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| 1 | Understanding divergent domestication traits from the whole-genome sequencing of swamp-and river-buffalo populations显示文摘Domesticated buffaloes have been integral to rice-paddy agro-ecosystems formillennia,yet relatively little is known about the buffalo genomics.Here,we sequenced and assembled reference genomes for both swamp and river buffaloes and we re-sequenced 230 individuals(132 swamp buffaloes and 98 river buffaloes)sampled from across Asia and Europe.Beyond the many actionable insights that our study revealed about the domestication,basic physiology and breeding of buffalo,we made the striking discovery that the divergent domestication traits between swamp and river buffaloes can be explained with recent selections of genes on social behavior,digestion metabolism,strengths and milk production. | Xier Luo Yu Zhou Bing Zhang Yi Zhang Xiaobo Wang Tong Feng Zhipeng Li Kuiqing Cui Zhiqiang Wang Chan Luo Hui Li Yanfei Deng Fenghua Lu Jianlin Han Yongwang Miao Huaming Mao Xiaoyan Yi Cheng Ai Shigang Wu Alun Li Zhichao Wu Zijun Zhuo Do Da Giang Bikash Mitra Mohammad Farhad Vahidi Shahid Mansoor Sahar Ahmed Al-Bayatti Eka Meutia Sari Neena Amatya Gorkhali Sigit Prastowo Laiba Shafique Guoyou Ye Qian Qian Baoshan Chen Deshun Shi Jue Ruan Qingyou Liu | 2020 | National Science Review2020，7，3： | 3 |
| 2 | Expression Pattern and Target Gene of bbu-miR-103-1 in Buffalo(Bubalus bubalis) at Lactation and Non-lactation Periods显示文摘[Objective] The paper aimed to investigate the expression pattern of bbu-miR-103-1 in buffalo( Bubalus bubalis) at lactation and non-lactation periods,and to predict its target gene and function. [Method]Expression pattern of bbu-miR-103-1 at lactation and non-lactation periods were detected by qRT-PCR.The precursor expression plasmid of bbu-miR-103-1 was constructed and named LpEZX-pre-miR-103-1. It was packaged and propagated to produce high-titer lentivirus in 293 T cell lines,which could be used to infect buffalo mammary epithelial cells( BMECs) and over express bbu-miR-103-1. The inhibitor of bbu-miR-103-1 was chemically synthesized and transfected into BMECs to suppress bbu-miR-103-1 at the same time. The relative expression of pantothenate kinase 3( PANK3) and milk fat metabolism related genes were detected by qRT-PCR. [Result]The relative expression of bbu-miR-103-1 at lactation period was 5. 29 times higher than that at non-lactation period in buffalo( P < 0. 01). The LpEZX-pre-miR-103-1 had been successfully constructed and packaged with the infection titer of 3. 47 × 10~6 PFU/m L. Overexpress or suppress of bbu-miR-103-1 extremely down-regulated or up-regulated the expression level of PANK3 in BMECs( P < 0. 01).Over expression of bbu-miR-103-1 extremely enhanced the expression of Acetyl-CoA carboxylase alpha( ACACA),Glycerol-3-phosphate acyltransferase 1 mitochondrial( GPAM),Diacylglycerol Oacyltransferase 1( DGAT1) and Pyruvate dehydrogenase lipoamide kinase isozyme 4( PDK4)( P < 0. 01),and also significantly up-regulated the expression of sterol regulatory element binding protein-1c( SREBP1c),Adipose differentiation-related protein( ADFP),Cluster of differentiation36( CD36),Acetyl-Co A synthetase short-chain subfamily member 1( ACSS1)( P < 0. 05). Over expression of bbu-miR-103-1 down-regulated the expression of PANK3,and improved the mRNA level of SREBP1c by feedback regulation,finally promoting the de novo synthesis of fatty acid beginning with ACACA.[Conclusion] bbu-miR-103-1 plays an important role in enhancing milk fatty acid synthesis,which provides a molecular base for revealing formation and regulatory mechanism of high-level milk fat in buffalo. | Cai Xiaoyan Li Sheng Chen Qiuping Wang Ping Deng Kai Liu Qingyou Shi Deshun | 2017 | Animal Husbandry and Feed Science2017，9，3： | 1 |
| 3 | Co - culture embedded in cumulus clumps promotes matu- ration of denuded oocytes and reconstructs gap junc- tions between oocytes and cumulus cells显示文摘 | Guixue Feng Deshun Shi Shufang Yang | 2012 | Zygote2012，3，： | 1 |
| 4 | Optimized production of transgenic buffalo embryos and offspring by cytoplasmic zygote injection显示文摘Background:Cytoplasmic injection of exogenous DNA into zygotes is a promising technique to generate transgenic livestock.However,it is still relatively inefficient and has not yet been demonstrated to work in buffalo.We sought to improve two key technical parameters of the procedure,namely i) how much linear DNA to inject and ii) when to inject it.For this,we introduced a constitutively expressed enhanced green fluorescent protein(EGFP) plasmid into buffalo zygotes.Results:First,we found that the proportion of EGFP-expressing blastocysts derived from zygotes injected with 20 or 50 ng/μL DNA was significantly higher than from those injected with 5 μg/mL However,50 ng/μL exogenous DNA compromised blastocyst development compared to non-injected IVF controls.Therefore the highest net yield of EGFP-positive blastocysts was achieved at 20 ng/μL DNA.Second,zygotes injected early(7-8 h post-insemination[hpi]) developed better than those injected at mid(12-13 hpi) or late(18-19 hpi) time points.Blastocysts derived from early injections were also more frequently EGFP-positive.As a consequence,the net yield of EGFP-expressing blastocysts was more than doubled using early vs late injections(16.4%vs 7.7%).With respect to blastocyst quality,we found no significant difference in cell numbers of EGFP-positive blastocysts vs non-injected blastocysts.Following embryo transfer of six EGFP-positive blastocysts into four recipient animals,two viable buffalo calves were born.Biopsied ear tissues from both buffalo calves were analyzed for transgene presence and expression by Southern blot,PCR and confocal laser scanning microscopy,respectively.This confirmed that both calves were transgenic.Conclusions:Our cytoplasmic injection protocol improved generation of transgenic embryos and resulted in the first transgenic buffalo calves produced by this method. | Fanli Meng Hui Li Xiaoli Wang Guangsheng Qin Bj?rn Oback Deshun Shi | 2015 | Journal of Animal Science and Biotechnology2015，6，4： | 0 |
| 5 | Whole‑genome transcriptome and DNA methylation dynamics of pre‑implantation embryos reveal progression of embryonic genome activation in buffaloes显示文摘Background During mammalian pre-implantation embryonic development(PED),the process of maternal-to-zygote transition(MZT)is well orchestrated by epigenetic modification and gene sequential expression,and it is related to the embryonic genome activation(EGA).During MZT,the embryos are sensitive to the environment and easy to arrest at this stage in vitro.However,the timing and regulation mechanism of EGA in buffaloes remain obscure.Results Buffalo pre-implantation embryos were subjected to trace cell based RNA-seq and whole-genome bisulfite sequencing(WGBS)to draw landscapes of transcription and DNA-methylation.Four typical developmental steps were classified during buffalo PED.Buffalo major EGA was identified at the 16-cell stage by the comprehensive analy-sis of gene expression and DNA methylation dynamics.By weighted gene co-expression network analysis,stage-spe-cific modules were identified during buffalo maternal-to-zygotic transition,and key signaling pathways and biological process events were further revealed.Programmed and continuous activation of these pathways was necessary for success of buffalo EGA.In addition,the hub gene,CDK1,was identified to play a critical role in buffalo EGA.Conclusions Our study provides a landscape of transcription and DNA methylation in buffalo PED and reveals deeply the molecular mechanism of the buffalo EGA and genetic programming during buffalo MZT.It will lay a foundation for improving the in vitro development of buffalo embryos. | Penghui Fu Du Zhang Chunyan Yang Xiang Yuan Xier Luo Haiying Zheng Yanfei Deng Qingyou Liu Kuiqing Cui Fei Gao Deshun Shi | 2023 | Journal of Animal Science and Biotechnology2023，14，6： | 0 |
| 6 | Individual variation in buffalo somatic cell cloning efficiency is related to glycolytic metabolism显示文摘Mammalian individuals differ in their somatic cell cloning efficiency,but the mechanisms leading to this variation is poorly understood.Here we found that high cloning efficiency buffalo fetal fibroblasts(BFFs)displayed robust energy metabolism,looser chromatin structure,high H3 K9 acetylation and low heterochromatin protein 1α(HP1α)expression.High cloning efficiency BFFs had more H3 K9 ac regions near to the upstream of glycolysis genes by Ch IP-seq,and involved more openness loci related to glycolysis genes through ATAC-seq.The expression of these glycolysis genes was also found to be higher in high cloning efficiency BFFs by q RT-PCR.Two key enzymes of glycolysis,PDKs and LDH,were confirmed to be associated with histone acetylation and chromatin openness of BFFs.Treatment of low cloning efficiency BFFs with PS48(activator of PDK1)resulted in an increase in the intracellular lactate production and H3 K9 acetylation,decrease in histone deacetylase activity and HP1αexpression,less condensed chromatin structure and more cloning embryos developing to blastocysts.These results indicate that the cloning efficiency of buffalo somatic cells is associated with their glycolytic metabolism and chromatin structure,and can be improved by increasing glycolytic metabolism. | Chan Luo Zhiqiang Wang Jinling Wang Feng Yun Fenghua Lu Jiayuan Fu Qingyou Liu Deshun Shi | 2022 | Science China(Life Sciences)2022，65，10： | 0 |
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