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Carbon Catabolite Repressor UvCreA is Required for Development and Pathogenicity in Ustilaginoidea virens

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rice science 2024年第2期31卷 203-214,I0029-I0031页

作者： XIE Shuwei SHI Huanbin WEN Hui LIU Zhiquan QIU Jiehua JIANG Nan KOU Yanjun state key laboratory of rice biology and breeding China National Rice Research InstituteHangzhou 311400China

The rice false smut disease, caused by Ustilaginoidea virens, has emerged as a significantglobal threat to rice production. The mechanism of carbon catabolite repression plays a crucial role in theefficient utilization of carbon nutrients and enzyme regulation in the presence of complex nutritionalconditions. Although significant progress has been made in understanding carbon catabolite repression infungi such as Aspergillus nidulans and Magnaporthe oryzae, its role in U. virens remains unclear. Toaddress this knowledge gap, we identified UvCreA, a pivotal component of carbon catabolite repression,in U. virens. Our investigation revealed that UvCreA localized to the nucleus. Deletion of UvCreA resultedin decreased growth and pathogenicity in U. virens. Through RNA-seq analysis, it was found that theknockout of UvCreA led to the up-regulation of 514 genes and down-regulation of 640 genes. Moreover,UvCreA was found to be involved in the transcriptional regulation of pathogenic genes and genesassociated with carbon metabolism in U. virens. In summary, our findings indicated that UvCreA isimportant in fungal development, virulence, and the utilization of carbon sources through transcriptionalregulation, thus making it a critical element of carbon catabolite repression.

关键词： Ustilaginoidea virens virulence carbon catabolite repression Oryza sativa rice false smut

Gapless Genome Assembly of ZH8015 and Preliminary Multi-Omics Analysis to Investigate ZH8015's Responses Against Brown Planthopper Infestation

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rice science 2024年第3期31卷 317-327,I0042-I0045页

作者： LI Dian DUAN Wenjing LIU Qun’en WU Weixun ZHAN Xiaodeng SUN Lianping ZHANG Yingxin CHENG Shihua state key laboratory of rice biology and breeding China National Rice Research InstituteHangzhou 310006China

Accurate genomic information is essential for advancing genetic breeding research in specific rice varieties.This study presented a gapless genome assembly of the indica rice cultivar Zhonghui 8015(ZH8015)using Pac Bio HiFi,Hi-C,and ONT(Oxford Nanopore Technologies)ultra-long sequencing technologies,annotating 43037 gene structures.Subsequently,utilizing this genome along with transcriptomic and metabolomic techniques,we explored ZH8015's response to brown planthopper(BPH)infestation.Continuous transcriptomic sampling indicated significant changes in gene expression levels around 48 h after BPH feeding.Enrichment analysis revealed particularly significant alterations in genes related to reactive oxygen species scavenging and cell wall formation.Metabolomic results demonstrated marked increases in levels of several monosaccharides,which are components of the cell wall and dramatic changes in flavonoid contents.Omics association analysis identified differentially expressed genes associated with key metabolites,shedding light on ZH8015's response to BPH infestation.In summary,this study constructed a reliable genome sequence resource for ZH8015,and the preliminary multi-omics results will guide future insect-resistant breeding research.

关键词： brown planthopper gapless genome genome assembly multi-omics Nilaparvata lugens rice

Two H3K36 methyltransferases differentially associate with transcriptional activity and enrichment of facultative heterochromatin in rice blast fungus

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aBIOTECH 2024年第1期5卷 1-16页

作者： Mengting Xu Ziyue Sun Huanbin Shi Jiangnan Yue Xiaohui Xiong Zhongling Wu Yanjun Kou Zeng Tao Ministry of Agriculture key laboratory of Molecular biology of Crop Pathogens and Insects Institute of BiotechnologyZhejiang UniversityHangzhou 310058China state key Lab of rice biology and breeding China National Rice Research InstituteHangzhou 310021China

Di-and tri-methylation of lysine 36 on histone H3(H3K36me2/3)is catalysed by histone methyltransferase Set2,which plays an essential role in transcriptional regulation.Although there is a single H3K36 methyltransferase in yeast and higher eukaryotes,two H3K36 methyltransferases,Ash1 and Set2,were present in many filamentous fungi.However,their roles in H3K36 methylation and transcriptional regulation remained unclear.Combined with methods of RNA-seq and ChIP-seq,we revealed that both Ash1 and Set2 are redundantly required for the full H3K36me2/3 activity in Magnaporthe oryzae,which causes the devastating worldwide rice blast disease.Ash1 and Set2 distinguish genomic H3K36me2/3-marked regions and are differentially associated with repressed and activated transcription,respectively.Furthermore,Ash1-catalysed H3K36me2 was co-localized with H3K27me3 at the chromatin,and Ash1 was required for the enrichment and transcriptional silencing of H3K27me3-occupied genes.With the different roles of Ash1 and Set2,in H3K36me2/3 enrichment and transcriptional regulation on the stress-responsive genes,they differentially respond to various stresses in M.oryzae.Overall,we reveal a novel mechanism by which two H3K36 methyltransferases catalyze H3K36me2/3 that differentially associate with transcriptional activities and contribute to enrichment of facultative heterochromatin in eukaryotes.

关键词： Ash1 Facultative heterochromatin H3K36me2/3 Magnaporthe oryzae Set2 Transcriptional regulation

Hi-TOM 2.0:an improved platform for high-throughput mutation detection

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Science China(Life Sciences) 2024年第7期67卷 1532-1534页

作者： Tingting Sun Qing Liu Xi Chen Fengyue Hu Kejian Wang state key laboratory of rice biology and breeding China National Rice Research InstituteChinese Academy of Agricultural SciencesHangzhou 310006China Hainan Seed Industry laboratory Sanya 572025China

Dear Editor,CRISPR/Cas systems,which can create novel mutations by manipulating the genome or transcriptome,have been developed as a powerful molecular tool for gene editing in various organisms(Cheng et al.,2022;Gao,2021).However,identifying mutations in large samples and decoding chimeric mutations are time-consuming,labor-intensive.

关键词： CRISPR/Cas consuming mutation

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 breeding.Plants with mutated necrotic lesion genes often have persistent broad-spectrum resistance,but this broad-spectrum resistance usually comes at the expense of yield.Currently,many necrotic lesion mutants in rice have been identified,and these genes are involved in disease resistance pathways.This review provides a detailed introduction to the characteristics,classification,and molecular mechanisms of necrotic lesion formation.Additionally,we review the molecular regulatory pathways of genes involved in rice disease resistance.Concurrently,we summarize the relationship between resistance and yield in rice using newly developed gene editing methods.We 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

Oriented Generation of Novel Thermo-Sensitive Genic Male Sterile Lines with Improved Grain Shape and Outcrossing Rate in Early-Season rice

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rice science 2024年第2期31卷 129-133,I0001-I0016页

作者： ZHANG Huali CHEN Junyu LI Ruiqing WANG Huimei DAI Dongqing LIANG Minmin WU Mingyue MA Liangyong state key laboratory of rice biology and breeding/Chinese National Center for rice Improvement China National Rice Research InstituteHangzhou 310006China

Two-line hybrid rice with excellent quality is preferred in the Chinese market.However,there is a trade-off between reducing costs for hybrid seed production and lowering the outcrossing rate of the sterile line,which is largely determined by the stigma exsertion rate(SER).In this study,we constructed mutants of male sterility lines with improved grain length(GL)and SER in three elite early-season indica rice varieties through targeted manipulation of the TMS5 and GS3 genes using CRISPR/Cas9-mediated multiplex systems.We obtained a series of marker-free gs3 single mutants and gs3tms5 double mutants with significantly higher SER,longer grains,and increased 1000-grain weight compared with the wild type(WT).Importantly,the typically thermo-sensitive genic male sterile(TGMS)trait with a higher SER was observed in gs3tms5 mutants,and their F1 hybrids exhibited remarkable improvements in grain shape and yield-related traits.Our findings provided an efficient method to generate new valuable TGMS germplasm with improved SER through the mutagenesis of GS3 and TMS5 synergistically,and demonstrated that GS3 had pleiotropic effects on grain size,SER,and grain quality in early-season indica rice.

关键词： sterile elite season

A polygalacturonase gene OsPG1 modulates water homeostasis in rice

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The Crop Journal 2024年第1期12卷 79-91页

作者： Qinwen Zou Ranran Tu Jiajun Wu Tingting Huang Zhihao Sun Zheyan Ruan Hongyu Cao Shihui Yang Xihong Shen Guanghua He Hong Wang rice Research Institute Key Laboratory of Application and Safety Control of Genetically Modified CropsAcademy of Agricultural SciencesSouthwest UniversityChongqing 400715China state key laboratory of rice biology and breeding Key Laboratory for Zhejiang Super Rice ResearchChina National Center for Rice ImprovementChina National Rice Research InstituteHangzhou 311401ZhejiangChina

A dynamic plant architecture is the basis of plant adaptation to changing environments.Although many genes regulating leaf rolling have been identified,genes directly associated with water homeostasis are largely unknown.Here,we isolated a rice mutant,dynamic leaf rolling 1(dlr1),characterized by‘leaf unfolding in the morning-leaf rolling at noon-leaf unfolding in the evening’during a sunny day.Water content was decreased in rolled leaves and water sprayed on leaves caused reopening,indicating that in vivo water deficiency induced the leaf rolling.Map-based cloning and expression tests demonstrated that an A1400G single base mutation in Oryza sativa Polygalacturonase 1(OsPG1)/PHOTO-SENSITIVE LEAF ROLLING 1(PSL1)was responsible for the dynamic leaf rolling phenotype in the dlr1 mutant.OsPG1 encodes a polygalacturonase,one of the main enzymes that degrade demethylesterified homogalacturonans in plant cell walls.OsPG1 was constitutively expressed in various tissues and was enriched in stomata.Mutants of the OsPG1 gene exhibited defects in stomatal closure and decreased stomatal density,leading to reduced transpiration and excessive water loss under specific conditions,but had normal root development.Further analysis revealed that mutation of OsPG1 led to reduced pectinase activity in the leaves and increased demethylesterified homogalacturonans in guard cells.Our findings reveal a mechanism by which OsPG1 modulates water homeostasis to control dynamic leaf rolling,providing insights for plants to adapt to environmental variation.

关键词： Photosynthesis Stomata Transpiration Leaf rolling

OsbZIP01 Affects Plant Growth and Development by Regulating OsSD1 in rice

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rice science 2024年第1期31卷 77-86,I0018,I0019页

作者： DONG Xinli ZHOU Yang ZHANG Yaqi RONG Fuxi DU Jiahong HONG Zheyuan HU Peisong LÜYusong College of Agriculture and Biotechnology Zhejiang UniversityHangzhou 310058China state key laboratory of rice biology and breeding/China National Center for rice Improvement China National Rice Research InstituteHangzhou 310006China

As the‘Green Revolution’gene,SD1(encoding GA20ox2),has been widely applied to improve yield in rice breeding.However,research on its transcriptional regulation is limited.Here,we identified a transcription factor OsbZIP01,which can suppress the expression of SD1 and regulate gibberellin(GA)biosynthesis in rice.Knockout mutants of OsbZIP01 exhibited increased plant height,while the overexpression lines showed a semi-dwarf phenotype and diminished germination rate.Furthermore,the semi-dwarf phenotype of OE-bZIP01,was caused by the reduced internode length,which was accompanied by a thin stem width.The predominant expression of OsbZIP01 was observed in leaves and sheaths.OsbZIP01 protein was localized in the nucleus and showed transcriptional repression activity.In addition,OsbZIP01 could directly bind to the promoter of the OsSD1 gene,and inhibit its transcription.The semi-dwarf phenotype of OE-bZIP01 could be rescued by exogenous GA_(3).Meanwhile,the bzip01 sd1 double mutant showed a shorter shoot length compared with the wild type,indicating that OsbZIP01 regulated plant growth mainly through the GA biosynthesis pathway.Collectively,OsbZIP01 negatively regulates GA biosynthesis by restraining SD1 transcription,thereby affecting plant growth and development.

关键词： OsbZIP01 SD1 gibberellin biosynthesis dwarf and germination

A 48-bp deletion upstream of LIGULELESS 1 alters rice panicle architecture

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The Crop Journal 2024年第2期12卷 354-363页

作者： Linhua Wu Min Hu Shuwei Lyu Wenfeng Chen Hang Yu Qing Liu Wei He Chen Li Zuofeng Zhu rice Research Institute Guangdong Academy of Agricultural SciencesGuangzhou 510640GuangdongChina National Center for Evaluation of Agricultural Wild Plants(rice) Department of Plant Genetics and BreedingChina Agricultural UniversityBeijing 100193China state key laboratory for rice biology and breeding China National Rice Research InstituteHangzhou 310006ZhejiangChina key laboratory of Genetics and breeding of High Quality rice in Southern China(Co-construction by Ministry and Province) Ministry of Agriculture and Rural AffairsGuangzhou 510640GuangdongChina Guangdong key laboratory of New Technology in rice breeding Guangzhou 510640GuangdongChina Guangdong rice Engineering laboratory Guangzhou 510640GuangdongChina

Panicle architecture is an agronomic determinant of crop yield and a target for cereal crop improvement.To investigate its molecular mechanisms in rice,we performed map-based cloning and characterization of OPEN PANICLE 1(OP1),a gain-of-function allele of LIGULELESS 1(LG1),controlling the spread-panicle phenotype.This allele results from a 48-bp deletion in the LG1 upstream region and promotes pulvinus development at the base of the primary branch.Increased OP1 expression and altered panicle phenotype in chimeric transgenic plants and upstream-region knockout mutants indicated that the deletion regulates spread-panicle architecture in the mutant spread panicle 1(sp1).Knocking out BRASSINOSTEROID UPREGULATED1(BU1)gene in the background of OP1 complementary plants resulted in compact panicles,suggesting OP1 may regulate inflorescence architecture via the brassinosteroid signaling pathway.We regard that manipulating the upstream regulatory region of OP1 or genes involved in BR signal pathway could be an efficient way to improve rice inflorescence architecture.

关键词： Upstream region Panicle architecture Gene expression BR rice