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| 1 | Engineering Herbicide-Resistant Rice Plants through CRISPR/Cas9-Mediated Homologous Recombination of Acetolactate Synthase显示文摘 | Sun, Yongwei Zhang, Xin Wu, Chuanyin He, Yubing Ma, Youzhi Hou, Han Guo, Xiuping Du, Wenming Zhao, Yunde Xia, Lanqin | 2016 | Molecular Plant2016，9，4： | 94 |
| 2 | Generation of Targeted Point Mutations in Rice by a Modified CRISPR/Cas9 System显示文摘 | Jingying Li Yongwei Sun Jinlu Du Yunde Zhao Lanqin Xia | 2017 | Molecular Plant2017，10，3： | 72 |
| 3 | Precise Modifications of Both Exogenous and Endogenous Genes in Rice by Prime Editing显示文摘Dear Editor,Harnessing genetic diversity and the introduction of elite alleles from wild relatives or landraces into commercial cultivars has been a major goal in crop breeding programs.Precise modification of the plant genome through clustered regularly interspaced short palindromic repeat(CRISPR)/CRISPR-associated protein(Cas)(CRISPR/Cas)-mediated homology-directed repair(HDR)offers a great promise to introduce elite alleles from wild relatives or landraces into commercialized cultivars in the short term. | Huiyuan Li Jingying Li Jilin Chen Lei Yan Lanqin Xia | 2020 | Molecular Plant2020，13，5： | 30 |
| 4 | Toward Precision Genome Editing in Crop Plants显示文摘Precision genome editing through homology-directed repair(HDR)in plants remains very challenging due to the innately low occurrence of HDR and obstacles in the delivery of sufficient donor repair template(DRT)into plant cells.For single-base substitution,cytidine or adenine base editors have been used successfully in crop plants in recent years.However,base editing is constrained by the distance between the targeted base and PAM motif and cannot install predefined transversion mutations or insertions and deletions(indels).Here,we briefly summarize the strategies reported so far for precision genome editing in plants.Based on the recently developed prime editing strategy,which enables gene replacement without double-strand breaks(DSBs)or DRT in both human cells and plants,we provide our perspectives on exploiting diverse strategies to achieve precise targeted gene/allele replacement toward crop improvement and resilience for sustainable agricultural development. | Jingying Li Huiyuan Li Jilin Chen Lei Yan Lanqin Xia | 2020 | Molecular Plant2020，13，6： | 13 |
| 5 | Increasing yield potential through manipulating of an ARE1 ortholog related to nitrogen use efficiency in wheat by CRISPR/Cas9显示文摘Wheat(Triticum aestivum L.)is a staple food crop consumed by more than 30%of world population.Nitrogen(N)fertilizer has been applied broadly in agriculture practice to improve wheat yield to meet the growing demands for food production.However,undue N fertilizer application and the low N use efficiency(NUE)of modern wheat varieties are aggravating environmental pollution and ecological deterioration.Under nitrogen-limiting conditions,the rice(Oryza sativa)abnormal cytokinin response1 repressor1(are1)mutant exhibits increased NUE,delayed senescence and consequently,increased grain yield.However,the function of ARE1 ortholog in wheat remains unknown.Here,we isolated and characterized three TaARE1 homoeologs from the elite Chinese winter wheat cultivar ZhengMai 7698.We then used CRISPR/Cas9-mediated targeted mutagenesis to generate a series of transgene-free mutant lines either with partial or triple-null taare1 alleles.All transgene-free mutant lines showed enhanced tolerance to N starvation,and showed delayed senescence and increased grain yield in field conditions.In particular,the AABBdd and aabbDD mutant lines exhibited delayed senescence and significantly increased grain yield without growth defects compared to the wild-type control.Together,our results underscore the potential to manipulate ARE1 orthologs through gene editing for breeding of high-yield wheat as well as other cereal crops with improved NUE. | Jiahui Zhang Huating Zhang Shaoya Li Jingying Li Lei Yan Lanqin Xia | 2021 | Journal of Integrative Plant Biology2021，63，9： | 13 |
| 6 | Efficient allelic replacement in rice by gene editing: A case study of the NRT1.1B gene显示文摘Precise replacement of an existing allele in commercial cultivars with an elite allele is a major goal in crop breeding. A single nucleotide polymorphism in the NRT1.1 B gene between japonica and indica rice is responsible for the improved nitrogen use efficiency in indica rice. Herein, we precisely replaced the japonica NRT1.1 B allele with the indica allele, in just one generation, using CRISPR/Cas9 gene-editing technology.No additional selective pressure was needed to enrich the precise replacement events. This work demonstrates the feasibility of replacing any genes with elite alleles within one generation, greatly expanding our ability to improve agriculturally important traits. | Jingying Li Xin Zhang Yongwei Sun Jiahui Zhang Wenming Du Xiuping Guo Shaoya Li Yunde Zhao Lanqin Xia | 2018 | Journal of Integrative Plant Biology2018，60，7： | 11 |
| 7 | Base editing in plants: Current status and challenges显示文摘Genome editing technologies have revolutionized the field of plant science by enabling targeted modification of plant genomes and are emerging as powerful tools for both plant gene functional analyses and crop improvement. Although homology-directed repair(HDR)is a feasible approach to achieve precise gene replacement and base substitution in some plant species, the dominance of the non-homologous end joining pathway and low efficiency of HDR in plant cells have limited its application. Base editing has emerged as an alternative tool to HDR-mediated replacement, facilitating precise editing of plant genome by converting one single base to another in a programmable manner without a doublestranded break and a donor repair template. In this review, we summarize the latest developments in base-editing technologies as well as their underlying mechanisms. We review current applications of these technologies in plant species. Finally, we address the challenges and future perspectives of this emerging technology in plants. | Sutar Suhas Bharat Shaoya Li Jingying Li Lei Yan Lanqin Xia | 2020 | The Crop Journal2020，8，3： | 8 |
| 8 | Expanding the Scope of CRISPR/Cpfl-Mediatec Senome Editing in Rice显示文摘 | Shaoya Li Xin Zhang Wensheng Wang Xiuping Guo Zhichao wu Wenming Du Yunde Zhao Lanqin Xia | 2018 | Molecular Plant2018，11，7： | 6 |
| 9 | Expression of an(E)-β-farnesene synthase gene from Asian peppermint in tobacco affected aphid infestation显示文摘Aphids are major agricultural pests that cause significant yield losses in crop plants each year.(E)-β-farnesene(EβF) is the main or only component of an alarm pheromone involved in chemical communication within aphid species and particularly in the avoidance of predation. EβF also occurs in the essential oil of some plant species, and is catalyzed by EβF synthase. By using oligonucleotide primers designed from the known sequence of an EβF synthase gene from black peppermint(Mentha × piperita), two cDNA sequences, MaβFS1 and MaβFS2, were isolated from Asian peppermint(Mentha asiatica). Expression pattern analysis showed that the MaβFS1 gene exhibited higher expression in flowers than in roots, stems and leaves at the transcriptional level. Overexpression of MaβFS1 in tobacco plants resulted in emission of pure EβF ranging from 2.62 to 4.85 ng d-1g-1of fresh tissue. Tritrophic interactions involving peach aphids(Myzus persicae), and predatory lacewing(Chrysopa septempunctata) larvae demonstrated that transgenic tobacco expressing MaβFS1 had lower aphid infestation. This result suggested that the EβF synthase gene from Asian peppermint could be a good candidate for genetic engineering of agriculturally important crop plants. | Xiudao Yu Yongjun Zhang Youzhi Ma Zhaoshi Xu Genping Wang Lanqin Xia | 2013 | The Crop Journal2013，1，1： | 6 |
| 10 | Pyramiding favorable alleles in an elite wheatvariety in one generation by CRISPR-Cas9-mediated multiplex gene editing显示文摘Dear Editor,Common wheat(Triticum aestivum,2n=6x=42,AABBDD)is amajor staple crop consumed by more than 30%of the world’spopulation.It is the main source of cereal-based processed prod-ucts,such as bread,cookies,pasta,and noodles.Althoughwheat production increased by 10-fold following the Green revo-lution and maker-assisted breeding over the past decades,it isstill facing unprecedented challenges in the context of globalclimate changes,growing world population,decreased farm-lands,as well as water shortages in arid and semi-arid lands.Meanwhile,the functional redundancy of genes in hexaploidywheat makes a forward genetics approach to select a desiredphenotype,especially for pyramiding of several agronomicallyimportant traits in a modern variety,very time-consuming and in some cases,impossible because of gene linkage or genedrag. | Jinman Luo Shaoya Li Jiajing Xu Lei Yan Youzhi Ma Lanqin Xia | 2021 | Molecular Plant2021，14，6： | 6 |
| 11 | Precise gene replacement in plants through CRISPR/Cas genome editing technology:current status and future perspectives显示文摘CRISPR/Cas,as a simple,versatile,robust and cost-effective system for genome manipulation,has dominated the genome editing field over the past few years.The application of CRISPR/Cas in crop improvement is particularly important in the context of global climate change,as well as diverse agricultural,environmental and ecological challenges.Various CRISPR/Cas toolboxes have been developed and allow for targeted mutagenesis at specific genome loci,transcriptome regulation and epigenome editing,base editing,and precise targeted gene/allele replacement or tagging in plants.In particular,precise replacement of an existing allele with an elite allele in a commercial variety through homology-directed repair(HDR)is a holy grail in genome editing for crop improvement as it has been very difficult,laborious and time-consuming to introgress the elite alleles into commercial varieties without any linkage drag from parental lines within a few generations in crop breeding practice.However,it still remains very challenging in crop plants.This review intends to provide an informative summary of the latest development and breakthroughs in gene replacement using CRISPR/Cas technology,with a focus on achievements,potential mechanisms and future perspectives in plant biological science as well as crop improvement. | Shaoya Li Lanqin Xia | 2020 | aBIOTECH2020，1，1： | 5 |
| 12 | Multiplex precision gene editing by a surrogate prime editor in rice显示文摘Dear Editor,Development of a multiplex precision gene editing system is highly desirable for pyramiding beneficial alleles in crop improve-ment.Prime editing is a newly developed genome-editing tool that can precisely enable the installation of all 12 nucleotide sub-stitutions,short insertions,and deletions without exogenous DNA donor repair template and double-strand breaks(Anzalone et al.,2019).Among the prime editing systems,prime editor 3(PE3),which consists of a prime editing guide RNA(pegRNA)and an additional nicking single guide RNA(sgRNA)to nick the non-edited strand,enhances editing efficiency. | Huiyuan Li Ziwei Zhu Shaoya Li Jingying Li Lei Yan Chen Zhang Youzhi Ma Lanqin Xia | 2022 | Molecular Plant2022，15，7： | 4 |
| 13 | Present and future prospects for wheat improvement through genome editing and advanced technologies显示文摘Wheat(Triticum aestivum,2n=6x=42,AABBDD)is one of the most important staple food crops in the world.Despite the fact that wheat production has significantly increased over the past decades,future wheat production will face unprecedented challenges from global climate change,increasing world population,and water shortages in arid and semi-arid lands.Furthermore,excessive applications of diverse fertilizers and pesticides are exacerbating environmental pollution and ecological deterioration.To ensure global food and ecosystem security,it is essential to enhance the resilience of wheat production while minimizing environmental pollution through the use of cutting-edge technologies.However,the hexaploid genome and gene redundancy complicate advances in genetic research and precision gene modifications for wheat improvement,thus impeding the breeding of elite wheat cultivars.In this review,we first introduce state-of-the-art genome-editing technologies in crop plants,especially wheat,for both functional genomics and genetic improvement.We then outline applications of other technologies,such as GWAS,high-throughput genotyping and phenotyping,speed breeding,and synthetic biology,in wheat.Finally,we discuss existing challenges in wheat genome editing and future prospects for precision gene modifications using advanced genome-editing technologies.We conclude that the combination of genome editing and other molecular breeding strategies will greatly facilitate genetic improvement ofwheat for sustainable global production. | Shaoya Li Chen Zhang Jingying Li Lei Yan Ning Wang Lanqin Xia | 2021 | Plant Communications2021，2，4： | 4 |
| 14 | Integration and inheritance stability of foreign Bt toxin gene in the bivalent insect-resistant transgenic cotton plants显示文摘Genetic and expressional stability of Bt toxin gene is crucial for the breeding of insect-resistant transgenic cotton varieties and their commercialization. Genomic Southern blot analysis of R3, R4 and R5 generations of bivalent transgenic insect-resistant cotton plants was done in order to determine the integration, the copy number and the inheritance stability of Bt toxin gene in the transgenic cotton plants. The results indicated that there was a 4.7 kb positive band in the Southern blot when the genomic DNA of the bivalent transgenic insect-resistant cotton plants and the positive control (the plasmid) were digested with HindⅢ respectively. This result proved that the Bt toxin gene had been integrated into the genome of the cotton in full length. There is only one XhoⅠ restriction site in the Bt toxin gene. Southern blot analysis indicated that many copies of Bt toxin gene had been integrated into the genome of the cotton when the genomic DNA of transgenic plants was digested with XhoⅠ. Among them, there were four copies (about 17.7, 8, 5.5 and 4.7 kb in size) existing in all the tested plants of R3, R4 and R5 generations. The preliminary conclusion was that there were more than four copies of Bt toxin gene integrated into the genome of the cotton, among them, more than one copy can express and inherit steadily. This result provides a scientific basis for the breeding of the bivalent insect-resis- tant transgenic cotton plants and its commercialization. | XIA Lanqin GUO Sandui | 2001 | Chinese Science Bulletin2001，46，16： | 2 |
| 15 | Plant genome editing using xCas9 with expanded PAM compatibility显示文摘CRISPR/Cas enables robust genome editing and has revolution-ized both functional genomics and crop breeding.The specificity of Cas-directed DNA cleavage is strictly determined by a chimeric single guide RNA(SgRNA)and a short protospacer adjacent motif(PAM)in the genome(Cong et al,2013;Zetsche et al,2015).The widely used Cas9 from Streptococcus pyogenes(SpCas9)generally recognizes the canonical NGG PAM(where N indicates any nucleicacid base)(Miao et al.,2013;Ma et al,2015),making many regionsuntargetable by Cas9.SpCas9 VQR and VRER variants,which recog-nize the non-canonical PAM sequences of NGA and NGCG,respectively,have been used to expand targetable sequences in plants(Hu et al.,2016).In addition,the applications of other Cas endonucleases such as SaCas9(Staphylococcus aureus Cas9)(Ran et al..2015). | Jingying Li Jinman Luo Meilian Xu Shaoya Li Jiahui Zhang Huiyuan Li Lei Yan Yunde Zhao Lanqin Xia | 2019 | Journal of Genetics and Genomics2019，46，5： | 2 |
| 16 | Plant base editing and prime editing:The current status and future perspectives显示文摘Precise replacement of an allele with an elite allele controlling an important agronomic trait in a predefined manner by gene editing technologies is highly desirable in crop improvement.Base editing and prime editing are two newly developed precision gene editing systems which can introduce the substitution of a single base and install the desired short indels to the target loci in the absence of double-strand breaks and donor repair templates,respectively.Since their discoveries,various strategies have been attempted to optimize both base editor(BE)and prime editor(PE)in order to improve the precise editing efficacy,specificity,and expand the targeting scopes.Here,we summarize the latest development of various BEs and PEs,as well as their applications in plants.Based on these progresses,we recommend the appropriate BEs and PEs for both basic plant research and crop improvement.Moreover,we propose the perspectives for further optimization of these two editors.We envision that both BEs and PEs will become the routine and customized precise gene editing tools for both plant biological research and crop improvement in the near future. | Jingying Li Chen Zhang Yubing He Shaoya Li Lei Yan Yucai Li Ziwei Zhu Lanqin Xia | 2023 | Journal of Integrative Plant Biology2023，65，2： | 1 |
| 17 | (E)-β-Farnesene synthase genes affect aphid (Myzus persicae) infestation in tobacco (Nicotiana tabacum)显示文摘 | Xiudao Yu Huw Jones Youzhi Ma Genping Wang Zhaoshi Xu Baoming Zhang Yongjun Zhang Guangwei Ren John Pickett Lanqin Xia | 2012 | Functional & Integrative Genomics2012，，1： | 1 |
| 18 | Occurrence of puroindoline alleles in Chinese winter wheats显示文摘 | Lanqin Xia Feng Chen Zhonghu He | 2005 | Cereal Chem2005，82，1： | 1 |
| 19 | Artificial evolution of OsEPSPS through an improved dual cytosine and adenine base editor generated a novel allele conferring rice glyphosate tolerance显示文摘Exploiting novel endogenous glyphosate-tolerant alleles is highly desirable and has promising potential for weed control in rice breeding. Here,through fusions of different effective cytosine and adenine deaminases with nCas9-NG, we engineered an effective surrogate two-component composite base editing system, STCBE-2, with improved C-to-T and A-to-G base editing efficiency and expanded the editing window. Furthermore,we targeted a rice endogenous OsEPSPS gene for artificial evolution through STCBE-2-mediated near-saturated mutagenesis. After hygromycin and glyphosate selection, we identified a novel OsEPSPS allele with an Asp-213-Asn(D213N)mutation(OsEPSPS-D213N) in the predicted glyphosate-binding domain, which conferred rice plants reliable glyphosate tolerance and had not been reported or applied in rice breeding. Collectively, we developed a novel dual base editor which will be valuable for artificial evolution of important genes in crops. And the novel glyphosate-tolerant rice germplasm generated in this study will benefit weeds management in rice paddy fields. | Chen Zhang Xue Zhong Shaoya Li Lei Yan Jingying Li Yubing He Yong Lin Yangjun Zhang Lanqin Xia | 2023 | Journal of Integrative Plant Biology2023，65，9： | 1 |
| 20 | The power and versatility of genome editing tools in crop improvement显示文摘Increasing world population,global climate change,decreased farmland,environmental pollution and ecological deterioration represent unprecedent challenges for crop production to ensure global food security(Hickey et al.,2019;Li et al.,2021 a).It is estimated that by the year 2050,50% more food is needed to feed the increasing population(Bailey-Serres et al.,2019).Thus,it is urgent to boost crop production by using cutting-edge technologies. | Lanqin Xia Kejian Wang Jian-Kang Zhu | 2021 | Journal of Integrative Plant Biology2021，63，9： | 0 |
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