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Development of plant cytosine base editors with the Cas12a system

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The Crop Journal 2023年第5期11卷 1451-1457页

作者： Huanhuan Wang Jing Liang Like Chen Bufang Deng Dongfang Gu Xiaoshuang Liu Shan Jin Rongfang Xu Ruiying Qin Yitong Zhu Liangxia Zhao Dourong Kou Yanjun Chen Yingli Jiang Juan Li Pengcheng Wei College of Agronomy Anhui Agricultural UniversityHefei 230036AnhuiChina Key Laboratory of rice Genetic breeding of Anhui Province Rice Research InstituteAnhui Academy of Agricultural SciencesHefei 230031AnhuiChina

Base editors of the Cas9 system have been widely used for precise nucleotide substitution in crops. In this study, Cas12a was applied to construct plant cytosine base editors(CBEs). The main elements of Cas12aCBEs were engineered and their efficiency was evaluated in stably transformed rice cells. An optimized ttCas12a-hyA3Bctd editor, consisting of a LbCas12a variant carrying catalytic inactive D832A and temperature-tolerance D156R double mutations, a truncated human APOBEC3B deaminase, a human RAD51 single-stranded DNA-binding domain, and double copies of UGI, outperformed other Cas12aCBEs in base editing efficiency. In T0transgenic rice plants, ttCas12a-hyA3Bctd edited an average of42.01% and a maximum of 68.75% of lines at six genomic targets. A-to-G conversions were generated in rice by an adenine base editor with a similar architecture to the optimized CBE. Our results provide preliminary evidence for the feasibility of robust and efficient plant Cas12a base editing systems, which could be useful for precise crop breeding.

关键词： Cas12a Base editing rice ABE CBE

Melatonin activates the OsbZIP79–OsABI5 module that orchestrates nitrogen and ROS homeostasis to alleviate nitrogen-limitation stress in rice

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Plant Communications 2023年第6期4卷 113-133页

作者： Meng Jiang Yue Song Ruifang Yang Chenfan Zheng Yunchao Zheng Huali Zhang Shan Li Yuanyuan Tan Jianzhong Huang Qingyao Shu Ruiqing Li Hainan Institute Zhejiang UniversityYazhou Bay Sci-Tech CitySanyaChina National Key Laboratory of rice breeding and Biology and Zhejiang Provincial Key Laboratory of Crop Germplasm The Advanced Seed InstituteZhejiang UniversityHangzhouChina College of Agronomy Anhui Agricultural UniversityHefeiChina Crop breeding and Cultivation Research Institute Shanghai Academy of Agricultural SciencesShanghaiChina School of Life Sciences Westlake UniversityHangzhouChina State Key Laboratory of rice breeding and Biology and Chinese National Center for rice Improvement China National Rice Research InstituteHangzhouChina

Melatonin(Mel)has previously been reported to effectively alleviate nitrogen-limitation(N-L)stress and thus increase nitrogen-use efficiency(NUE)in several plants,but the underlying mechanism remains ***,we revealed that OsbZIP79(BASIC LEUCINE ZIPPER 79)is transcriptionally activated under N-L conditions,and its expression is further enhanced by exogenous *** the combined use of omics,genetics,and biological techniques,we revealed that the OsbZIP79–OsABI5(ABSCISIC ACID INSENSITIVE 5)module stimulated regulation of reactive oxygen species(ROS)homeostasis and the uptake and metabolismof nitrogen under conditions of indoor nitrogen limitation(1/16 normal level).OsbZIP79 activated the transcription of OsABI5,and OsABI5 then bound to the promoters of target genes,including genes involved in ROS homeostasis and nitrogen metabolism,activating their *** module was also indispensable for upregulation of several other genes involved in abscisic acid catabolism,nitrogen uptake,and assimilation under N-L and Mel treatment,although these genes were not directly transactivated by *** experiments demonstrated that Mel significantly improved rice growth under low nitrogen(L-N,half the normal level)by the same mechanism revealed in the nitrogen-limitation *** application produced a 28.6%yield increase under L-N and thus similar increases in ***,two OsbZIP79-overexpression lines grown in L-N field plots had significantly higher NUE(+13.7%and+21.2%)than their wild ***,our data show that an OsbZIP79–OsABI5 module regulates the rice response to N insufficiency(N limitation or low N),which is important for increasing NUE in rice production.

关键词： melatonin peroxidase nitrogen starvation allantoinase ROS signaling

A comparative study on the role of conventional,chemical,and nanopriming for better salt tolerance during seed germination of direct seeding rice

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Journal of Integrative Agriculture 2024年第12期23卷 3998-4017页

作者： Yixue Mu Yusheng Li Yicheng Zhang Xiayu Guo Shaokun Song Zheng Huang Lin Li Qilin Ma Mohammad Nauman Khan Lixiao Nie School of breeding and Multiplication(Sanya Institute of breeding and Multiplication)of Hainan University Hainan UniversitySanya 572000China College of Tropical Crops Hainan UniversityHaikou 570228China National Innovation Center of Saline–Alkali Tolerant rice in Sanya Sanya 572000China Hunan Hybrid rice Research Center Changsha 410125China

Salinity is one of the most significant risks to crop production and food security as it harms plant physiology and *** salt stress during the rice emergence stages severely hampers the seed germination and seedling growth of direct-seeded ***,nanoparticles(NPs)have been reported to be effectively involved in many plant physiological processes,particularly under abiotic *** our knowledge,no comparative studies have been performed to study the efficiency of conventional,chemical,and seed nanopriming for better plant stress ***,we conducted growth chamber and field experiments with different salinity levels(0,1.5,and 3‰),two rice varieties(CY1000 and LLY506),and different priming techniques such as hydropriming,chemical priming(ascorbic acid,salicylic acid,and γ-aminobutyric acid),and nanopriming(zinc oxide nanoparticles).Salt stress inhibited rice seed germination,germination index,vigor index,and seedling ***,salt stress increased the over accumulation of reactive oxygen species(H_(2)O_(2) and O_(2)^(-)·)and malondialdehyde(MDA)***,salt-stressed seedlings accumulated higher sodium(Na^(+))ions and significantly lower potassium(K^(+))***,the findings of our study demonstrated that,among the different priming techniques,seed nanopriming with zinc oxide nanoparticles(NanoZnO)significantly contributed to rice salt *** nanopriming improved rice seed germination and seedling growth in the pot and field experiments under salt *** possible mechanism behind ZnO nanopriming improved rice salt tolerance included higher contents of α-amylase,soluble sugar,and soluble protein and higher activities of antioxidant enzymes to sustain better seed germination and seedling ***,another mechanism of ZnO nanopriming induced rice salt tolerance was associated with better maintenance of(K^(+))ions *** research concluded that NanoZnO could promote plant salt tolerance and be

关键词： rice salinity ROS scavenging seed nanopriming germination mechanism

SH3P2,an SH3 domain-containing protein that interacts with both Pib and AvrPib,suppresses effector-triggered,Pib-mediated immunity in rice

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Molecular Plant 2022年第12期15卷 1931-1946页

作者： Yunjie Xie Yupeng Wang Xiangzhen Yu Yuelong Lin Yongsheng Zhu Jinwen Chen Hongguang Xie Qingqing Zhang Lanning Wang Yidong Wei Yanjia Xiao Qiuhua Cai Yanmei Zheng Mo Wang Huaan Xie Jianfu Zhang State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops Fujian Agriculture and Forestry UniversityFuzhou 350002China rice Research Institute Fujian Academy of Agricultural SciencesFuzhou 350018China Key Laboratory of Germplasm Innovation and Molecular breeding of Hybrid rice for South China Ministry of Agriculture and AffairsFuzhouP.R.China Incubator of National Key Laboratory of Germplasm Innovation and Molecular breeding between Fujian and Ministry of Sciences and Technology FuzhouChina Fuzhou Branch National Rice Improvement Center of ChinaFuzhouChina Fujian Engineering Laboratory of Crop Molecular breeding FuzhouChina Fujian Key Laboratory of rice Molecular breeding Fuzhou 350003China

Plants usually keep resistance(R)proteins in a static state under normal conditions to avoid autoimmunity and save energy for growth,but R proteins can be rapidly activated upon perceiving pathogen ***,the first cloned blast disease R gene in rice,encoding a nucleotide-binding leucine-rich repeat(NLR)protein,mediates resistance to the blast fungal(Magnaporthe oryzae)isolates carrying the avirulence gene ***,the molecular mechanisms about how Pib recognizes AvrPib and how it is inactivated and activated remain largely *** this study,through map-based cloning and CRISPR-Cas9 gene editing,we proved that Pib contributes to the blast disease resistance of rice cultivar Yunyin(YY).Furthermore,an SH3 domain-containing protein,SH3P2,was found to associate with Pib mainly at clathrin-coated vesicles in rice cells,via direct binding with the coiled-coil(CC)domain of ***,overexpression of SH3P2 in YY compromised Pib-mediated resistance to *** isolates carrying AvrPib and Pib-AvrPib recognition-induced cell ***3P2 competitively inhibits the self-association of the Pib CC domain in vitro,suggesting that binding of SH3P2 with Pib undermines its ***,SH3P2 can also interact with AvrPib and displays higher affinity to AvrPib than to Pib,which leads to dissociation of SH3P2 from Pib in the presence of *** together,our results suggest that SH3P2 functions as a“protector”to keep Pib in a static state by direct interaction during normal growth but could be triggered off by the invasion of AvrPib-carrying *** *** study reveals a new mechanism about how an NLR protein is inactivated under normal conditions but is activated upon pathogen infection.

关键词： rice blast fungus Pib-AvrPib recognition SH3 domain-containing protein protector

Stay-Green Panicle Branches Improve Processing Quality of Elite rice Cultivars

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rice science 2023年第1期30卷 11-14页

作者： CHEN Yibo ZHAO Lei WANG Chongrong LI Hong HUANG Daoqiang WANG Zhidong ZHOU Degui PAN Yangyang GONG Rong ZHOU Shaochuan rice Research Institute Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Laboratory for Lingnan Modern AgricultureGuangzhou 510640China

rice panicle branches are key routes for transportation of photo synthetic products to *** senescence is an important trait that the breeders considered when breeding elite rice cultivars in South ***,little is known about the mechanisms underlying the contributions of stay-green panicle branches to rice yield and ***,we reported stay-green branches that continuously maintained transportation function and provided carbohydrates for basal grain development at the late stages of rice *** ensured the coordination of development between apical and basal grains,and further improved the processing quality of elite *** findings provided strategies for improving the fullness and quality of rice grains and presented an important basis for cultivating elite rice.

关键词： elite breeding cultivar

Application of an Improved 2-Dimensional High-Throughput Soybean Root Phenotyping Platform to Identify Novel Genetic Variants Regulating Root Architecture Traits

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Plant Phenomics 2023年第4期5卷 728-745页

作者： Rahul Chandnani Tongfei Qin Heng Ye Haifei Hu Karim Panjvani Mutsutomo Tokizawa Javier Mora Macias Alma Armenta Medina Karine C.Bernardino Pierre-Luc Pradier Pankaj Banik Ashlyn Mooney Jurandir V.Magalhaes Henry T.Nguyen Leon V.Kochian Global Institute for Food Security University of SaskatchewanSaskatoonSKCanada NRGene Canada 110 Research Dr Suite 101SaskatoonSKCanada division of Plant Sciences and Technology University of MissouriColumbiaM065211USA School of Biological Sciences The University of Western AustraliaCrawleyWA 6009Australia rice Research Institute Guangdong Academy of Agricultural Sciences&Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China(Co-construction by Ministry and Province)Ministry of Agriculture and Rural Affairs&Guangdong Key Laboratory of New Technology in Rice Breeding&Guangdong Rice Engineering LaboratoryGuangdongChina Embrapa Maize and Sorghum Sete LagoasBrazil

Nutrient-efficient root system architecture(RSA)is becoming an important breeding objective for generating crop varieties with improved nutrient and water acquisition *** variants shaping soybean RSA is key in improving nutrient and water ***,we report on the use of an improved 2-dimensional high-throughput root phenotyping platform that minimizes background noise by imaging pouch-grown root systems submerged in *** also developed a background image cleaning Python pipeline that computationally removes images of small pieces of debris and filter paper fibers,which can be erroneously quantified as root *** platform was used to phenotype root traits in 286 soybean lines genotyped with 5.4 million single-nucleotide *** was a substantially higher correlation in manually counted number of root tips with computationally quantified root tips(95%correlation),when the background was cleaned of nonroot materials compared to root images without the background corrected(79%).Improvements in our RSA phenotyping pipeline significantly reduced overestimation of the root traits influenced by the number of root ***-wide association studies conducted on the root phenotypic data and quantitative gene expression analysis of candidate genes resulted in the identification of 3 putative positive regulators of root system depth,total root length and surface area,and root system volume and surface area of thicker roots(DOF1-like zinc finger transcription factor,protein of unknown function,and C2H2 zinc finger protein).We also identified a putative negative regulator(gibberellin 20 oxidase 3)of the total number of lateral roots.

关键词： Python Root submerged

The UDP-glycosyltransferase OsUGT706D2 positively regulates cold and submergence stress tolerance in rice

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The Crop Journal 2024年第3期12卷 732-742页

作者： Qing Liu Lanlan Zhang Shuwei Lyu Hang Yu Wenjie Huang Liqun Jiang Jing Zhang Bingrui Sun Xingxue Mao Pingli Chen Junlian Xing Wenfeng Chen Zhilan Fan Shijuan Yan Chen Li Guangdong Key Laboratory of New Technology in rice breeding/Guangdong rice Engineering Laboratory/Key Laboratory of Genetics and breeding of High Quality rice in Southern China(Co-construction by Ministry and Province) Ministry of Agriculture and Rural AffairsRice Research InstituteGuangdong Academy of Agricultural SciencesGuangzhou 510640GuangdongChina Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization Agro-biological Gene Research CenterGuangdong Academy of Agricultural SciencesGuangzhou 510640GuangdongChina

In a genome-wide association study,we identified a rice UDP-glycosyltransferase gene,OsUGT706D2,whose transcription was activated in response to cold and submergence stress and to exogenous abscisic acid(ABA).OsUGT706D2 positively regulated the biosynthesis of tricin-4’-O-(syringyl alcohol)ether-7-O-glucoside at both the transcriptional and metabolic ***706D2 mediated cold and submergence tolerance by modulating the expression of stress-responsive genes as well as the abscisic acid(ABA)signaling *** of function of OsUGT706D2 increased cold and submergence tolerance and loss of function of OsUGT706D2 reduced cold *** positively regulated OsUGT706D2-mediated cold tolerance but reduced submergence *** findings suggest the potential use of OsUGT706D2 for improving abiotic stress tolerance in rice.

关键词： UDP-glycosyltransferase rice Cold tolerance Submergence tolerance ABA

A KNOX II transcription factor suppresses the NLR immune receptor BRG8-mediated immunity in rice

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Plant Communications 2024年第10期5卷 121-138页

作者： Siliang Xu Xinghua Wei Qinqin Yang Dongxiu Hu Yuanyuan Zhang Xiaoping Yuan Fengyu Kang Zhaozhong Wu Zhiqin Yan Xueqin Luo Yanfei Sun Shan Wang Yue Feng Qun Xu Mengchen Zhang Yaolong Yang China National Center for rice Improvement/State Key Laboratory of rice Biology and breeding China National Rice Research InstituteHangzhou 310006China National Nanfan Research Institute(Sanya) Chinese Academy of Agricultural SciencesSanya 572024China

Nucleotide-binding site and leucine-rich repeat(NLR)proteins are activated by detecting pathogen effectors,which in turn trigger host defenses and cell *** many NLRs have been identified,the mechanisms responsible for NLR-triggered defense responses are still poorly *** this study,through a genome-wide association study approach,we identified a novel NLR gene,Blast Resistance Gene 8(BRG8),which confers resistance to rice blast and bacterial blight ***8 overexpression and complementation lines exhibit enhanced resistance to both *** localization assays showed that BRG8 is localized in both the cytoplasm and the *** evidence revealed that nuclear-localized BRG8 can enhance rice immunity without a hypersensitive response(HR)-like *** also demonstrated that the coiled-coil domain of BRG8 not only physically interacts with itself but also interacts with the KNOX II protein HOMEOBOX ORYZA SATIVA59(HOS59).Knockout mutants of HOS59 in the BRG8 background show enhanced resistance to Magnaporthe oryzae strain CH171 and Xoo strain CR4,similar to that of the BRG8 *** contrast,overexpression of HOS59 in the BRG8 background will compromise the HR-like phenotype and resistance *** analysis revealed that HOS59 promotes the degradation of BRG8 via the 26S proteasome ***,our study highlights HOS59 as an NLR immune regulator that fine-tunes BRG8-mediated immune responses against pathogens,providing new insights into NLR associations and functions in plant immunity.

关键词： rice NLR protein KNOX II protein rice blast bacterial blight

Cry1Ab rice does not impact biological characters and functional response of Cyrtorhinus lividipennis preying on Nilaparvata lugens eggs

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Journal of Integrative Agriculture 2015年第10期14卷 2011-2018页

作者： CHEN Yang LAI Feng-xiang SUN Yan-qun HONG Li-ying TIAN Jun-ce ZHANG Zhi-tao FU Qiang State Key Laboratory of rice Biology China National Rice Research Institute State Key Laboratory of breeding Base for Zhejiang Sustainable Pest and Disease Control Institute of Plant Protection and Microbiology Zhejiang Academy of Agricultural Sciences

One concern about the use of transgenic plants is their potential risk to natural enemies. In this study, using the eggs of the rice brown planthopper, Nilaparvata lugens, as a food source, we investigated the effects of Cry1 Ab rice on the biological characteristics and functional response of an important predator Cyrtorhinus lividipennis. The results showed that the survival ability（adult emergence rate and egg hatching rate）, development（egg duration, nymphal developmental duration）, adult fresh weight, adult longevity and fecundity of C. lividipennis on Bt rice plants were not significantly different compared to those on non-Bt rice plants. Furthermore, two important parameters of functional response（instantaneous search rate and handling time） were not significantly affected by Bt rice. In conclusion, the tested Cry1 Ab rice does not adversely impact the biological character and functional response of C. lividipennis.

关键词： Bt rice safety assessment non-target organism natural enemy