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Insights into genetic diversity and phenotypic variations in domestic geese through comprehensive population and pan-genome analysis

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Journal of Animal Science and Biotechnology 2024年第1期15卷 88-107页

作者： Guangliang Gao Hongmei Zhang jiangping ni Xianzhi Zhao Keshan Zhang Jian Wang Xiangdong Kong Qigui Wang Chongqing Academy of Animal Science Rongchang DistrictChongqing 402460China Livestock and Poultry Multi‑Omics Key Laboratory of Ministry of Agriculture and Rural Affairs College of Animal Science and TechnologySichuan Agricultural UniversityChengdu 611130China Chongqing Engineering Research Center of Goose Genetic Improvement Rongchang DistrictChongqing 402460China Department of Cardiovascular Ultrasound and Non‑Invasive Cardiology Sichuan Academy of Medical Sciences and Sichuan Provincial People’s HospitalUniversity of Electronic Science and Technology of ChinaChengdu611731China Ultrasound in Cardiac Electrophysiology and Biomechanics Key Laboratory of Sichuan Province University of Electronic Science and Technology of ChinaChengdu611731China JiguangGene Biotechnology Co. Ltd.Nanjing210032China Jiangsu Agri-Animal Vocational College Taizhou225300China Poultry Science Institute Chongqing Academy of Animal ScienceNo.51 Changzhou AvenueRongchang DistrictChongqing 402460P.R.China

Background Domestic goose breeds are descended from either the Swan goose(Anser cygnoides)or the Greylag goose(Anser anser),exhibiting variations in body size,reproductive performance,egg production,feather color,and other phenotypic *** a pan-genome facilitates a thorough identification of genetic variations,thereby deepening our comprehension of the molecular mechanisms underlying genetic diversity and phenotypic *** To comprehensively facilitate population genomic and pan-genomic analyses in geese,we embarked on the task of 659 geese whole genome resequencing data and compiling a database of 155 RNA-seq *** constructing the pan-genome for geese,we generated non-reference contigs totaling 612 Mb,unveiling a collection of 2,813 novel genes and pinpointing 15,567 core genes,1,324 softcore genes,2,734 shell genes,and 878 cloud genes in goose ***,we detected an 81.97 Mb genomic region showing signs of genome selection,encompassing the TGFBR2 gene correlated with variations in body weight among ***-wide association studies utilizing single nucleotide polymorphisms(SNPs)and presence-absence variation revealed significant genomic associations with various goose meat quality,reproductive,and body composition *** instance,a gene encoding the SVEP1 protein was linked to carcass oblique length,and a distinct gene-CDS haplotype of the SVEP1 gene exhibited an association with carcass oblique ***,the pan-genome analysis revealed enrichment of variable genes in the“hair follicle maturation”Gene Ontology term,potentially linked to the selection of feather-related traits in geese.A gene presence-absence variation analysis suggested a reduced frequency of genes associated with“regulation of heart contraction”in domesticated geese compared to their wild *** study provided novel insights into gene expression features and functions by integrating gene expression patterns across multiple orga

关键词： Gene-CDS haplotype Goose GWAS Pan-genome Presence-absence variation Selection signal

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Pangenome and multi-tissue gene atlas provide new insights into the domestication and highland adaptation of yaks

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Journal of Animal Science and Biotechnology 2024年第5期15卷 1832-1850页

作者： Daoliang Lan Wei Fu Wenhui Ji Tserang‑Donko Mipam Xianrong Xiong Shi Ying Yan Xiong Peng Sheng jiangping ni Lijun Bai Tongling Shan Xiangdong Kong Jian Li Ministry of Education of Key Laboratory of Qinghai‑Tibetan Plateau Animal Genetic Resource and Utilization Southwest Minzu UniversityChengduChina College of Animal&Veterinary Sciences Southwest Minzu UniversityChengduChina Institute of Qinghai‑Tibetan Plateau Southwest Minzu UniversityChengduChina Jiguang Gene Biotechnology Co. Ltd.NanjingChina Chengdu Genepre Technology Co. Ltd.ChengduChina Shanghai Veterinary Research Institute Chinese Academy of Agricultural SciencesShanghaiChina

Background The genetic diversity of yak,a key domestic animal on the Qinghai-Tibetan Plateau(QTP),is a vital resource for domestication and breeding *** study presents the first yak pangenome obtained through the de novo assembly of 16 yak *** We discovered 290 Mb of nonreference sequences and 504 new *** pangenome-wide presence and absence variation(PAV)analysis revealed 5,120 PAV-related genes,highlighting a wide range of variety-specific genes and genes with varying frequencies across yak *** component analysis(PCA)based on binary gene PAV data classified yaks into three new groups:wild,domestic,and ***,we pro-posed a‘two-haplotype genomic hybridization model'for understanding the hybridization patterns among breeds by integrating gene frequency,heterozygosity,and gene PAV data.A gene PAV-GWAS identified a novel gene(Bos-Gru3G009179)that may be associated with the multirib trait in Jinchuan ***,an integrated transcrip-tome and pangenome analysis highlighted the significant differences in the expression of core genes and the muta-tional burden of differentially expressed genes between yaks from high and low *** analysis across multiple species revealed that yaks have the most unique differentially expressed m RNAs and lnc RNAs(between high-and low-altitude regions),especially in the heart and lungs,when comparing high-and low-altitude *** The yak pangenome offers a comprehensive resource and new insights for functional genomic studies,supporting future biological research and breeding strategies.

关键词： High-and low-altitude Novel genes Pangenome PAV-GWAS Yak

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SCR7和RS-1对酿酒酵母中CRISPR/Cas9编辑效率的影响

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宁夏医科大学学报 2024年第8期46卷 770-776,781页

作者：倪江萍杨兰张轩宁夏医科大学基础医学院银川750004 宁夏回族自治区人民医院宁夏医科大学第三临床医学院银川750002

目的研究SCR7和RS-1对酿酒酵母中CRISPR/Cas9编辑效率的影响。方法 CRISPR/Cas9系统能特异性地切断DNA双链,产生双链断裂(DSB),在真核细胞中DSB的修复方式主要有两种,非同源末端连接(NHEJ)和同源重组修复(HDR)。小分子化合物SCR7和RS-1... 详细信息

目的研究SCR7和RS-1对酿酒酵母中CRISPR/Cas9编辑效率的影响。方法 CRISPR/Cas9系统能特异性地切断DNA双链,产生双链断裂(DSB),在真核细胞中DSB的修复方式主要有两种,非同源末端连接(NHEJ)和同源重组修复(HDR)。小分子化合物SCR7和RS-1在DNA修复过程中能通过抑制NHEJ或增强HDR提高CRISPR/Cas9精准基因编辑效率。本研究将探究用不同浓度的SCR7和RS-1分别处理酿酒酵母,验证YPL062W基因的删除效率。结果本研究发现,添加5、10、15、20μmol SCR7后,YPL062W基因的删除效率分别为80%、90%、90%和80%,添加1、5、10、15、20μmol RS-1后,YPL062W基因的删除效率分别为70%、70%、80%、70%和70%,添加小分子化合物组合10μmol SCR7+10μmol RS-1和15μmol SCR7+10μmol RS-1后,YPL062W基因的删除效率分别为70%和80%。结论 SCR7和RS-1能显著增强酿酒酵母中CRISPR/Cas9系统基因编辑效率。

关键词： CRISPR/Cas9系统 SCR7 RS-1 酿酒酵母

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Simultaneously down-regulation of multiplex branch pathways using CRISPRi and fermentation optimization for enhancingβ-amyrin production in Saccharomyces cerevisiae

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Synthetic and Systems Biotechnology 2019年第2期4卷 79-85页

作者： jiangping ni Genlin Zhang Lei Qin Jun Li Chun Li Institute for Synthetic Biosystem Department of Biochemical EngineeringSchool of Chemistry and Chemical EngineeringBeijing Institute of Technology5 ZhongGuanCunNan RoadBeijing 100081China School of Chemistry and Chemical Engineering Key Laboratory for Green Processing of Chemical Engineering of Xinjiang BingtuanShihezi UniversityShihezi 832003China

The production ofβ-amyrin in Saccharomyces cerevisiae is still low due to the inability of effectively regulating the endogenous metabolic pathway for competitive synthesis ofβ-amyrin *** this study,we focused on two branches ofβ-amyrin synthetics pathway that consumeβ-amyrin precursors(2,3-oxidosqualene and cytosolic acetyl-CoA)and regulated related genes(ADH1,ADH4,ADH5,ADH6,CIT2,MLS2 and ERG7).We developed a CRISPRi method by constructing a multi-gRNA plasmid to down-regulate the seven genes simultaneously,which is reported for the first time in *** average transcription inhibition efficiency of the seven genes reached as high as 75.5%.Furthermore,by optimizing the fermentation condition(including pH,inoculum size,initial glucose concentration and feed of glucose or ethanol)and increasing extracellular transportation via supplying methyl-β-cyclodextrin,β-amyrin concentration of engineered strain SGibSdCg increased by 44.3%compared with the parent strain SGib,achieving 156.7 mg/L which was the highest concentration ofβ-amyrin reported in *** one-step down-regulation of multiple genes using CRISPRi showed high efficiency and promising future in improving the yields of natural products.

关键词： β-amyrin CRISPRi Transcriptional regulation Saccharomyces cerevisiae

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Boosting hydrogen production of ammonia decomposition via the construction of metal-oxide interfaces

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结构化学 2024年第2期43卷 49-59页

作者： jiangping Chen Hongju Ren Kai Wu Huihuang Fang Chongqi Chen Li Lin Yu Luo Lilong Jiang National Engineering Research Center for Chemical Fertilizer Catalyst(NERC-CFC) School of Chemical EngineeringFuzhou UniversityFuzhou350002China National Engineering Research Center for Chemical Fertilizer Catalyst(NERC-CFC) School of Chemical EngineeringFuzhou UniversityFuzhou350002China Qingyuan Innovation Laboratory QuanzhouFujian362801China

The ammonia decomposition for the production of carbon-free hydrogen has triggered great attention yet still remains challenging due to its sluggish kinetics,posting the importance of precise design of efficient catalysts for ammonia decomposition under low *** the metal-support interaction and interface is one of the most important strategies for promoting *** this work,by coating ceria onto the ni nanoparticles(NPs),we discover that the ni-CeO2 interfaces create an exceptional effect to enhance the catalytic decomposition of ammonia by over 10 folds,compared with the pristine *** kinetic analysis demonstrates that the recombinative N2 desorption is the rate-determining step(RDS)and the ni-CeO2 interface greatly increases the *** on these understandings,a strategy to fabricate the ni/CeO2 catalyst with abundant ni-Ce-O in-terfaces via one-pot sol-gel method was employed(hereafter denoted to s-ni/CeC2).The s-ni/CeO2 catalyst shows a high activity for ammonia decomposition,achieving a H2 formation rate of 10.5 mmol gcat1 min-1 at 550 ℃.Combined with a series of characterizations,the relationship between the catalyst structure and the performance was investigated for further understanding the effect of metal-oxide interfaces.

关键词： Metal-support interaction Ammonia decomposition nickel Cerium oxide Metal-oxide interfaces

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高校实验室存在的管理问题及相应对策

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山东化工 2021年第5期50卷 186-187页

作者：倪江萍郭凤英薛姝婧于飞飞王玫宁夏医科大学宁夏银川750004

实验室是高校培养人才的重要场所,具有极重要地位。但是高校实验室也是最容易出事故的地方,充分说明在管理上仍存在许多问题。因此,本文从实验室安全管理、实验室建设、实验管理人员的管理机制及实验室信息化管理四个方面存在的问题及... 详细信息

实验室是高校培养人才的重要场所,具有极重要地位。但是高校实验室也是最容易出事故的地方,充分说明在管理上仍存在许多问题。因此,本文从实验室安全管理、实验室建设、实验管理人员的管理机制及实验室信息化管理四个方面存在的问题及对策进行了深入剖析。

关键词：实验室管理问题对策

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Identifying the genes of unconventional high temperature superconductors

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Science Bulletin 2016年第7期61卷 561-569页

作者： jiangping Hu Beijing National Laboratory for Condensed Matter Physics Institute of Physics Chinese Academy of Sciences Beijing 100190 China Collaborative Innovation Center of Quantum Matter Beijing 100190 China

We elucidate a recently emergent framework in unifying the two families of high temperature （high To） superconductors, cuprates and iron-based superconductors. The unification suggests that the latter is simply the counterpart of the former to realize robust extended s-wave pairing symmetries in a square lattice. The unification identifies that the key ingredients （gene） of high Tc superconductors is a quasi two dimensional electronic environment in which the d-orbitals of cations that partic- ipate in strong in-plane couplings to the p-orbitals of anions are isolated near Fermi energy. With this gene, the superexchange magnetic interactions mediated by anions could maximize their contributions to superconductivity. Creating the gene requires special arrangements between local electronic structures and crystal lattice structures. The speciality explains why high Tc superconductors are so rare. An explicit prediction is made to realize high Tc superconductivity in Co/ni-based materials with a quasi two dimensional hexagonal lattice structure formed by trigonal bipyramidal complexes.

关键词： Cuprates Iron-based superconductors Unconventional high Tc superconducotors Superexchange

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A possible new family of unconventional high temperature superconductors

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Science Bulletin 2017年第3期62卷 212-217页

作者： jiangping Hu Congcong Le Beijing Notional Laboratory for Condensed Matter Physics and Institute of Physics Chinese Academy of Sciences Beijing 100190 China Collaborative Innovation Center of Quantum Matter Beijing 100871 China School of Physics University of Chinese Academy of Sdences Beijing 100049 China

We suggest a new family of Co[ni-based materials that may host unconventional high temperature superconductivity （high-To）. These materials carry layered square lattices with each layer being formed by vertex-shared transition metal tetrahedra cation-anion complexes. The electronic physics in these materials is determined by the two dimensional layer and is fully attributed to the three near degenerated t2g d-orbitals close to a d7 filling configuration in the d-shell of CoJni atoms. The electronic structure meets the necessary criteria for unconventional high Tc materials proposed recently by us to unify the two known high-Tc families, cuprates and iron-based superconductors. We predict that they host superconducting states with a d-wave pairing symmetry with Tc potentially higher than those of iron-based superconductors. These materials, if realized, can be a fertile new ground to study strongly correlated electronic Physics and provide decisive evidence for superconducting pairing mechanism.

关键词： Iron-based superconductors Cuprates d-Wave pairing symmetry Cobalt chalcogenides

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Predicting diamond-like Co-based chalcogenides as unconventional high temperature superconductors

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Science Bulletin 2018年第20期63卷 1338-1344页

作者： jiangping Hu Yuhao Gu Congcong Le Beijing National Laboratory for Condensed Matter Physics and Institute of PhysicsChinese Academy of SciencesBeijing 100190China Kavli Institute of Theoretical Sciences University of Chinese Academy of SciencesBeijing 1O0190China Collaborative Innovation Center of Quantum Matter Beijing 100049China Beijing National Laboratory for Molecular Sciences State Key Laboratory of Rare Earth Materials Chemistry and ApplicationsInstitute of Theoretical and Computational ChemistryCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing 100871China

We predict Co-based chalcogenides with a diamond-like structure can host unconventional high temperature superconductivity(high-Tc). The essential electronic physics in these materials stems from the Co layers with each layer being formed by vertex-shared CoA_4(A=S, Se, Te) tetrahedra complexes, a material genome proposed recently by us to host potential unconventional high-Tcclose to a d7 filling configuration in 3 d transition metal compounds. We calculate the magnetic ground states of different transition metal compounds with this structure. It is found that(Mn, Fe, Co)-based compounds all have a G-type antiferromagnetic(AFM) insulating ground state while ni-based compounds are paramagnetic *** AFM interaction is the largest in the Co-based compounds as the three t2 gorbitals all strongly participate in AFM superexchange interactions. The abrupt quenching of the magnetism from the Co to ni-based compounds is very similar to those from Fe to Co-based pnictides in which a C-type AFM state appears in the Fe-based ones but vanishes in the Co-based ones. This behavior can be considered as an electronic signature of the high-Tcgene. Upon doping, as we predicted before, this family of Co-based compounds favor a strong d-wave pairing superconducting state.

关键词： Iron-based superconductors Cuprates Cobalt chalcogenides d-wave pairing symmetry

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基因编辑与诊断工具酶LwCas13a的克隆表达、纯化与酶活性鉴定

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宁夏医科大学学报 2023年第12期45卷 1208-1213页

作者：李晓雨倪江萍朱玥杨玉玛薛依凡张斯涵妥蓉蓉杨延辉宁夏医科大学基础医学院宁夏常见传染病防治重点实验室银川750004

目的开发可大量制备具有天然酶活性的基因编辑与诊断工具酶LwCas13a的技术,为研究基因编辑或开发基因诊断试剂提供稳定的酶。方法以LwCas13a蛋白基因序列为模板,采用PCR技术扩增目的基因LwCas13a,运用NotⅠ和BamHⅠ进行双酶切,将酶切产... 详细信息

目的开发可大量制备具有天然酶活性的基因编辑与诊断工具酶LwCas13a的技术,为研究基因编辑或开发基因诊断试剂提供稳定的酶。方法以LwCas13a蛋白基因序列为模板,采用PCR技术扩增目的基因LwCas13a,运用NotⅠ和BamHⅠ进行双酶切,将酶切产物与相同酶切获得的载体pC013用T4 DNA连接酶连接构建成含有融合表达His标签的原核表达载体pC013-Twinstrep-SUMO-huLwCas13a,选择经酶切和测序鉴定均正确的质粒转化到*** BL21感受态细胞中,用0.5 mmol·L^(-1)的异丙基-β-D-硫代丰乳糖苷在16℃条件下诱导16 h,表达LwCas13a酶,产物经SDS-PAGE电泳检测,获得可溶性表达条件后,进行大量蛋白诱导表达,使用ni^(2+)亲和层析法,纯化LwCas13a蛋白。利用LwCas13a酶的“侧向切割活性”检测纯化获得的酶。结果PCR扩增获得3479 bp序列完全正确的LwCas13a基因,重组蛋白以融合蛋白形式可溶性高效表达,纯度达到98%。经比较优于商业化的LwCas13a酶。结论成功获得具有天然侧向剪切活性的LwCas13a酶,为开发使用LwCas13a酶的分子诊断试剂提供原材料奠定了基础。

关键词： LwCas13a酶原核表达蛋白纯化酶活性鉴定

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