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园艺学报（英文版）
园艺学报（英文版）
园艺学报（英文版）/CSTPCDSCI
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    Turnip mosaic virus pathogenesis and host resistance mechanisms in Brassica

    Guanwei WuXinxin FangTianqi YuJianping Chen...
    947-960页
    查看更多>>摘要：Turnip mosaic virus(TuMV)is a devastating potyvirus pathogen that infects a wide variety of both cultivated and wild Brassicaceae plants.We urgently need more information and understanding of TuMV pathogenesis and the host responses involved in disease development in cruciferous crops.TuMV displays great versatility in viral pathogenesis,especially in its replication and intercellular movement.Moreover,in the coevolutionary arms races between TuMV and its hosts,the virus has evolved to co-opt host factors to facilitate its infection and counter host defense responses.This review mainly focuses on recent advances in understanding the viral factors that contribute to the TuMV infection cycle and the host resistance mechanism in Brassica.Finally,we propose some future research directions on TuMV pathogenesis and control strategies to design durable TuMV-resistant Brassica crops.
      原文链接:
    • NETL
    • NSTL
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    Improved genome annotation of Brassica oleracea highlights the importance of alternative splicing

    Yinqing YangLei ZhangQi TangLingkui Zhang...
    961-970页
    查看更多>>摘要：Brassica oleracea has been developed into many important crops,including cabbage,kale,cauliflower,broccoli and so on.The genome and gene annotation of cabbage(cultivar JZS),a representative morphotype of B.oleracea,has been widely used as a common reference in biological research.Although 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 59 452 genes and 75 684 transcripts.Additionally,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 11 908 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 stress.Meanwhile,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 analysis.Overall,JZSv3 provides a valuable resource for exploring gene function,especially for obtaining a deeper understanding of AS regulation mechanisms.
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    Gene expression,transcription factor binding and histone modification predict leaf adaxial-abaxial polarity related genes

    Wei SunZhicheng ZhangGuusje BonnemaXiaowu Wang...
    971-982页
    查看更多>>摘要：Leaf adaxial-abaxial(ad-abaxial)polarity is crucial for leaf morphology and function,but the genetic machinery governing this process re-mains unclear.To uncover critical genes involved in leaf ad-abaxial patterning,we applied a combination of in silico prediction using machine learning(ML)and experimental analysis.A Random Forest model was trained using genes known to influence ad-abaxial polarity as ground truth.Gene expression data from various tissues and conditions as well as promoter regulation data derived from transcription factor chromatin immunoprecipitation sequencing(ChIP-seq)was used as input,enabling the prediction of novel ad-abaxial polarity-related genes and additional transcription factors.Parallel to this,available and newly-obtained transcriptome data enabled us to identify genes differentially expressed across leaf ad-abaxial sides.Based on these analyses,we obtained a set of 111 novel genes which are involved in leaf ad-abaxial specialization.To explore implications for vegetable crop breeding,we examined the conservation of expression patterns between Arabidopsis and Brassica rapa using single-cell transcriptomics.The results demonstrated the utility of our computational approach for predicting candidate genes in crop species.Our findings expand the understanding of the genetic networks governing leaf ad-abaxial differentiation in agriculturally important vegetables,enhancing comprehension of natural variation impacting leaf morphology and development,with demonstrable breeding applications.
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    An efficient and universal protoplast-based transient gene expression system for genome editing in Brassica crops

    Xiaoxiao YuJintai YuYin LuWenjing Li...
    983-994页
    查看更多>>摘要：Protoplast-based transient gene expression system has been widely used in plant genome editing because of its simple operation and less time-consuming.In order to establish a universal protoplast-based transient transfection system for verifying activities of genome editing vectors containing targets in Brassica,we systematically optimized factors affecting protoplast isolation and transient gene expression.We established an efficient protoplast-based transient gene expression system(PTGE)in Chinese cabbage,achieving high protoplast yield of 4.9 × 105·g-1FW,viability over 95％,and transfection efficiency of 76％.We showed for the first time that pretreatment of protoplasts with a hypotonic MMG could significantly enhance the transfection efficiency.Furthermore,protoplasts incubated at 37 ℃ for 6 min improved the transfection efficiency to 86％.We also demonstrated that PTGE worked well(more than 50％transfection efficiency)in multiple Brassica species including cabbage,Pak Choi,Chinese kale,and turnip.Finally,PTGE was used for validating the activities of CRISPR/Cas9 vectors containing targets in Chinese cabbage,cabbage,and pak choi,demonstrating the broad applicability of the established PTGE for genome editing in Brassica crops.
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    UV-B irradiation enhances the accumulation of beneficial glucosinolates induced by melatonin in Chinese kale sprout

    Mengyu WangJiansheng WangYuhe YangZhiqing Li...
    995-1006页
    查看更多>>摘要：Cruciferous sprout is a new form of vegetable product rich in bioactive compounds,especially glucosinolates.Previous studies have focused on increasing the accumulation of glucosinolates in cruciferous sprouts by applying different chemical regulators,with a particular focus on their contribution to nutritional quality and health benefits.Nevertheless,the effects of melatonin and UV-B irradiation on glucosinolate biosynthesis remain unclear.In this study,it was found that changes in melatonin concentrations significantly affected the contents of in-dividual as well as total aliphatic and indolic glucosinolates.The 5 μmol·L-1 melatonin was decided as the optimum concentration that could increase the content of beneficial glucosinolates including glucoraphanin and 4-methoxy glucobrassicin in Chinese kale sprouts.Notably,the enhancement of glucosinolate accumulation by melatonin treatment could be further amplified by UV-B irradiation.Furthermore,our results showed that R2R3-MYB transcription factor BoaMYB28 and BoaMYB51,which are central regulators of aliphatic and indolic glucosinolate biosynthesis respectively,were both involved in the regulation of glucosinolate biosynthesis by melatonin and UV-B irradiation.Additionally,the expression of glucosinolate biosynthetic genes,including BoaCYP79F1,BoaCYP83A1,BoaSUR1,BoaUGT74B1,BoaCYP79B2,BoaCYP79B3,and BoaCYP83B1 participated in the formation of core structures and BoaFMOGS-OX5,BoaAOP2,BoaCYP81F2,and BoaIGMT1 involved in the side-chain modification of aliphatic and indolic glucosinolate,was regulated by melatonin or UV-B irradiation.Taken together,these findings provide a potential strategy for improving the nutritional quality and resistance of Chinese kale sprouts.
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    Expression changes of miRNA-regulated genes associated with the formation of the leafy head in cabbage

    Jorge Alemán-BáezJose Fernando Acevedo-ZamoraJohan BucherChengcheng Cai...
    1007-1019页
    查看更多>>摘要：The vegetative development of cabbage(Brassica oleracea var.capitata)passes through seedling,rosette,folding and heading stages.Leaves that form the rosette are large and mostly flat.In the following developmental stages,the plants produce leaves that curve inward to produce the leafy head.Many microRNAs and their target genes have been described participating in leaf development and leaf curvature.The aim of this study is to investigate the role of miRNA-regulated genes in the transition from the rosette to the heading stage.We compared the miRNA and gene abundances between emerging rosette and heading leaves.To remove transcripts(miRNAs and genes)whose regulation was most likely asso-ciated with plant age rather than the change from rosette to heading stage,we utilized a non-heading collard green(B.oleracea var.acephala)morphotype as control.This resulted in 33 DEMs and 1 998 DEGs with likely roles in the transition from rosette to heading stage in cabbage.Among these 1 998 DEGs,we found enriched GO terms related to DNA-binding transcription factor activity,transcription regulator activity,iron ion binding,and photosynthesis.We predicted the target genes of these 33 DEMs and focused on the subset that was differentially expressed(1 998 DEGs)between rosette and heading stage leaves to construct miRNA-target gene interaction networks.Our main finding is a role for miR396b-5p targeting two Arabidopsis thaliana orthologues of GROWTH REGULATING FACTORS 3(GRF3)and 4(GRF4)in pointed cabbage head formation.
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    Editing of eIF(iso)4E.c confers resistance against Turnip mosaic virus in Brassica rapa

    Yujia LiuXiaoyun XinPeirong LiWeihong Wang...
    1020-1034页
    查看更多>>摘要：Turnip mosaic virus(TuMV)constitutes one of the primary diseases affecting Brassica rapa,severely impacting its production and resulting in crop failures in various regions worldwide.Recent research has demonstrated the significance of plant translation initiation factors,specifically the eIF4E and eIF4G family genes,as essential recessive disease resistance genes.In our study,we conducted evolutionary and gene expression studies,leading us to identify eIF(iso)4E.c as a potential TuMV-resistant gene.Leveraging CRISPR/Cas9 technology,we obtained mutant B.rapa plants with edited eIF(iso)4E.c gene.We confirmed eIF(iso)4E.c confers resistance against TuMV through phenotypic observations and virus content evaluations.Furthermore,we employed ribosome profiling assays on eif(iso)4e.c mutant seedlings to unravel the translation landscape in response to TuMV.Interestingly,we observed a moderate correlation between the fold changes in gene expression at the transcriptional and translational levels(R2=0.729).Comparative analysis of ribosome profiling and RNA-seq data revealed that plant-pathogen interaction,and MAPK signaling pathway-plant pathways were involved in eIF(iso)4E.c-mediated TuMV resistance.Further analysis revealed that sequence features,coding sequence length,and normalized minimal free energy,influenced the translation efficiency of genes.Our study highlights that the loss of eIF(iso)4E.c can result in a highly intricate translation mechanism,acting synergistically with transcription to confer resistance against TuMV.
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    Studies on the temporal,structural,and interacting features of the clubroot resistance gene Rcr1 using CRISPR/Cas9-based systems

    Hao HuFengqun Yu
    1035-1048页
    查看更多>>摘要：Clubroot disease is a severe threat to Brassica crops globally,particularly in western Canada.Genetic resistance,achieved through pyr-amiding clubroot resistance(CR)genes with different modes of action,is the most important strategy for managing the disease.However,studies on the CR gene functions are quite limited.In this study,we have conducted investigations into the temporal,structural,and inter-acting features of a newly cloned CR gene,Rcr1,using CRISPR/Cas9 technology.For temporal functionality,we developed a novel CRISPR/Cas9-based binary vector,pHHIGR-Hsp18.2,to deliver Rcr1 into a susceptible canola line(DH12075)and observed that early expression of Rcr1 is critical for conferring resistance.For structural functionality,several independent mutations in specific domains of Rcr1 resulted in loss-of-function,highlighting their importance for CR phenotype.In the study of the interacting features of Rcr1,a cysteine protease gene and its homologous allele in canola were successfully disrupted via CRISPR/Cas9 as an interacting component with Rcr1 protein,resulting in the conversion from clubroot resistant to susceptible in plants carrying intact Rcr1.These results indicated an indispensable role of these two cysteine proteases in Rcr1-mediated resistance response.This study,the first of its kind,provides valuable insights into the functionality of Rcr1.Further,the new vector pHHIGR-Hsp18.2 demonstrated an inducible feature on the removal of add-on traits,which should be useful for functional genomics and other similar research in brassica crops.
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    Development of a rapid and efficient system for CR genes identification based on hairy root transformation in Brassicaceae

    Wenlin YuLu YangYuanyuan XiangRongde Li...
    1049-1060页
    查看更多>>摘要：Many economically important crops and vegetables belonging to the cruciferous family are heavily endangered by clubroot disease caused by Plasmodiophora brassicae infection.Breeding of clubroot resistant cultivars based on mapping and cloning of resistant genes is commonly regarded as the most cost-effective and efficient way to fight against this disease.The traditional way of R gene functional validation requires stable transformation that is both time-and labor-consuming.In this study,a rapid and efficient hairy-root transgenic protocol mediated by Agrobacterium rhizogenes was developed.The transformation positive rate was over 80％in Brassica napus showed by GUS reporter gene and this transformation only took 1/6 of the time compared with stable transformation.The system was applicable to different B.napus varieties and other cruciferous crops including Brassica rapa and Brassica oleracea.In particular,two known CR genes,CRA3.7.1 and CRA8.2.4 were used respectively,as example to show that the system works well for CR gene study combined with subsequent P.brassicae infection in B.napus.Most importantly,it works both in over-expression that led to disease resistance,as well as in RNAi which led to disease susceptible phenotype.Therefore,this system can be used in batch-wise identification of CR genes,and also offered the possibility of manipulating key genes within the P.brassicae genome that could improve our knowledge on host-pathogen interaction.
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