooled corresponding mRNAs of monotocous Liaoning Cashmere goats, as drivers. A total of 1,458 true-positive clones--including 955 known genes and 481 known and 22 unknown expressed sequence tags--were obtained from the SSH libraries by sequencing and alignment. The known genes were categorized into cellular processes and signaling information storage and processing, and metabolism. Three genes (FTH1, GH, and SAA) were selected to validate the SSH results by quantitative real-time PCR; all three were up-regulated in the corresponding tissues in the tester group indicating that these are candidate genes associated with the large litter size of Jining Grey goats. Several other identified genes may affect embryo survival, follicular development, and health during pregnancy. This study provides insights into the mechanistic basis by which the caprine hypothalamic-pituitary-gonadal axis affects reproductive traits and provides a theoretical basis for goat production and breeding.
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Affiliation(s)
- Tao Feng
- Key Laboratory of Farm Animal Genetic Resources Germplasm Innovation of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China; Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Science, Beijing, China
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Zhang P, Liu P, Dou H, Chen L, Chen L, Lin L, Tan P, Vajta G, Gao J, Du Y, Ma RZ. Handmade cloned transgenic sheep rich in omega-3 Fatty acids. PLoS One 2013; 8:e55941. [PMID: 23437077 PMCID: PMC3577796 DOI: 10.1371/journal.pone.0055941] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 01/07/2013] [Indexed: 01/31/2023] Open
Abstract
Technology of somatic cell nuclear transfer (SCNT) has been adapted worldwide to generate transgenic animals, although the traditional procedure relies largely on instrumental micromanipulation. In this study, we used the modified handmade cloning (HMC) established in cattle and pig to produce transgenic sheep with elevated levels of omega-3 (n−3) fatty acids. Codon-optimized nematode mfat-1 was inserted into a eukaryotic expression vector and was transferred into the genome of primary ovine fibroblast cells from a male Chinese merino sheep. Reverse transcriptase PCR, gas chromatography, and chromosome analyses were performed to select nuclear donor cells capable of converting omega-6 (n−6) into n−3 fatty acids. Blastocysts developed after 7 days of in vitro culture were surgically transplanted into the uterus of female ovine recipients of a local sheep breed in Xinjiang. For the HMC, approximately 8.9% (n = 925) of reconstructed embryos developed to the blastocyst stage. Four recipients became pregnant after 53 blastocysts were transplanted into 29 naturally cycling females, and a total of 3 live transgenic lambs were produced. Detailed analyses on one of the transgenic lambs revealed a single integration of the modified nematode mfat-1 gene at sheep chromosome 5. The transgenic sheep expressed functional n−3 fatty acid desaturase, accompanied by more than 2-folds reduction of n−6/n−3 ratio in the muscle (p<0.01) and other major organs/tissues (p<0.05). To our knowledge, this is the first report of transgenic sheep produced by the HMC. Compared to the traditional SCNT method, HMC showed an equivalent efficiency but proved cheaper and easier in operation.
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Affiliation(s)
- Peng Zhang
- State Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- Graduate University of the Chinese Academy of Sciences, Beijing, China
| | - Peng Liu
- BGI ARK Biotechnology Co., Ltd, Shenzhen, China
| | - Hongwei Dou
- BGI ARK Biotechnology Co., Ltd, Shenzhen, China
| | - Lei Chen
- State Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Longxin Chen
- State Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Lin Lin
- BGI ARK Biotechnology Co., Ltd, Shenzhen, China
| | - Pingping Tan
- State Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Gabor Vajta
- BGI ARK Biotechnology Co., Ltd, Shenzhen, China
- IRIS, Central Queensland University, Rockhampton, Australia
| | - Jianfeng Gao
- School of Life Sciences, Shihezi University, Shihezi, China
| | - Yutao Du
- BGI ARK Biotechnology Co., Ltd, Shenzhen, China
- BGI-Shenzhen, Shenzhen, China
- * E-mail: (RZM); (YD)
| | - Runlin Z. Ma
- State Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- Graduate University of the Chinese Academy of Sciences, Beijing, China
- * E-mail: (RZM); (YD)
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