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The RNA binding protein EHD6 recruits the m^(6)A reader YTH07 and sequesters OsCOL4 mRNA into phase-separated ribonucleoprotein condensates to promote rice flowering

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Molecular Plant 2024年第6期17卷 935-954页

作者： Song Cui Peizhe Song Chaolong Wang Saihua Chen Benyuan Hao Zhuang Xu Liang Cai Xu Chen Shanshan Zhu Xiangchao Gan Hui Dong Yuan Hu Liang Zhou Haigang Hou Yunlu Tian Xi Liu Liangming Chen Shijia Liu Ling Jiang Haiyang Wang Guifang Jia Shirong Zhou Jianmin Wan state key laboratory for crop genetics&germplasm enhancement and utilization Zhongshan Biological Breeding LaboratoryNational Observation and Research Station of Rice Germplasm ResourcesNanjing Agricultural UniversityNanjing 210095China state key laboratory for crop Gene Resources and Breeding Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijing 100081China Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular SciencesKey Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of EducationCollege of Chemistry and Molecular EngineeringPeking-Tsinghua Center for Life SciencesBeijing Advanced Center of RNA BiologyPeking UniversityBeijingChina Jiangsu key laboratory of crop Genomics and Molecular Breeding Agricultural College of Yangzhou UniversityYangzhou 225009China Max Planck Institute for Plant Breeding Research Carl-von-Linne´-Weg 1050829 KolnGermany

N6-Methyladenosine(m^(6)A)is one of the most abundant modifications of eukaryotic mRNA,but its comprehensive biological functionality remains further *** this study,we identified and characterized a new flowering-promoting gene,EARLY HEADING DATE6(EHD6),in ***6 encodes an RNA recognition motif(RRM)-containing RNA binding protein that is localized in the non-membranous cytoplasm ribonucleoprotein(RNP)granules and can bind both m^(6)A-modified RNA and unmodified RNA *** found that EHD6 can physically interact with YTH07,a YTH(YT521-B homology)domain-containing m^(6)A *** showed that their interaction enhances the binding of an m^(6)A-modified RNA and triggers relocation of a portion of YTH07 from the cytoplasm into RNP granules through phase-separated *** these condensates,the mRNA of a rice flowering repressor,CONSTANS-like 4(OsCOL4),becomes sequestered,leading to a reduction in its protein abundance and thus accelerated flowering through the Early heading date 1 *** together,these results not only shed new light on the molecular mechanism of efficient m^(6)A recognition by the collaboration between an RNA binding protein and YTH family m^(6)A reader,but also uncover the potential for m^(6)A-mediated translation regulation through phaseseparated ribonucleoprotein condensation in rice.

关键词： N6-methyladenosine m^(6)A EHD6 YTH domain-containing protein phase separation heading date

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Improved genome annotation of Brassica oleracea highlights the importance of alternative splicing

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Horticultural Plant Journal 2024年第4期10卷 961-970页

作者： Yinqing Yang Lei Zhang Qi Tang Lingkui Zhang Xing Li Shumin Chen Kang Zhang Ying Li Xilin Hou Feng Cheng state key laboratory of crop genetics and germplasm enhancement College of HorticultureNanjing Agricultural UniversityNanjing 210095China state key laboratory of Vegetable Biobreeding Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural AffairsSino-Dutch Joint Laboratory of Horticultural GenomicsBeijing 100081China

Brassica oleracea has been developed into many important crops,including cabbage,kale,cauliflower,broccoli and so *** genome and gene annotation of cabbage(cultivar JZS),a representative morphotype of ***,has been widely used as a common reference in biological *** its genome assembly has been updated twice,the current gene annotation still lacks information on untranslated regions(UTRs)and alternative splicing(AS).Here,we constructed a high-quality gene annotation(JZSv3)using a full-length transcriptome acquired by nanopore sequencing,yielding a total of 59452 genes and 75684 ***,we re-analyzed the previously reported transcriptome data related to the development of different tissues and cold response using JZSv3 as a reference,and found that 3843 out of 11908 differentially expressed genes(DEGs)underwent AS during the development of different tissues and 309 out of 903 cold-related genes underwent AS in response to cold ***,we also identified many AS genes,including BolLHCB5 and BolHSP70,that displayed distinct expression patterns within variant transcripts of the same gene,highlighting the importance of JZSv3 as a pivotal reference for AS ***,JZSv3 provides a valuable resource for exploring gene function,especially for obtaining a deeper understanding of AS regulation mechanisms.

关键词： Brassica oleracea Oxford nanopore technologies Gene annotation Alternative splicing

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Efficient genome editing in rice with miniature Cas12f variants

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aBIOTECH 2024年第2期5卷 184-188页

作者： Zhengyan Ye Yuanyan Zhang Shiqi He Shaokang Li Longjiong Luo Yanbiao Zhou Junjie Tan Jianmin Wan Sanya Institute of Nanjing Agricultural University State Key Laboratory of Crop Genetics&Germplasm Enhancement and UtilizationProvince and Ministry Co-sponsored Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjing 210095China Zhongshan Biological Breeding laboratory No.50 Zhongling StreetNanjing 210014China key laboratory of Southern Rice Innovation&Improvement Ministry of Agriculture and Rural Affairs/Hunan Engineering Laboratory of Disease and Pest Resistant Rice BreedingYuan Longping High-Tech Agriculture Co.LtdChangsha 410001China

Genome editing,particularly using the CRISPR/Cas system,has revolutionized biological research and crop *** the widespread use of CRISPR/Cas9,it faces limitations such as PAM sequence requirements and challenges in delivering its large protein into plant *** hypercompact Cas12f,derived from Acidibacillus sulfuroxidans(AsCas12f),stands out due to its small size of only 422 amino acids and its preference for a T-rich motif,presenting advantageous features over ***,its editing efficiency is extremely low in *** studies have generated two AsCas12f variants,AsCas12f-YHAM and AsCas12f-HKRA,demonstrating higher editing efficiencies in mammalian cells,yet their performance in plants remains *** this study,through a systematic investigation of genome cleavage activity in rice,we unveiled a substantial enhancement in editing efficiency for both AsCas12f variants,particularly for AsCas12f-HKRA,which achieved an editing efficiency of up to 53%.Furthermore,our analysis revealed that AsCas12f predominantly induces deletion in the target DNA,displaying a unique deletion pattern primarily concentrated at positions 12,13,23,and 24,resulting in deletion size mainly of 10 and 11 bp,suggesting significant potential for targeted DNA deletion using *** findings expand the toolbox for efficient genome editing in plants,offering promising prospects for precise genetic modifications in agriculture.

关键词： CRISPR/Cas Cas12 AsCas12f Rice Genome editing

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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

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Genome-wide association with transcriptomics reveals a shade-tolerance gene network in soybean

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The crop Journal 2024年第1期12卷 232-243页

作者： Yanzhu Su Xiaoshuai Hao Weiying Zeng Zhenguang Lai Yongpeng Pan Can Wang Pengfei Guo Zhipeng Zhang Jianbo He Guangnan Xing Wubin Wang Jiaoping Zhang Zudong Sun Junyi Gai Soybean Research Institute/MARA National Center for Soybean Improvement MARA key laboratory of Biology and Genetic Improvement of Soybean/state key laboratory for crop genetics and germplasm enhancement/state Innovation Platform for Integrated Production and Education in Soybean Bio-breeding/Jiangsu Collaborative Innovation Center for Modern crop Production Nanjing Agricultural UniversityNanjing 210095JiangsuChina Guangxi Academy of Agricultural Sciences Nanning 530007GuangxiChina

Shade tolerance is essential for soybeans in inter/relay cropping systems.A genome-wide association study(GWAS)integrated with transcriptome sequencing was performed to identify genes and construct a genetic network governing the trait in a set of recombinant inbred lines derived from two soybean parents with contrasting shade *** improved GWAS procedure,restricted two-stage multi-locus genome-wide association study based on gene/allele sequence markers(GASM-RTM-GWAS),identified 140 genes and their alleles associated with shade-tolerance index(STI),146 with relative pith cell length(RCL),and nine with *** of these genes by biological categories allowed the construction of a protein–protein interaction network by 187 genes,of which half were differentially expressed under shading and non-shading conditions as well as at different growth *** the identified genes,three ones jointly identified for both traits by both GWAS and transcriptome and two genes with maximum links were chosen as beginners for entrance into the ***,both STI and RCL gene systems worked for shade-tolerance with genes interacted each other,this confirmed that shadetolerance is regulated by more than single group of interacted genes,involving multiple biological functions as a gene network.

关键词： Soybean(Glycine max(L.)Merr.) Shade-tolerance Restricted two-stage multi-locus genomewide association study based on gene/allele sequence markers(GASM-RTM-GWAS) Shade-tolerance index(STI) Relative cell length(RCL) Transcriptome

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Recombination and repeat-induced point mutation landscapes reveal trade-offs between the sexual and asexual cycles of Magnaporthe oryzae

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Journal of genetics and Genomics 2024年第7期51卷 723-734页

作者： Xifang Zong Yaxin Lou Mengshuang Xia Kunyang Zhao Jingxuan Chen Ju Huang Sihai Yang Long Wang state key laboratory of Pharmaceutical Biotechnology School of Life SciencesNanjing UniversityNanjingJiangsu 210000China state key laboratory for crop genetics and germplasm enhancement Bioinformatics CenterAcademy for Advanced Interdisciplinary StudiesNanjing Agricultural UniversityNanjingJiangsu 210000China Co-Innovation Center for Sustainable Forestry in Southern China Nanjing Forestry UniversityNanjingJiangsu 210000China

The fungal disease caused by Magnaporthe oryzae is one of the most devastating diseases that endanger many crops *** shows that sexual reproduction can be advantageous for fungal diseases as hybridization facilitates ***,the pervasive clonal lineages of *** observed in natural fields contradict this expectation.A better understanding of the roles of recombination and the fungi-specific repeat-induced point mutation(RIP)in shaping its evolutionary trajectory is essential to bridge this knowledge *** we systematically investigate the RIP and recombination landscapes in *** using a whole genome sequencing data from 252 population samples and 92 cross *** data reveal that the RIP can robustly capture the population history of ***,and we provide accurate estimations of the recombination and RIP rates across different *** ***,our results highlight a parent-of-origin bias in both recombination and RIP rates,tightly associating with their sexual potential and variations of effector *** bias suggests a critical trade-off between generating novel allelic combinations in the sexual cycle to facilitate host-jumping and stimulating transposon-associated diversification of effectors in the asexual cycle to facilitate host *** findings provide unique insights into understanding the evolution of blast fungus.

关键词： Magnaporthe oryzae Crossover Repeat-induced point mutation(RiP) Effectors Sexual reproduction

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Temporal control of the Aux/IAA genes BnIAA32 and BnIAA34 mediates Brassica napus dual shade responses

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Journal of Integrative Plant Biology 2024年第5期66卷 928-942页

作者： Yafei Li Yiyi Guo Yue Cao Pengguo Xia Dongqing Xu Ning Sun Lixi Jiang Jie Dong Institute of crop Science College of Agriculture and BiotechnologyZhejiang UniversityHangzhou 310058China key laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province College of Life Sciences and MedicineZhejiang Sci-TechUniversityHangzhou310018China state key laboratory of crop genetics and germplasm enhancement College of AgricultureNanjing Agricultural UniversityNanjing 210095China key laboratory of Growth Regulation and Transformation Research of Zhejiang Province School of Life SciencesWestlake UniversityHangzhou 310024China

Precise responses to changes in light quality are crucial for plant growth and *** example,hypocotyls of shade-avoiding plants typically elongate under shade *** this typical shade-avoidance response(TSR)has been studied in Arabidopsis(Arabidopsis thaliana),the molecular mechanisms underlying shade tolerance are poorly *** we report that ***(Brassica napus)seedlings exhibit dual shade *** addition to the TSR,*** seedlings also display an atypical shade response(ASR),with shorter hypocotyls upon perception of early-shade ***-wide selective sweep analysis indicated that ASR is associated with light and auxin ***,genetic studies demonstrated that phytochrome A(BnphyA)promotes ASR,whereas BnphyB inhibits *** ASR,YUCCA8 expression is activated by early-shade cues,leading to increased auxin *** inhibits hypocotyl elongation,as young *** seedlings are highly sensitive to ***,two non-canonical AUXIN/INDOLE-3-ACETIC ACID(Aux/IAA)repressor genes,BnIAA32 and BnIAA34,are expressed during this early ***32 and BnIAA34 inhibit hypocotyl elongation under shade conditions,and mutations in BnIAA32 and BnIAA34 suppress ***,our study demonstrates that the temporal expression of BnIAA32 and BnIAA34 determines the behavior of *** seedlings following shade-induced auxin biosynthesis.

关键词： Brassica napus high-density planting IAA32/34 light signal transduction shade response temporal gene expression

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Comparative Transcriptomic Analysis of Two Tomato Cultivars with Different Shelf-Life Traits

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Phyton-International Journal of Experimental Botany 2024年第8期93卷 2075-2093页

作者： Abdul Karim Amin Yan He Xianglong Wang Pengwei Li Muhammad Ahmad Hassan Mohammad Yousof Soltani Yiling Zhang Mohammad Alem Amin Ahmad Shah Ahmadzai Yajing Liu Songhu Wang Anhui Province key laboratory of Horticultural crop Quality Biology School of HorticultureAnhui Agricultural UniversityHefei230036China Anhui Academy of Agricultural Sciences Hefei230001China Anhui Province key laboratory of Soybean Molecular Breeding and crop Quality Biology School of AgronomyAnhui Agricultural UniversityHefei230036China Department of Horticulture Ghazni UniversityGhazni2301Afghanistan state key laboratory of crop genetics and germplasm enhancement College of HorticultureNanjing Agricultural UniversityNanjing210095China

Tomato(Solanum lycopersicum)is a perishable fruit because of its fast water loss and susceptibility to pathogens in the post-harvest stage,which leads to huge economic losses every *** this study,firstly from 19 tomato cultivars,we screened out two cultivars,Riogrand and SalarF1,having long and short shelf-life spans,***,shelf-life analysis was carried out for both cultivars at room *** exhibited that Riogrand showed higher firmness and less weight loss than *** ethylene production was higher in SalarF1,compared with Riogrand during post-harvest *** performed transcriptomic analysis of both cultivars in different storage *** discovered 2913,2188,and 11,119 differentially expressed genes(DEGs)for three post-harvest stages(0,20,and 40 Days Post-Harvest(DPH)),*** genes are enriched in ethylene biosynthesis and response,as well as cell wall-related *** response factor(ERF)ERF2 and ERF4 were highly expressed in SalarF1 with a short shelf life in 40 DPH,and the ethylene biosynthetic genes ACO1,ACO4,ACS6,and ACS2 were significantly upregulated in *** cell wall loosening and cell wall-related genes XTH3,XTH7,XTH23,1,3;1,4-β-D-Gluc-like,pGlcT1,Cellulase,PGH1,PL5,PL-like 1,PL-like 2 exhibited the highest levels of significance,being notably upregulated in the last stage of *** quantitative real-time polymerase chain reaction(qRT-PCR)analysis validated these gene expressions,which is in line with the transcriptome *** findings suggested that the extension of tomato fruit shelf life is mostly dependent on ethylene biosynthesis,signaling pathway genes,cell wall loosening,and cell wall-associated genes.

关键词： Shelf life transcriptome analysis tomato differentially expressed genes(DEGs) ethylene

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D53 represses rice blast resistance by directly targeting phenylalanine ammonia lyases

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Journal of Integrative Plant Biology 2024年第9期66卷 1827-1830页

作者： Haitao Ye Qingqing Hou Haitao Lv Hui Shi Duo Wang Yujie Chen Tangshuai Xu Mei Wang Min He Junjie Yin Xiang Lu Yongyan Tang Xiaobo Zhu Lijuan Zou Xuewei Chen Jiayang Li Bing Wang Jing Wang state key laboratory of crop Gene Exploration and utilization in Southwest China Sichuan Agricultural UniversityChengdu 611130China key laboratory of Seed Innovation Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China Yazhouwan National laboratory Sanya 572024China

Phytohormones play important roles in orchestrating plantimmune responses to pathogen ***(SLs),a group of carotenoid-derived phytohormones,modulate diverse biological processes in plants,including shoot branching,plant height,root architecture,leaf senescence,seed germination of parasitic plants,and symbiosis of arbuscular mycorrhizal fungi(Burger and Chory,2020).Recently,increasing evidence has indicated potential roles for SLs in regulating responses against biotic stresses,including defense responses against certain pathogenic fungi and bacteria in roots and leaves(Yi et al.,2023).

关键词： ammonia resistance branching

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Construction of apricot variety search engine based on deep learning

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Horticultural Plant Journal 2024年第2期10卷 387-397页

作者： Chen Chen Lin Wang Huimin Liu Jing Liu Wanyu Xu Mengzhen Huang Ningning Gou Chu Wang Haikun Bai Gengjie Jia Tana Wuyun state key laboratory of Tree genetics and Breeding Research Institute of Non-timber ForestryChinese Academy of ForestryZhengzhouHenan 450003China Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdong 518120China Kernel-Apricot Engineering and Technology Research Center of state Forestry and Grassland Administration ZhengzhouHenan 450003China key laboratory of Non-timber Forest germplasm enhancement and utilization of National Forestry and Grassland Administration ZhengzhouHenan 450003China

Apricot has a long history of cultivation and has many varieties and types. The traditional variety identification methods are timeconsuming and labor-consuming, posing grand challenges to apricot resource management. Tool development in this regard will help researchers quickly identify variety information. This study photographed apricot fruits outdoors and indoors and constructed a dataset that can precisely classify the fruits using a U-net model (F-score:99%), which helps to obtain the fruit's size, shape, and color features. Meanwhile, a variety search engine was constructed, which can search and identify variety from the database according to the above features. Besides, a mobile and web application (ApricotView) was developed, and the construction mode can be also applied to other varieties of fruit ***, we have collected four difficult-to-identify seed datasets and used the VGG16 model for training, with an accuracy of 97%, which provided an important basis for ApricotView. To address the difficulties in data collection bottlenecking apricot phenomics research, we developed the first apricot database platform of its kind (ApricotDIAP, http://***/) to accumulate, manage, and publicize scientific data of apricot.

关键词： Apricot Variety Convolutional neural network Deep learning Database platform Mobile application Image retrieval

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