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Genome editing opens a new era of genetic improvement in polyploid crops

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The Crop Journal 2019年第2期7卷 141-150页

作者： qamar u.zaman Chao Li Hongtao Cheng Qiong Hu Oil Crops Research Institute Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of Agriculture Graduate School of Chinese Academy of Agricultural Sciences

Sequence-specific nucleases(SSN) that generate double-stranded DNA breaks(DSBs) in genes of interest are the key to site-specific genome editing in plants. Genome editing has developed into one method of reducing undesirable traits in crops by the induction of knockout mutations. Different SSN-mediated genome-editing systems, including LAGLIDADG homing endonucleases or meganucleases, zinc-finger nucleases, transcription activator-like effector nucleases and clustered regularly interspaced short palindromic repeats, are emerging as robust tools for introducing functional mutations in polyploid crops including citrus, wheat, cotton, soybean, rapeseed, potato, grapes, Camelina sativa,dandelion, and tobacco. The approach utilizes knowledge of biological mechanisms for targeted induction of DSBs and their error-prone repair, allowing highly specific changes at designated genome loci. In this review, we briefly describe genome-editing technologies and their application to genetic improvement of polyploid crops.

关键词： Genome editing CRISPR Site-specific mutagenesis Polyploid Crop improvement

Computational Tools and Resources for CRISPR/Cas Genome Editing

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Genomics, Proteomics & Bioinformatics 2023年第1期21卷 108-126页

作者： Chao Li Wen Chu Rafaqat Ali Gill Shifei Sang Yuqin Shi Xuezhi Hu Yuting Yang qamar u.zaman Baohong Zhang Oil Crops Research Institute Chinese Academy of Agricultural SciencesKey Laboratory for Biology and Genetic Improvement of Oil CropsMinistry of Agriculture and Rural AffairsWuhan 430062China Graduate School of Chinese Academy of Agricultural Sciences Beijing 100081China Department of Biology East Carolina UniversityGreenvilleNC 27858USA

The past decade has witnessed a rapid evolution in identifying more versatile clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein(Cas)nucleases and their functional variants,as well as in developing precise CRISPR/Cas-derived genome *** programmable and robust features of the genome editors provide an effective RNAguided platform for fundamental life science research and subsequent applications in diverse scenarios,including biomedical innovation and targeted crop *** of the most essential principles is to guide alterations in genomic sequences or genes in the intended manner without undesired off-target impacts,which strongly depends on the efficiency and specificity of single guide RNA(sgRNA)-directed recognition of targeted DNA *** advances in empirical scoring algorithms and machine learning models have facilitated sgRNA design and off-target *** this review,we first briefly introduce the different features of CRISPR/Cas tools that should be taken into consideration to achieve specific ***,we focus on the computer-assisted tools and resources that are widely used in designing sgRNAs and analyzing CRISPR/Cas-induced on-and off-target ***,we provide insights into the limitations of available computational tools that would help researchers of this field for further ***,we suggest a simple but effective workflow for choosing and applying web-based resources and tools for CRISPR/Cas genome editing.

关键词： Genome editing Efficiency and specificity CRISPR/Cas9 sgRNA Computational tool Algorithm

Complete organelle genomes of Sinapis arvensis and their evolutionary implications

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The Crop Journal 2020年第4期8卷 505-514页

作者： Shifei Sang Hongtao Cheng Desheng Mei Li Fu Hui Wang Jia Liu Wenxiang Wang qamar u.zaman Kede Liu Qiong Hu Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory for Biology and Genetic Improvement of Oil Crops Ministry of Agriculture and Rural AffairsWuhan 430062HubeiChina National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhan 430070HubeiChina

Sinapis arvensis,belonging to the genus Sinapis of the family Brassicaceae,has good agronomic characters that make it a valuable genetic resource for crop improvement and is a cytoplasmic source of heterologous cytoplasmic male sterility(CMS).In addition,*** has played an important role in the evolution of the six major cultivated Brassica species involved in the triangle of *** next-generation sequencing,we assembled and revealed the gene composition of *** cytoplasmic *** chloroplast genome comprises 153,590 bp,with 112 individual genes,including 4 r RNA,29 t RNA,and 79 proteincoding *** mitochondrial genome comprises 240,024 bp,with 54 genes,including 18 t RNA,three r RNA and 33 protein-coding *** structure and evolutionary analysis indicated that the sequences of the *** organellar genomes were more similar to those of Brassica nigra and *** than to those of other Brassicaceae *** mitochondrial open reading frames displaying chimeric structural features and encoding hypothetical proteins with transmembrane domains may account for the infertility of Nsa CMS previously derived from somatic cell hybridization between *** and *** results will not only contribute to utilize the germplasm resource of ***,and comprehend the evolution of organelle genomes within the Brassicaceae family,but also help to identify genes conditioning the alloplasmic male sterility of Nsa CMS in ***.

关键词： species. organelle evolutionary

An efficient approach for obtaining plant organelle genomes

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Oil Crop Science 2020年第3期5卷 129-135页

作者： Shifei Sang Desheng Mei qamar u.zaman Jia Liu Hongtao Cheng Li Fu Wenxiang Wang Hui Wang Qiong Hu Key Laboratory for Biology and Genetic Improvement of Oil Crops Ministry of Agriculture and Rural AffairsOil Crops Research InstituteChinese Academy of Agricultural SciencesWuhanChina

Plant organelle(plastid and mitochondrial)genomes contain substantial information for plant evolution and ***,it’s important to reveal plant whole-genome sequences including plastid and mitochondrial *** decode these sequences,it is required to efficiently separate organelle genomic DNA from nucleus genome,which is difficult and *** this study,an efficient procedure was established to obtain plant organelle genomes without extraction of plastid and *** DNA was extracted from three materials including Sinapis arvensis var.‘Yeyou 18’,a cytoplasmic male sterile line(Nsa CMS)and its corresponding maintainer line‘Zhongshuang 4’.DNA was sequenced by Roche 454 FLXt and Illumina Miseq *** genomes were assembled using the generated reads and public organelle genome *** research presented a procedure that efficiently assembled organelle genomes and subsequent fill gaps by extending the consensus contig *** method enabled us to assemble plant plastid and mitochondrial genomes *** obtained organelle genomes could accelerate understanding of mitochondrial rearrangements and laid a foundation for further study of Sinapis arvensis evolution and sterility gene of Nsa CMS.

关键词： Plastid Mitochondrial Genome sequence Nsa CMS organelle genome

Seed Priming with Potassium Nitrate Can Enhance Salt Stress Tolerance in Maize

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Phyton-International Journal of Experimental Botany 2024年第8期93卷 1819-1838页

作者： Bushra Rehman Asma Zulfiqar Houneida Attia Rehana Sardar Muneera A.Saleh Khalid H.Alamer Ibtisam M.Alsudays Faisal Mehmood qamar uz zaman Institute of Botany University of the PunjabLahore54590Pakistan Department of Biology College of ScienceTaif UniversityTaif21944Saudi Arabia Department of Botany Emerson UniversityMultan60000Pakistan Biological Sciences Department Faculty of Science and ArtsKing Abdulaziz UniversityRabigh21911Saudi Arabia Department of Biology College of ScienceQassim UniversityBurydah52571Saudi Arabia Department of Chemistry Sciences The University of LahoreLahore54590Pakistan Department of Environmental Sciences The University of LahoreLahore54590Pakistan

Salinity is a major abiotic stress that hinders plant development and productivity and influences agricultural *** priming is a technique used to boost germination and seedling growth under abiotic stress.A pot experiment was conducted to evaluate the impact of seed priming with potassium nitrate(KNO_(3))at various levels(0%,0.50%,1.00%and 1.50%)under salt stress(0,75,100 mM NaCl)on two maize verities(MNH360 and 30T60)for the growth,development and metabolic attributes results revealed that in maize variety MNH360,KNO_(3)priming’s significantly enhanced growth parameters than in maize variety 30T60 under control and salt-stressed *** with KNO_(3)enhanced carotenoids and total chlorophyll in the 30T60 variety that protected the maize plants from salt ***,it was shown that priming with 1.00%KNO_(3)acts as safeguarded to protect them from oxidative damage by salt stress minimizing reactive oxygen species(ROS)formation through increased levels of malondialdehyde(MDA),catalase(CAT),peroxidase(POD),ascorbate peroxidase(APX),and total soluble *** findings of the present study confirm that the use of the KNO_(3)seed priming technique is a lowcost,environmentally friendly technique for mitigating adverse impacts of salt stress in maize crops by activating the antioxidant defense system and improving chlorophyll and osmolyte contents.

关键词： Salinity Zea mays antioxidant enzymes growth seedlings oxidative damage

Combined Application of Biostimulants and EDTA Improved Wheat Productivity under Cadmium Stress

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Phyton-International Journal of Experimental Botany 2024年第7期93卷 1647-1665页

作者： Abida Aziz Shafiqa Bano Mubshar Hussain Muhammad Farooq Azhar Ghulam Yasin Naila Hadayat Iqra Arooj Abeer Hashem Ajay Kumar Elsayed Fathi Abd_Allah qamar uz zaman Department of Botany The Women UniversityMultan54500Pakistan Institute of Agronomy Bahauddin Zakariya UniversityMultan60800Pakistan Department of Forestry and Range Management Bahauddin Zakariya UniversityMultan60800Pakistan Department of Botany Division of Science&TechnologyUniversity of EducationLahore54770Pakistan Department of Microbiology&Molecular Genetics The Women UniversityMultan54500Pakistan Botany and Microbiology Department College of ScienceKing Saud UniversityRiyadh201313Saudi Arabia Amity Institute of Biotechnology Amity UniversityNoida201313India Plant Production Department College of Food and Agricultural SciencesKing Saud UniversityRiyadh11451Saudi Arabia School of Agriculture Yunnan UniversityKunmingYunan650504China Department of Environmental Sciences The University of LahoreLahore54590Pakistan

Wheat(Triticum aestivum L.)exhibits a greater capacity for cadmium(Cd)absorption compared to other cereal crops,leading to elevated daily Cd intake,and posing a signiﬁcant threat to public *** the mitigation of Cd stress in sustainable and environmentally friendly way,a pot study was designed by using exogenous application of various biostimulants,i.e.,Nigella sativa and Ocimum sanctum extracts:0%,10%,and 20%in combination with the chelating agent ethylenediaminetetraacetic acid(EDTA)using 0 and 5 mg kg^(-1) under various levels of Cd stress(i.e.,0,5,10,and 15 mg kg^(-1) soil).Results revealed that Cd stress signiﬁcantly reduced the seed emergence,growth,root,and allometric characters and yield-related parameters of wheat *** most observable reduc-tion was documented in wheat plants exposed to a higher Cd concentration(15 mg kg^(-1)),followed by the lower Cd level(control).The combined application of bio-stimulants and EDTA minimized the negative impacts of Cd *** highest increase in seedling emergence(5.44%),leaf area(50.60%),number of tillers(31.02%),grain yield per plant(24.28%),biological yield(13.97%),and decrease in Cd levels in grains(40%)was noticed where 20%foliar application of *** and 10%of *** biostimulants were done using 5 mg kg^(-1) of soil-applied *** intervention demonstrated a notable reduction in Cd-induced negative effects,highlighting the potential of these substances in promoting sustainable wheat cultivation in contaminated ***,it is an eco-friendly and approachable method at theﬁeld level able to ensure food safety.

关键词： Abiotic stress allometric characters antioxidant activity crop yield seed emergence grain yield

Reducing carbon emissions with Geoscience solutions:A look at the contributions of nuclear energy,technology,and green finance

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Geoscience Frontiers 2024年第4期15卷 411-426页

作者： Aifeng Liu Muhammad Imran Abdelmohsen A.Nassani Rima H.Binsaeed Khalid zaman International Business School Shaanxi Normal UniversityXi’anChina Department of Economics The University of HaripurHaripur Khyber Pakhtunkhwa 22620Pakistan Department of Management College of Business AdministrationKing Saud UniversityP.O.Box 71115Riyadh 11587Saudi Arabia

Standards for Low-Carbon Energy Portfolios(LC-EPS)mandate that a certain percentage of a region's electricity generation originate from zero-or low-emissions *** 1995Q1 through 2020Q4,the study used the ARDL-Bounds testing technique to estimate coefficient parameters,Granger causality to draw causal inferences,and variance decomposition analysis to anticipate the factors that will have the greatest impact on carbon emissions in the uS *** power significantly impacts carbon emissions,as seen by an inverted u-shaped environmental Kuznets curve,whereas long-term impact of innovation leads to lower *** the other hand,exports of sophisticated technology reduce carbon *** growth has a discernible effect on carbon emissions,nuclear power,innovation,and environmentally friendly ***-tech exports will likely impact carbon emissions most,followed by a demand for nuclear power,innovation,economic expansion,and sustainable finance for the next ten *** results give policymakers helpful insight into how the uS economy may reduce carbon emissions and fight climate change via renewable energy and green finance.

关键词： Nuclear energy demand High technology exports Innovation Economic growth Green finance uSA

A Diagnostic Study of Record Heavy Rain in Twin Cities Islāmābad-Rāwalpindi

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Advances in Atmospheric Sciences 2004年第6期21卷 976-988页

作者： Ghulam RASuL qamar-uz-zaman CHAuDHRY 赵思雄曾庆存 Meteorological Service of Pakistan P. O. Box 1214 Islāamāabad-Pakistan Institute of Atmospheric Physics Chinese Academy of Sciences Beijing 100029 Graduate School Chinese Academy of Sciences Beijing 100039

using surface and NCEP reanalysis data along with radar and satellite images, diagnosis has been carried out to probe the reasons for the very heavy rainfall that occurred in Islāmābad-Rāwalpindi on 23 July 2001. It has been revealed that the sudden evolution of this meso-scale severe weather system was the direct result of strong surface convection in moist and unstable lower layers of the atmosphere. The subsequent rapid development was the combined effect of the presence of the mid latitude westerly’s trough in the north and moisture feeding through monsoon flow along the Himalayas and also the direct south-westerly current from the Arabian Sea. After the westward shifting of the Sub-Tropical High (STH) from the north of India, the strong divergence zone on its eastern edge contributed positively to the development of upward motion. Initially the convective systems moved towards the south and then southeastward following the steering current in the middle troposphere. Based on these analyses, the physical model of the sudden record heavy rainfall has been proposed and a comparison between the heavy rainfall in this case and one in China has been conducted.

关键词： monsoon circulation mesoscale systems heavy rainfall

Depositional facies and reservoir characteristics of the Early Cretaceous Lower Goru Formation,Lower Indus Basin Pakistan:Integration of petrographic and gamma-ray log analysis

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Petroleum 2023年第3期9卷 331-341页

作者： qamar uZ zaman Dar Pu Renhai Shahid Ghazi Shakeel Ahme Rana Imran Ali Mubashir Mehmood Department of Geology Northwest UniversityXi'an710069China Institute of Geology University of the PunjabLahore54000Pakistan Oil and Gas Development Company Limited Islamabad44000Pakistan Kuwait Foreign Petroleum Exploration Company(Kufpec) Islamabad44000Pakistan Department of Geology Abdul Wali Khan UniversityMardan23130Pakistan

The sand intervals of the Early Cretaceous Lower Goru Formation are a conventional reservoir,generally distributed in the Middle and Lower Indus Basin of *** formation is classified into two parts;the upper parts are predominantly composed of shale,siltstone,and thin layers of alternate shale and sandstone,while the lower parts are composed of sandstone with interlayering of shale and *** sandstone of the Lower Goru Formation has been further divided into A,B,C,and D sand intervals based on reservoir *** depositional facies and reservoir characteristics are essential for the evaluation of hydrocarbon exploration and *** paper aims to evaluate the depositional environment and reservoir characterization of the siliciclastic reservoir of the Early Cretaceous Lower Goru Formation by integrating the gamma-ray log patterns and petrographic analysis and scanning electron microscopic(SEM)*** characterization of the sand intervals and Gamma-ray log signatures were used for the interpretation of the depositional environment of the reservoir *** analysis reveals that the sandstone of the Lower Goru Formation is fine-to medium-grained,well-sorted,arkose or feldspathic *** intergranular macroporosity,secondary intragranular macropores,and Intercrystalline micropores were identified within the sandstone by the SEM *** diagenetic analysis suggests that the sandstone possesses high porosity,low permeability,and has undergone significant alterations such as compaction,quartz cementation,feldspar dissolution,and clay minerals *** electrofacies are interpreted based on gamma-ray log patterns including(1)funnel shape(FA);(2)bell shape(FB);(3)cylindrical shape(FC);(4)bow shape(FD);and(5)serrated shape(FE)*** interpreted facies results reveal shoreface environment for A-sand,Tidal flat for B-sand,mixed tidal flat for C sand,Tide dominated mixed fo

关键词： Depositional facies Early cretaceous Electrofacies Gamma-ray pattern Lower goru Petrographic analysis