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In maize,co-expression of GAT and GR79-EPSPS provides high glyphosate resistance,along with low glyphosate residues

aBIOTECH 2023年第4期4卷 277-290页

作者： Shengyan Li Pengcheng Li Xiangyin Li Ning Wen Yinxiao Wang Wei Lu Min Lin Zhihong Lang Biotechnology research institute Chinese Academy of Agricultural SciencesBeijingChina National Nanfan Research Institute(Sanya) Chinese Academy of Agricultural SciencesSanyaHainanChina

Herbicide tolerance has been the dominant trait introduced during the global commercialization of genetically modified(GM)crops.Herbicide-tolerant crops,especially glyphosate-resistant crops,offer great advantages for weed management;however,despite these benefits,glyphosate-resistant maize(Zea mays L.)has not yet been commercially deployed in China.To develop a new bio-breeding resource for glyphosate-resistant maize,we introduced a codon-optimized glyphosate N-acetyltransferase gene,gat,and the enolpyruvyl-shikimate-3-phosphate synthase gene,gr79-epsps,into the maize variety B104.We selected a genetically stable high glyphosate resistance(GR)transgenic event,designated GG2,from the transgenic maize population through screening with high doses of glyphosate.A molecular analysis demonstrated that single copy of gat and gr79-epsps were integrated into the maize genome,and these two genes were stably transcribed and translated.Field trials showed that the transgenic event GG2 could tolerate 9000 g acid equivalent(a.e.)glyphosate per ha with no effect on phenotype or yield.A gas chromatography-mass spectrometry(GC–MS)analysis revealed that,shortly after glyphosate application,the glyphosate(PMG)and aminomethylphosphonic acid(AMPA)residues in GG2 leaves decreased by more than 90%compared to their levels in HGK60 transgenic plants,which only harbored the epsps gene.Additionally,PMG and its metabolic residues(AMPA and N-acetyl-PMG)were not detected in the silage or seeds of GG2,even when far more than the recommended agricultural dose of glyphosate was applied.The co-expression of gat and gr79-epsps,therefore,confers GG2 with high GR and a low risk of herbicide residue accumulation,making this germplasm a valuable GR event in herbicide-tolerant maize breeding.

关键词： Transgenic maize Glyphosate resistance Gr79-epsps gene Gat gene Low residues

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Plant base editing and prime editing:The current status and future perspectives

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Journal of Integrative Plant Biology 2023年第2期65卷 444-467页

作者： Jingying Li Chen Zhang Yubing He Shaoya Li Lei Yan Yucai Li Ziwei Zhu Lanqin Xia institute of Crop Sciences(ICS) Chinese Academy of Agricultural Sciences(CAAS)Beijing 100081China National Nanfan Research Institute(Sanya) Chinese Academy of Agricultural Sciences/Hainan Yazhou Bay Seed LaboratorySanya 572024China

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.

关键词： base editing CRISPR/Cas plants precision genome editing prime editing

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LSL1 controls cell death and grain production by stabilizing chloroplast in rice

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Science China(Life Sciences) 2022年第11期65卷 2148-2161页

作者： Deyong Ren Wei Xie Qiankun Xu Jiang Hu Li Zhu Guangheng Zhang Dali Zeng Qian Qian State Key Lab of Rice Biology China National Rice Research InstituteHangzhou 310006China College of Modern Agriculure Zhejiang A&F UniversityHangzhou 31006China National Nanfan Research Institute Chinese Academy of Agricultural SciencesSanya 572024China

Lesion mutants can be valuable tools to reveal the interactions between genetic factors and environmental signals and to improve grain production.Here we identified a rice(Oryza sativa)mutant,lesion spotleaf1(lsl1),which produces necrotic leaf lesions throughout its life cycle.LSL1 encodes a protein of unknown function and belongs to a grass-specific clade.The lesion phenotype of the lsl1 mutant was sharply induced by shading,and its detached leaves incubated in 6-benzylamino purine similarly formed lesions in the dark.In addition,the lsl1 mutant exhibited reactive oxygen species accumulation and cell death.The terminal deoxynucleotidyl transferase d UTP nick end-labeling(TUNEL)and comet assays revealed that the lsl1 mutant contained severe DNA damage,resulting in reduced grain yield and quality.RNA sequencing,gene expression,and protein activity analyses indicate that LSL1 is required for chloroplast function.Furthermore,LSL1 interacts with Psa D and PAP10 to form a regulatory module that functions in chlorophyll synthesis and chloroplast development to maintain redox balance.Our results reveal that LSL1 maintains chloroplast structure,redox homeostasis,and DNA stability,and plays important roles in the interaction between genetic factors and environmental signals and in regulating grain size and quality.

关键词： lesion formation chloroplast function redox homeostasis grain size and quality LSL1 rice

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Population analysis reveals the roles of DNA methylation in tomato domestication and metabolic diversity

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Science China(Life Sciences) 2023年第8期66卷 1888-1902页

作者： Hao Guo Peng Cao Chao Wang Jun Lai Yuan Deng Chun Li Yingchen Hao Zeyong Wu Ridong Chen Qi Qiang Alisdair RFernie Jun Yang Shouchuang Wang Sanya Nanfan Research Institute of Hainan University Hainan Yazhou Bay Seed LaboratorySanya 572025China College of Tropical Crops Hainan UniversityHaikou 572208China Max-Planck-institute of Molecular Plant Physiology Potsdam-Golm 144776Germany

DNA methylation is an important epigenetic marker,yet its diversity and consequences in tomato breeding at the population level are largely unknown.We performed whole-genome bisulfite sequencing(WGBS),RNA sequencing,and metabolic profiling on a population comprising wild tomatoes,landraces,and cultivars.A total of 8,375 differentially methylated regions(DMRs)were identified,with methylation levels progressively decreasing from domestication to improvement.We found that over 20%of DMRs overlapped with selective sweeps.Moreover,more than 80%of DMRs in tomato were not significantly associated with single-nucleotide polymorphisms(SNPs),and DMRs had strong linkages with adjacent SNPs.We additionally profiled 339 metabolites from 364 diverse accessions and further performed a metabolic association study based on SNPs and DMRs.We detected 971 and 711 large-effect loci via SNP and DMR markers,respectively.Combined with multi-omics,we identified 13 candidate genes and updated the polyphenol biosynthetic pathway.Our results showed that DNA methylation variants could complement SNP profiling of metabolite diversity.Our study thus provides a DNA methylome map across diverse accessions and suggests that DNA methylation variation can be the genetic basis of metabolic diversity in plants.

关键词： DNA methylation domestication multi-omics mGWAS mEWAS metabolic diversity tomato

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Metabolomics-centered mining of plant metabolic diversity and function:Past decade and future perspectives

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Molecular Plant 2023年第1期16卷 43-63页

作者： Shuangqian Shen Chuansong Zhan Chenkun Yang Alisdair R.Fernie 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 Potsdam-Golm 14476Germany

Plants are natural experts in organic synthesis,being able to generate large numbers of specific metabolites with widely varying structures that help them adapt to variable survival challenges.Metabolomics is a research discipline that integrates the capabilities of several types of research including analytical chemistry,statistics,and biochemistry.Its ongoing development provides strategies for gaining a systematic understanding of quantitative changes in the levels of metabolites.Metabolomics is usually performed by targeting either a specific cell,a specific tissue,or the entire organism.Considerable advances in science and technology over the last three decades have propelled us into the era of multi-omics,in which metabolomics,despite at an earlier developmental stage than genomics,transcriptomics,and proteomics,offers the distinct advantage of studying the cellular entities that have the greatest influence on end phenotype.Here,we summarize the state of the art of metabolite detection and identification,and illustrate these techniques with four case study applications:(i)comparing metabolite composition within and between species,(ii)assessing spatio-temporal metabolic changes during plant development,(iii)mining characteristic metabolites of plants in different ecological environments and upon exposure to various stresses,and(iv)assessing the performance of metabolomics as a means of functional gene identification,metabolic pathway elucidation,and metabolomics-assisted breeding through analyzing plant populations with diverse genetic variations.In addition,we highlight the prominent contributions of joint analyses of plant metabolomics and other omics datasets,including those from genomics,transcriptomics,proteomics,epigenomics,phenomics,microbiomes,and ion-omics studies.Finally,we discuss future directions and challenges exploiting metabolomics-centered approaches in understanding plant metabolic diversity.

关键词： metabolomics multi-omics high-throughput metabolic profiling bioactive markers

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

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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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Recent progression and future perspectives in cotton genomic breeding

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Journal of Integrative Plant Biology 2023年第2期65卷 548-569页

作者： Zhaoen Yang Chenxu Gao Yihao Zhang Qingdi Yan Wei Hu Lan Yang Zhi Wang Fuguang Li Zhengzhou research Base State Key Laboratory of Cotton BiologySchool of Agricultural SciencesZhengzhou UniversityZhengzhou 450000China State Key Laboratory of Cotton Biology Institute of Cotton Research of the Chinese Academy of Agricultural SciencesAnyang 455000China National Nanfan Research Institute(Sanya) Chinese Academy of Agricultural SciencesSanya 572000China Sanya institute Zhengzhou UniversitySanya 572000China

Upland cotton is an important global cash crop for its long seed fibers and high edible oil and protein content.Progress in cotton genomics promotes the advancement of cotton genetics,evolutionary studies,functional genetics,and breeding,and has ushered cotton research and breeding into a new era.Here,we summarize high-impact genomics studies for cotton from the last 10 years.The diploid Gossypium arboreum and allotetraploid Gossypium hirsutum are the main focus of most genetic and genomic studies.We next review recent progress in cotton molecular biology and genetics,which builds on cotton genome sequencing efforts,population studies,and functional genomics,to provide insights into the mechanisms shaping abiotic and biotic stress tolerance,plant architecture,seed oil content,and fiber development.We also suggest the application of novel technologies and strategies to facilitate genome-based crop breeding.Explosive growth in the amount of novel genomic data,identified genes,gene modules,and pathways is now enabling researchers to utilize multidisciplinary genomics-enabled breeding strategies to cultivate"super cotton",synergistically improving multiple traits.These strategies must rise to meet urgent demands for a sustainable cotton industry.

关键词： functional genomics genomic breeding germplasm resource Gossypium integrated breeding strategy major locus multi-omics

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Multiplex precision gene editing by a surrogate prime editor in rice

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Molecular Plant 2022年第7期15卷 1077-1080页

作者： Huiyuan Li Ziwei Zhu Shaoya Li Jingying Li Lei Yan Chen Zhang Youzhi Ma Lanqin Xia institute of Crop Sciences(ICS) Chinese Academy of Agricultural Sciences(CAAS)Be11ing 100081China Hainan Yazhou Bay Seed Laboratory/National Nanfan Research Institute(Sanya) Chinese Academy of Agricultural SciencesSanyaHainan Province 572024China

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.

关键词： editor editing template

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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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