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Cassava Me RS40 is required for the regulation of plant salt tolerance

Journal of Integrative Agriculture 2023年第5期22卷 1396-1411页

作者： MA Xiao-wen MA Qiu-xiang MA Mu-qing CHEN Yan-hang GU Jin-bao LI Yang HU Qing LUO Qing-wen WEN Ming-fu ZHANG Peng LI Cong WANG Zhen-yu institute of nanfan&Seed Industry Guangdong Academy of SciencesGuangzhou 510316P.R.China National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai 200032P.R.China Zhanjiang research Center Institute of Nanfan&Seed IndustryGuangdong Academy of SciencesZhanjiang 524300P.R.China

Soil salinity affects the expression of serine/arginine-rich(SR) genes and isoforms by alternative splicing, which in turn regulates the adaptation of plants to stress.We previously identified the cassava spliceosomal component 35 like(SCL) and SR subfamilies, belonging to the SR protein family, which are extensively involved in responses to abiotic stresses.However, the post-transcriptional regulatory mechanism of cassava arginine/serine-rich(RS) subfamily in response to salt stress remains to be explored.In the current study, we identified 37 genes of the RS subfamily from 11 plant species and systematically investigated the transcript levels of the RS40 and RS31 genes under diverse abiotic stress conditions.Subsequently, an analysis of the conserved protein domains revealed that plant RS subfamily genes were likely to preserve their conserved molecular functions and played critical functional roles in responses to abiotic stresses.Importantly, we found that overexpression of MeRS40 in Arabidopsis enhanced salt tolerance by maintaining reactive oxygen species homeostasis and up-regulating the salt-responsive genes.However,overexpression of MeRS40 gene in cassava reduced salt tolerance due to the depression of its endogenous gene expression by negative autoregulation of its own pre-mRNA.Moreover, the MeRS40 protein interacted with MeU1-70Ks(MeU1-70Ka and MeU1-70Kb) in vivo and in vitro, respectively.Therefore, our findings highlight the critical role of cassava SR proteins in responses to salt stress in plants.

关键词： cassava alternative splicing serine/arginine-rich proteins salt stress

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Design and experiment of pneumatic seed clearing mechanism for pin-hole tube wheat plot precision sowing device

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International Journal of Agricultural and Biological Engineering 2023年第4期16卷 85-95页

作者： Xirui Zhang Youming Yang Qingjie Wang Hongwen Li Zhifu Zhang Junxiao Liu School of Mechanical and Electrical Engineering Hainan UniversityHaikou 570228China College of Engineering China Agricultural UniversityBeijing 100083China Sanya nanfan research institute of Hainan University Sanya 572025HainanChina

For the problem that when wheat is sucked up by the air suction method,the seeds are aligned in a small area,making it difficult for the contact seed cleaning mechanism to clean the seeds.The mechanism of seed cleaning airflow on wheat seed was studied,the flow velocity distribution relationship of the jet section was defined,the mathematical model of the jet velocity of circular and plane sections was established,and the key factors that could have a significant influence on seed cleaning effect were explored.A non-contact positive pressure air flow seed cleaning method was proposed.After theoretical calculations,it is concluded that the core section lengths of the circular section jet and the inline jet are 24.8 mm and 28.8 mm,respectively.The clearing distance is set to 20 mm.Through the single-factor test,the best air tube nozzle shape was clarified as a vertical inline nozzle.The angle of seed cleaning,the air velocity of seed cleaning,and the negative supply pressure were selected as influencing factors,and the seed leakage index,seed reabsorption index,and seed qualification index as the evaluation indicators to conduct a 3-factor 5-horizontal rotation test.A mathematical regression model of influencing factors and evaluation indexes was established to analyze the influence of these factors and indexes.The optimal operation parameters were obtained as the seed cleaning Angle of 19°,the seed cleaning air velocity of 58 m/s,and the negative pressure of 8.5 kPa.Under the optimal parameters,the seed leakage suction index is 8.23%,the seed reabsorption index is 0.33%,and the seed qualification index is 91.44%,which meets the design requirements.

关键词： wheat precision seed-metering device clearing seed positive pressure airflow jet flow field

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Integration of high-throughput phenotyping,GWAS,and predictive models reveals the genetic architecture of plant height in maize

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Molecular Plant 2023年第2期16卷 354-373页

作者： Weixuan Wang Weijun Guo Liang Le Jia Yu Yue Wu Dongwei Li Yifan Wang Huan Wang Xiaoduo Lu Hong Qiao Xiaofeng Gu Jian Tian Chunyi Zhang Li Pu Biotechnology research institute Chinese Academy of Agricultural SciencesBeijing 100081China National nanfan research institute(Sanya) Chinese Academy of Agricultural SciencesSanya 572024China institute of Molecular Breeding for Maize Qilu Normal UniversityJinan 250200China institute for Cellular and Molecular Biology The University of Texas at AustinAustinTX 78712USA Department of Molecular Biosciences The University of Texas at AustinAustinTX 78712USA Sanya institute Hainan Academy of Agricultural SciencesSanya 572000China

Plant height(PH)is an essential trait in maize(Zea mays)that is tightly associated with planting density,biomass,lodging resistance,and grain yield in the field.Dissecting the dynamics of maize plant architecture will be beneficial for ideotype-based maize breeding and prediction,as the genetic basis controlling PH in maize remains largely unknown.In this study,we developed an automated high-throughput phenotyping platform(HTP)to systematically and noninvasively quantify 77 image-based traits(i-traits)and 20 field traits(f-traits)for 228 maize inbred lines across all developmental stages.Time-resolved i-traits with novel digital phenotypes and complex correlations with agronomic traits were characterized to reveal the dynamics of maize growth.An i-trait-based genome-wide association study identified 4945 traitassociated SNPs,2603 genetic loci,and 1974 corresponding candidate genes.We found that rapid growth of maize plants occurs mainly at two developmental stages,stage 2(S2)to S3 and S5 to S6,accounting for the final PH indicators.By integrating the PH-association network with the transcriptome profiles of specific internodes,we revealed 13 hub genes that may play vital roles during rapid growth.The candidate genes and novel i-traits identified at multiple growth stages may be used as potential indicators for final PH in maize.One candidate gene,ZmVATE,was functionally validated and shown to regulate PH-related traits in maize using genetic mutation.Furthermore,machine learning was used to build predictive models for final PH based on i-traits,and their performancewas assessed across developmental stages.Moderate,strong,and very strong correlations between predictions and experimental datasets were achieved from the early S4(tenth-leaf)stage.Colletively,our study provides a valuable tool for dissecting the spatiotemporal formation of specific internodes and the genetic architecture of PH,as well as resources and predictive models that are useful for molecular design breeding and predicting maize varieties with i

关键词： phenomics GWAS plant height machine learning prediction maize

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LncPheDB:a genome-wide lncRNAs regulated phenotypes database in plants

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aBIOTECH 2022年第3期3卷 169-177页

作者： Danjing Lou Fei Li Jinyue Ge Weiya Fan Ziran Liu Yanyan Wang Jingfen Huang Meng Xing Wenlong Guo Shizhuang Wang Weihua Qiao Zhenyun Han Qian Qian Qingwen Yang Xiaoming Zheng National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing100081China College of Life Science Shenyang Normal UniversityShenyang110034China National nanfan research institute(Sanya) Chinese Academy of Agricultural SciencesSanya572000China State Key Laboratory of Rice Biology China National Rice Research InstituteChinese Academy of Agricultural SciencesHangzhou310006China Agricultural Genomics institute at Shenzhen Chinese Academy of Agricultural SciencesShenzhen518120China International Rice research institute DAPO box 7777Metro ManilaThe Philippines

LncPheDB(https://***/)is a systematic resource of genome-wide long non-coding RNAs(lncRNAs)-phenotypes associations for multiple species.It was established to display the genome-wide lncRNA annotations,target genes prediction,variant-trait associations,gene-phenotype correlations,lncRNA-phenotype correlations,and the similar non-coding regions of the queried sequence in multiple species.LncPheDB sorted out a total of 203,391 lncRNA sequences,2000 phenotypes,and 120,271 variants of nine species(Zea mays L.,Gossypium barbadense L.,Triticum aestivum L.,Lycopersicon esculentum Mille,Oryza sativa L.,Hordeum vulgare L.,Sorghum bicolor L.,Glycine max L.,and Cucumis sativus L.).By exploring the relationship between lncRNAs and the genomic position of variants in genome-wide association analysis,a total of 68,862 lncRNAs were found to be related to the diversity of agronomic traits.More importantly,to facilitate the study of the functions of lncRNAs,we analyzed the possible target genes of lncRNAs,constructed a blast tool for performing similar fragmentation studies in all species,linked the pages of phenotypic studies related to lncRNAs that possess similar fragments and constructed their regulatory networks.In addition,LncPheDB also provides a user-friendly interface,a genome visualization platform,and multi-level and multi-modal convenient data search engine.We believe that LncPheDB plays a crucial role in mining lncRNA-related plant data.

关键词： LncRNA GWAS Phenotype SNP Plants

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Past and recent advances in sugarcane cytogenetics

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The Crop Journal 2023年第1期11卷 1-8页

作者： Kai Wang Hui Zhang Haris Khurshid Ayman Esh Caiwen Wu Qinnan Wang Nathalie Piperidis School of Life Sciences Nantong UniversityNantong 226019JiangsuChina Sugar research Australia Mackay 4740Australia institute of nanfan&Seed Industry Guangdong Academy of SciencesGuangzhou 510316GuangdongChina Sugarcane institute Yunnan Academy of Agricultural SciencesKaiyuan 661600YunnanChina Sugar Crops research institute Agriculture Research CenterGiza 12111Egypt Oilseeds research Program National Agricultural Research CentreIslamabad 44000Pakistan

The Saccharum genus comprises species with large and variable chromosome numbers, leading to challenges in genomic studies and breeding improvement. Cytogenetics, including classical and molecular approaches, has played a central role in deciphering the genome structure, classification, and evolution of the genus Saccharum. The application of fluorescence in situ hybridization using oligonucleotide probes significantly improved our understanding of the complex genomes of Saccharum species. This paper reviews the application and progress of cytogenetic techniques in Saccharum. Future applications of cytogenetics are discussed, as they could benefit both genomic studies and breeding of sugarcane as well as other plants with complex genomes.

关键词： Cytogenetics Sugarcane FISH Chromosome Oligo-FISH

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Natural variations of OsAUX5,a target gene of OsWRKY78,control the neutral essential amino acid content in rice grains

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Molecular Plant 2023年第2期16卷 322-336页

作者： Yuheng Shi Yuanyuan Zhang Yangyang Sun Ziyang Xie Yu Luo Qiyuan Long Jiahui Feng Xueqing Liu Bi Wang Dujun He Junxia Ren Peizhen Guo Junwei Xing Liqiang He Alisdair RFernie Wei Chen Xianqing Liu Yuehua Luo Cheng Jin Jie Luo Sanya nanfan research institute of Hainan University Hainan Yazhou Bay Seed LaboratorySanya 572025China College of Tropical Crops Hainan UniversityHaikou 570228China Max Planck institute of Molecular Plant Physiology 14476 Potsdam-GolmGermany National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene research(Wuhan) Huazhong Agricultural UniversityWuhan 430070China

Grain essential amino acid(EAA)levels contribute to rice nutritional quality.However,the molecular mechanisms underlying EAA accumulation and natural variation in rice grains remain unclear.Here we report the identification of a previously unrecognized auxin influx carrier subfamily gene,OsAUX5,which encodes an amino acid transporter that functions in uptake of multiple amino acids.We identified an elite haplotype of Pro::OsAUX5^(Hap2) that enhances grain EAA accumulation without an apparent negative effect on agronomic traits.Natural variations of OsAUX5 occur in the cis elements of its promoter,which are differentially activated because of the different binding affinity between OsWRKY78 and the W-box,contributing to grain EAA variation among rice varieties.The two distinct haplotypes were shown to have originated from different Oryza rufipogon progenitors,which contributed to the divergence between japonica and indica.Introduction of the indica-type Pro::OsAUX5^(Hap2) genotype into japonica could significantly increase EAA levels,indicating that indica-type Pro::OsAUX5^(Hap2) can be utilized to increase grain EAAs of japonica varieties.Collectively,our study uncovers an WRKY78–OsAUX5-based regulatory mechanism controlling grain EAA accumulation and provides a potential target for breeding EAA-rich rice.

关键词： amino acid natural variation transcriptional regulation Oryza sativa

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Hyper-seq:A novel,effective,and flexible marker-assisted selection and genotyping approach

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The Innovation 2022年第4期3卷 28-29页

作者： Meiling Zou Zhiqiang Xia Sanya nanfan research institute of Hainan University Hainan Yazhou Bay Seed LaboratorySanya 572025China College of Tropical Crops Hainan University Hainan UniversityHaikou 570288China The institute of Tropical Biosciences and Biotechnology Chinese Academy of Tropical Agriculture SciencesHaikou 571101China

Recently,a novel extremely low-cost,effective,flexible,and high-throughput DNA sequencing library preparation and genotyping approach has been developed named Hyper-seq.This new technology has been adopted by more than 15 research institutes and universities,which has significantly improved the efficiency of crop breeding.The collection and explanation of all DNA sequences froma species,known as pangenome,is the future and hotspot of genomics research.The effective and flexible identification of distinct genetic materials among individuals or populations from pangenome is crucial for exploring genetic and molecular biological processes.Single-nucleotide polymorphisms(SNPs)have become the preferred genetic component to examine humandiseases aswell as animal and plant resistance andmolecular breeding.1 Meanwhile,driven by next-generation sequencing(NGS)technology,the cost of DNA sequencing has been greatly decreased.Over the past decade,genomics-assisted breeding(GAB)has played an important role in utilizing the potential and characterization of modern genomic resources.

关键词： utilizing breeding explanation

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Single-cell RNA sequencing reveals the landscape of maize root tips and assists in identification of cell type-specific nitrate-response genes

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The Crop Journal 2022年第6期10卷 1589-1600页

作者： Xuhui Li Xiangbo Zhang Shuai Gao Fangqing Cui Weiwei Chen Lina Fan Yongwen Qi institute of nanfan&Seed Industry Guangdong Academy of ScienceGuangzhou 510316GuangdongChina College of Agriculture and Biology Zhongkai University of Agriculture and EngineeringGuangzhou 510325GuangdongChina

The root system is fundamental for maize growth and yield.Characterizing its heterogeneity and cell type-specific response to nitrate at the single-cell level will shed light on root development and nutrient uptake.We profiled the transcriptomes of>7000 cells derived from root tips of maize seedlings grown on media with or without nitrate,and identified 11 major cell types or tissues and 85 cell type-specific nitrate-response genes,including several known nitrate metabolic genes.A pseudotime analysis showed a continuous pseudotime series with the beginning at meristematic zone cells and showed that the root hair cell was derived by differentiation of a subset of epidermal cells.Interspecies comparison of root cells between maize and rice revealed the conservation and divergence of the root cell types and identified 57,216,and 80 conserved orthologous genes in root hair,endodermis,and phloem cells respectively.This study provides a global view of maize root tip developmental processes and responses to nitrate at the single-cell level.The genes described in the present work could serve as targets for further genetic analyses and accurate regulation of gene expression and phenotypic variation in specific cell types or tissues.

关键词： Maize Single-cell RNA sequencing Root Nitrate

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Disease resistance conferred by components of essential chrysanthemum oil and the epigenetic regulation of OsTPS1

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Science China(Life Sciences) 2023年第5期66卷 1108-1118页

作者： Chuansong Zhan Long Lei Hao Guo Shen Zhou Congping Xu Zixin Liu Zichen Wu Yuan Deng Yuanyuan Miao Yu Han Meng Zhang Hua Li Sishu Huang Chenkun Yang Feng Zhang Yufei Li Ling Liu Xianqing Liu Hafiz Muhammad Khalid Abbas Alisdair R.Fernie Meng Yuan Jie Luo College of Tropical Crops Hainan UniversityHaikou 570228China Sanya nanfan research institute of Hainan University Hainan Yazhou Bay Seed LaboratorySanya 572025China National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene research(Wuhan) Huazhong Agricultural UniversityWuhan 430070China Max Planck institute of Molecular Plant Physiology Am Mühlenberg 114476 Potsdam-GolmGermany

The sesquiterpene alpha-bisabolol is the predominant active ingredient in essential oils that are highly valued in the cosmetics industry due to its wound healing,anti-inflammatory,and skin-soothing properties.Alpha-bisabolol was thought to be restricted to Compositae plants.Here we reveal that alpha-bisabolol is also synthesized in rice,a non-Compositae plant,where it acts as a novel sesquiterpene phytoalexin.Overexpressing the gene responsible for the biosynthesis of alpha-bisabolol,Os TPS1,conferred bacterial blight resistance in rice.Phylogenomic analyses revealed that alpha-bisabolol-synthesizing enzymes in rice and Compositae evolved independently.Further experiments demonstrated that the natural variation in the disease resistance level was associated with differential transcription of Os TPS1 due to polymorphisms in its promoter.We demonstrated that Os TPS1 was regulated at the epigenetic level by JMJ705 through the methyl jasmonate pathway.These data reveal the cross-family accumulation and regulatory mechanisms of alpha-bisabolol production.

关键词： alpha-bisabolol epigenetic regulation natural variation

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Artificial evolution of OsEPSPS through an improved dual cytosine and adenine base editor generated a novel allele conferring rice glyphosate tolerance

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植物学报:英文版 2023年第9期65卷 2194-2203页

作者： Chen Zhang Xue Zhong Shaoya Li Lei Yan Jingying Li Yubing He Yong Lin Yangjun Zhang Lanqin Xia institute of Crop Sciences(ICS) Chinese Academy of Agricultural Sciences(CAAS)Beijing 100081China CAAS/Hainan Yazhou Bay Seed Laboratory National Nanfan Research Institute(Sanya)Sanya 572024China Key Laboratory of Gene Editing Technologies(Hainan) Ministry of Agricultural and Rural AffairsSanya 572024China Beijing Dabeinong Technology Group Co. LtdBeijing 10080China

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.

关键词： artificial evolution dual cytosine and adenine base editor nCas9‐NG rice(Oryza sativa L) near‐saturated mutagenesis

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