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Journal of Integrative plant Biology 2024年第1期66卷 86-102页

作者： Yufei Zhang Lingyan Wang Yuexin Wu Donghui Wang Xin‐Qiang He state key laboratory of protein and plant gene research School of Life SciencesPeking UniversityBeijing 100871China

Secondary vascular tissue(SVT)development and regeneration are regulated by *** this study,we used an in vitro SVT regeneration system to demonstrate that gibberellin(GA)treatment significantly promotes auxin-induced cambium *** GA content by overexpressing or knocking down ent-kaurene synthase(KS)affected secondary growth and SVT regeneration in *** poplar DELLA gene GIBBERELLIC ACID INSENSITIVE(PtoGAI)is expressed in a specific pattern during secondary growth and cambium regeneration after *** of PtoGAI disrupted poplar growth and inhibited cambium regeneration,and the inhibition of cambium regeneration could be partially restored by GA *** analysis of the PtaDR5:GUS transgenic plants,the localization of PIN-FORMED 1(PIN1)and the expression of auxin-related genes found that an additional GA treatment could enhance the auxin response as well as the expression of PIN1,which mediates auxin transport during SVT *** together,these findings suggest that GA promotes cambium regeneration by stimulating auxin signal transduction.

关键词： auxin cambium gibberellin Populus secondary vascular tissue regeneration

Molecular Evolution of protein Sequences and Codon Usage in Monkeypox Viruses

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Genomics, Proteomics & Bioinformatics 2024年第1期22卷 89-97页

作者： Ke-Jia Shan Changcheng Wu Xiaolu Tang Roujian Lu Yaling Hu Wenjie Tan Jian Lu state key laboratory of protein and plant gene research Center for BioinformaticsSchool of Life SciencesPeking UniversityBeijing 100871China Sinovac Biotech Ltd. Beijing 100085China NHC key laboratory of Biosafety National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing 100052China

The monkeypox virus(mpox virus,MPXV)epidemic in 2022 has posed a significant public health ***,the evolutionary principles of MPXV remain largely ***,we examined the evolutionary patterns of protein sequences and codon usage in *** first demonstrated the signal of positive selection in OPG027,specifically in the CladeⅠlineage of ***,we discovered accelerated protein sequence evolution over time in the variants responsible for the 2022 ***,we showed strong epistasis between amino acid substitutions located in different *** codon adaptation index(CAI)analysis revealed that MPXV genes tended to use more non-preferred codons compared to human genes,and the CAI decreased over time and diverged between clades,with CladeⅠ>Ⅱa andⅡb-A>Ⅱ*** the decrease in fatality rate among the three groups aligned with the CAI pattern,it remains unclear whether this correlation was coincidental or if the deoptimization of codon usage in MPXV led to a reduction in fatality *** study sheds new light on the mechanisms that govern the evolution of MPXV in human populations.

关键词： Mpox virus Positive selection OPG027 Accelerated evolution Codon usage bias

Microbe-induced gene silencing explores interspecies RNAi and opens up possibilities of crop protection

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Science China(Life Sciences) 2024年第3期67卷 626-628页

作者： Rongxiang Fang state key laboratory of plant Genomics Institute of MicrobiologyChinese Academy of Sciencesand National Plant Gene Research CenterBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

In most eukaryotes, small RNA(sRNA)-mediated RNA silencing(or RNA interference, RNAi) is an evolutionarily conserved mechanism that regulates gene expression in a sequence-specific ***, s RNAs are produced by the RNase III enzymes Dicers and then incorporated into Argonaute(AGO) proteins to regulate gene expression by mRNA degradation.

关键词： protection conserved manner

plant virology in the 21st century in China:Recent advances and future directions

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Journal of Integrative plant Biology 2024年第3期66卷 579-622页

作者： Jianguo Wu Yongliang Zhang Fangfang Li Xiaoming Zhang Jian Ye Taiyun Wei Zhenghe Li Xiaorong Tao Feng Cui Xianbing Wang Lili Zhang Fei Yan Shifang Li Yule Liu Dawei Li Xueping Zhou Yi Li state key laboratory for Ecological Pest Control of Fujian and Taiwan Crops Vector-borne Virus Research CenterCollege of Plant ProtectionFujian Agriculture and Forestry UniversityFuzhou 350002China state key laboratory of plant Environmental Resilience and Ministry of Agriculture key laboratory of Soil Microbiology College of Biological SciencesChina Agricultural UniversityBeijing 100193China state key laboratory for Biology of plant Diseases and Insect Pests Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing 100193China state key laboratory of Integrated Management of Pest Insects and Rodents Institute of ZoologyChinese Academy of SciencesBeijing 100101China CAS Center for Excellence in Biotic Interactions University of Chinese Academy of SciencesBeijing 100049China state key laboratory of plant Genomics Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China state key laboratory of Rice Biology Institute of BiotechnologyZhejiang UniversityHangzhou 310058China Department of plant Pathology The Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjing 210095China state key laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products Institute of Plant VirologyNingbo UniversityNingbo 315211China MOE key laboratory of Bioinformatics Center for Plant BiologySchool of Life SciencesTsinghua UniversityBeijing 100084China state key laboratory of protein and plant gene research School of Life SciencesPeking UniversityBeijing 100871China

plant viruses are a group of intracellular pathogens that persistently threaten global food *** advances in plant virology have been achieved by Chinese scientists over the last 20 years,including basic research and technologies for preventing and controlling plant viral ***,we review these milestones and advances,including the identification of new crop-infecting viruses,dissection of pathogenic mechanisms of multiple viruses,examination of multilayered interactions among viruses,their host plants,and virus-transmitting arthropod vectors,and in-depth interrogation of plantencoded resistance and susceptibility ***,various plant virus-based vectors have also been successfully developed for gene function studies and target gene expression in *** also recommend future plant virology studies in China.

关键词： China emerging plant viruses plant virology plant resistance/susceptibility to viral infection plant-virus transmission vector interactions plant virus-based vectors viral pathogenesis

The genetic basis and process of inbreeding depression in an elite hybrid rice

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Science China(Life Sciences) 2024年第8期67卷 1727-1738页

作者： Xiaodong Xu Yawen Xu Jian Che Xu Han Zhengji Wang Xianmeng Wang Qinghua Zhang Xu Li Qinglu Zhang Jinghua Xiao Xianghua Li Qifa Zhang Yidan Ouyang National key laboratory of Crop genetic Improvement and National Centre of plant gene research(Wuhan) Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China

Inbreeding depression refers to the reduced performance arising from increased homozygosity,a phenomenon that is the reverse of heterosis and exists among plants and *** a natural self-pollinated crop with strong heterosis,the mechanism of inbreeding depression in rice is largely *** understand the genetic basis of inbreeding depression,we constructed a successive inbreeding population from the F_(2)to F_(4)generation and observed inbreeding depression of all heterotic traits in the progeny along with the decay of heterozygosity in each *** expected depression effect was largely explained by 13 QTLs showing dominant effects for spikelets per panicle,11 for primary branches,and 12 for secondary branches,and these loci constitute the main correlation between heterosis and inbreeding ***,the genetic basis of inbreeding depression is also distinct from that of heterosis,such that a biased transmission ratio of alleles for QTLs with either dominant or additive effects in four segregation distortion regions would result in minor effects in expected ***,two-locus interactions may change the extent and direction of the depression effects of the target loci,and overall interactions would promote inbreeding depression among *** an F_(2:3)variation population,the actual performance of the loci showing expected depression was evaluated considering the heterozygosity decay in the background after *** found inconsistent or various degrees of background depression from the F_(2)to F_(3)generation assuming different genotypes of the target locus,which may affect the actual depression effect of the locus due to *** results suggest that the genetic architecture of inbreeding depression and heterosis is closely linked but also differs in their intrinsic mechanisms,which expand our understanding of the whole-genome architecture of inbreeding depression.

关键词： rice inbreeding depression spikelet development dominance segregation distortion epistasis

Increased long-distance and homo-trans interactions related to H3K27me3 in Arabidopsis hybrids

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Journal of Integrative plant Biology 2024年第2期66卷 208-227页

作者： Zhaoxu Gao Yanning Su Le Chang Guanzhong Jiao Yang Ou Mei Yang Chao Xu Pengtao Liu Zejia Wang Zewen Qi Wenwen Liu Linhua Sun Guangming He Xing Wang Deng Hang He School of Advanced Agriculture Sciences and School of Life Sciences State Key Laboratory of Protein and Plant Gene ResearchPeking UniversityBeijing 100871China College of Grassland Science Beijing Forestry UniversityBeijing 100083China Peking University Institute of Advanced Agricultural Sciences Shandong Laboratory of Advanced Agricultural Sciences in WeifangWeifang 261325China

In plants,the genome structure of hybrids changes compared with their parents,but the effects of these changes in hybrids remain *** reciprocal crosses between Col×C24 and C24×Col in Arabidopsis using high-throughput chromosome conformation capture assay(Hi-C)analysis,we found that hybrid three-dimensional(3D)chromatin organization had more long-distance interactions relative to parents,and this was mainly located in promoter regions and enriched in genes with heterosis-related *** interactions between euchromatin and heterochromatin were increased,and the compartment strength decreased in *** compartment domain(CD)boundaries,the distal interactions were more in hybrids than their *** the hybrids of CURLY LEAF(clf)mutants clfCol×clfC24and clfC24×clfCol,the heterosis phenotype was damaged,and the long-distance interactions in hybrids were fewer than in their parents with lower ***-seq data revealed higher levels of H3K27me3 in the region adjacent to the CD boundary and the same interactional homo-trans sites in the wild-type(WT)hybrids,which may have led to more long-distance *** addition,the differentially expressed genes(DEGs)located in the boundaries of CDs and loop regions changed obviously in WT,and the functional enrichment for DEGs was different between WT and clf in the longdistance interactions and loop *** findings may therefore propose a new epigenetic explanation of heterosis in the Arabidopsis hybrids and provide new insights into crop breeding and yield increase.

关键词： 3D chromatin organization H3K27me3 homo-trans hybrids long-distanceinteractions

Upgraded durian genome reveals the role of chromosome reshuffling during ancestral karyotype evolution,lignin biosynthesis regulation,and stress tolerance

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Science China(Life Sciences) 2024年第6期67卷 1266-1279页

作者： Wanwan Li Xin Chen Jianing Yu Yuxian Zhu College of Life Sciences Shaanxi Normal UniversityXi’an 710119China The state key laboratory of protein and gene research College of Life SciencesPeking UniversityBeijing 100871China The Institute for Advanced Studies Wuhan UniversityWuhan 430072China

Durian(Durio zibethinus)is a tropical fruit that has a unique flavor and *** occupies a significant phylogenetic position within the Malvaceae *** core-eudicot plants are reported to share seven ancestral karyotypes that have undergone reshuffling,resulting in an abundant genomic ***,the ancestral karyotypes of the Malvaceae family,as well as the evolution trajectory leading to the28 chromosomes in durian,remain poorly ***,we report the high-quality assembly of the durian genome with comprehensive comparative genomic *** analyzing the collinear blocks between cacao and durian,we inferred 11 Malvaceae ancestral *** blocks were present in a single-copy form in cacao and mainly in triplicates in durian,possibly resulting from a recent whole genome triplication(WGT)event that led to hexaploidization of the durian genome around 20(17–24)million years ago.A large proportion of the duplicated genes in durian,such as those involved in the lignin biosynthesis module for phenylpropane biosynthesis,are derived directly from whole genome duplication,which makes it an important force in reshaping its genomic *** studies have revealed that genes involved in feruloyl-Co A formations were highly preferentially expressed in fruit peels,indicating that the thorns produced on durian fruit may comprise guaiacyl and syringyl *** all the analyzed transcription factors(TFs),members of the heat shock factor family(HSF)were the most significantly upregulated under heat *** subfamilies of genes encoding heat shock proteins(HSPs)in the durian genome appear to have undergone *** potential interactions between HSF Dzi05.397 and HSPs were examined and experimentally *** study provides a high-quality durian genome and reveals the reshuffling mechanism of ancestral Malvaceae chromosomes to produce the durian *** also provide insights into the mechanism underlying lignin bi

关键词： Durio zibethinus whole genome duplication whole genome triplication Malvaceae ancestral karyotypes chromosome reshuffling lignin biosynthesis heat stress

Engineering disease-resistant plants with alternative translation efficiency by switching uORF types through CRISPR

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Science China(Life Sciences) 2024年第8期67卷 1715-1726页

作者： Jingjing Tian Zhijuan Tang Ruixia Niu Yulu Zhou Dan Yang Dan Chen Ming Luo Rui Mou Meng Yuan Guoyong Xu National key laboratory of Crop genetic Improvement National Centre of Plant Gene Research(Wuhan)Huazhong Agricultural UniversityWuhan 430070China state key laboratory of Hybrid Rice Institute for Advanced Studies(IAS)Wuhan UniversityWuhan 430072China Hubei Hongshan laboratory Wuhan 430070China

Engineering disease-resistant plants can be a powerful solution to the issue of food ***,it requires addressing two fundamental questions:what genes to express and how to control their *** find a solution,we screen CRISPR-edited upstream open reading frame(uORF)variants in rice,aiming to optimize translational control of disease-related *** switching uORF types of the 5′-leader from Arabidopsis TBF1,we modulate the ribosome accessibility to the downstream firefly *** assume that by switching uORF types using CRISPR,we could generate uORF variants with alternative translation efficiency(CRISPR-aTrE-uORF).These variants,capable of boosting translation for resistance-associated genes and dampening it for susceptible ones,can help pinpoint previously unidentified genes with optimal expression *** test the assumption,we screened edited uORF variants and found that enhanced translational suppression of the plastic glutamine synthetase 2 can provide broad-spectrum disease resistance in rice with minimal fitness *** strategy,which involves modifying uORFs from none to some,or from some to none or different ones,demonstrates how translational agriculture can speed up the development of disease-resistant *** is vital for tackling the food security challenges we face due to growing populations and changing climates.

关键词： disease-resistant plants broad-spectrum disease resistance uORF uORF types uORF variants CRISPR

genetic analysis and fine mapping of a grain size QTL in the smallgrain sterile rice line Zhuo201S

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Journal of Integrative Agriculture 2024年第7期23卷 2155-2163页

作者： Bin Lei Jiale Shao Feng Zhang Jian Wang Yunhua Xiao Zhijun Cheng Wenbang Tang Jianmin Wan College of Agronomy Hunan Agricultural UniversityChangsha 410128China National key Facility for Crop gene Resources and genetic Improvement/Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081China state key laboratory for Crop genetics and Germplasm Enhancement/Jiangsu plant gene Engineering research Center Nanjing Agricultural UniversityNanjing 210095China state key laboratory of Hybrid Rice Hunan Hybrid Rice Research CenterChangsha 410125China

The development and application of the small-grain rice sterile line Zhuo201S(Z201S)has demonstrated its potential for mechanized hybrid rice seed production,leading to significant cost ***,the molecular mechanism responsible for the small-grain size characteristic of Z201S remains *** this study,we conducted a genetic analysis using near-isogenic lines constructed from Z210S,a small-grain rice sterile line,and R2115,a normal-grain *** results revealed that the small-grain trait in Z201S is governed by a single partially dominant gene which also enhances grain *** mapping,we localized the causal gene to the short arm of chromosome 2,within a 113 kb physical region delimited by the molecular markers S2-4-1 and *** analysis and gene expression assays indicated LOC_Os02g14760 as the most likely candidate gene,suggesting that the small-grain size trait of Z201S is controlled by a novel locus that has not been previously identified.

关键词： rice grain size map-based cloning

Molecular Mechanism of Rice Necrotic Lesion for Optimized Yield and Disease Resistance

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Rice science 2024年第3期31卷 285-299页

作者： HOU Xinyue WANG Yuping QIAN Qian REN Deyong state key laboratory of Rice Biology and Breeding China National Rice Research InstituteHangzhou 310006China state key laboratory of Crop gene Exploration and Utilization in Southwest China Rice Research InstituteSichuan Agricultural UniversityChengdu 611130China

How to balance rice resistance and yield is an important issue in rice *** with mutated necrotic lesion genes often have persistent broad-spectrum resistance,but this broad-spectrum resistance usually comes at the expense of ***,many necrotic lesion mutants in rice have been identified,and these genes are involved in disease resistance *** review provides a detailed introduction to the characteristics,classification,and molecular mechanisms of necrotic lesion ***,we review the molecular regulatory pathways of genes involved in rice disease ***,we summarize the relationship between resistance and yield in rice using newly developed gene editing *** discuss a rational and precise breeding strategy to better utilize molecular design technology for breeding disease-resistant and high-yield rice varieties.

关键词： rice necrotic lesion regulation mechanism high yield high resistance