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Uncovering key salt-tolerant regulators through a combined eQTL and GWAS analysis using the super pan-genome in rice

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national science Review 2024年第4期11卷 55-69页

作者： Hua Wei Xianmeng Wang Zhipeng Zhang Longbo Yang Qianqian Zhang Yilin Li Huiying He Dandan Chen Bin Zhang Chongke Zheng Yue Leng Xinglan Cao Yan Cui Chuanlin Shi Yifan Liu Yang Lv Jie Ma Wenchuang He Xiangpei Liu Qiang Xu Qiaoling Yuan Xiaoman Yu Tianyi Wang Hongge Qian Xiaoxia Li Bintao Zhang Hong Zhang Wu Chen Mingliang Guo Xiaofan Dai Yuexing Wang Xiaoming Zheng Longbiao Guo Xianzhi Xie Qian Qian Lianguang Shang 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 Sciences institute of Wetland Agriculture and Ecology Shandong Academy of Agricultural Sciences State key laboratory of rice biology China National Rice Research Institute national key Facility for crop Gene Resources and Genetic Improvement Institute of Crop Science Chinese Academy of Agricultural Sciences Yazhouwan national laboratory

For sessile plants, gene expression plays a pivotal role in responding to salinity stress by activating or suppressing specific genes. However, our knowledge of genetic variations governing gene expression in response to salt stress remains limited in natural germplasm. Through transcriptome analysis of the Global Mini-Core rice Collection consisting of a panel of 202 accessions, we identified 22 345 and 27 610expression quantitative trait loci associated with the expression of 7787 and 9361 e Genes under normal and salt-stress conditions, respectively, leveraging the super pan-genome map. Notably, combined with genome-wide association studies, we swiftly pinpointed the potential candidate gene STG5—a major salt-tolerant locus known as q STS5. Intriguingly, STG5 is required for maintaining Na+/K+homeostasis by directly regulating the transcription of multiple members of the Os HKT gene family. Our study sheds light on how genetic variants influence the dynamic changes in gene expression responding to salinity stress and provides a valuable resource for the mining of salt-tolerant genes in the future.

关键词： super pan-genome expression quantitative trait loci GWAS salt tolerance rice

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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

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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 *** 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 ***,utilizing this genome along with transcriptomic and metabolomic techniques,we explored ZH8015's response to brown planthopper(BPH)*** transcriptomic sampling indicated significant changes in gene expression levels around 48 h after BPH *** analysis revealed particularly significant alterations in genes related to reactive oxygen species scavenging and cell wall *** results demonstrated marked increases in levels of several monosaccharides,which are components of the cell wall and dramatic changes in flavonoid *** association analysis identified differentially expressed genes associated with key metabolites,shedding light on ZH8015's response to BPH *** 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

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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

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OsATL32 ubiquitinates the reactive oxygen species-producing OsRac5-OsRbohB module to suppress rice immunity

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Journal of Integrative Plant biology 2024年第7期66卷 1459-1480页

作者： Yuqing Yan Hui Wang Yan Bi Jiajing Wang Muhammad Noman Dayong Li Fengming Song national key laboratory for rice biology and Breeding Institute of BiotechnologyZhejiang UniversityHangzhou 310058China Ministry of Agriculture key laboratory of Molecular biology of crop Pathogens and Insect Pests Institute of BiotechnologyZhejiang UniversityHangzhou 310058China key laboratory of biology of crop Pathogens and Insects of Zhejiang Province Institute of BiotechnologyZhejiang UniversityHangzhou 310058China

Ubiquitination-mediated protein degradation is integral to plant immunity,with E3 ubiquitin ligases acting as key factors in this ***,we report the functions of OsATL32,a plasma membrane-localized Arabidopsis Tóxicos En Levadura(ATL)-type E3 ubiquitin ligase,in rice(Oryza sativa)immunity and its associated regulatory *** found that the expression of OsATL32 is downregulated in both compatible and incompatible interactions between rice and the rice blast fungus Magnaporthe *** OsATL32 protein level declines in response to infection by a compatible *** strain or to chitin ***32 negatively regulates rice resistance to blast and bacterial leaf blight diseases,as well as chitin-triggered *** and genetic studies revealed that OsATL32 suppresses pathogen-induced reactive oxygen species(ROS)accumulation by mediating ubiquitination and degradation of the ROS-producing OsRac5–OsRbohB module,which enhances rice immunity against *** protein phosphatase PHOSPHATASE AND TENSIN HOMOLOG enhances rice blast resistance by dephosphorylating OsATL32 and promoting its degradation,preventing its negative effect on rice *** study provides insights into the molecular mechanism by which the E3 ligase OsATL32 targets a ROS-producing module to undermine rice immunity.

关键词： E3 ligase OsATL32 OsRac5-OsRbohB module phosphatase OsPTEN reactive oxygen species rice immunity

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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 *** many genes regulating leaf rolling have been identified,genes directly associated with water homeostasis are largely ***,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 *** content was decreased in rolled leaves and water sprayed on leaves caused reopening,indicating that in vivo water deficiency induced the leaf ***-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 ***1 encodes a polygalacturonase,one of the main enzymes that degrade demethylesterified homogalacturonans in plant cell ***1 was constitutively expressed in various tissues and was enriched in *** 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 *** analysis revealed that mutation of OsPG1 led to reduced pectinase activity in the leaves and increased demethylesterified homogalacturonans in guard *** 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

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OsbZIP53 Negatively Regulates Immunity Response by Involving in Reactive Oxygen Species and Salicylic Acid Metabolism in rice

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rice science 2024年第2期31卷 190-202,I0022-I0028页

作者： WU Lijuan HAN Cong WANG Huimei HE Yuchang LIN Hai WANG Lei CHEN Chen E Zhiguo State key laboratory of rice biology and Breeding China National Rice Research InstituteHangzhou 310006China Jiangsu key laboratory of crop Genetics and Physiology/key laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu key laboratory of crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain crops Agricultural College of Yangzhou UniversityYangzhou 225009China

The basic region/leucine zipper(bZIP)transcription factors play important roles in plant development and responses to abiotic and biotic ***53 regulates resistance to Magnaporthe oryzae in rice by analyzing APIP5-RNAi transgenic *** further investigate the biological functions of OsbZIP53,we generated osbzip53 mutants using CRISPR/Cas9 editing and also constructed OsbZIP53 over-expression transgenic *** analysis of phenotypical,physiological,and transcriptional data showed that knocking-out OsbZIP53 not only improved disease resistance by inducing a hypersensitivity response in plants,but also regulated the immune response through the salicylic acid ***,disrupting OsbZIP53 increased H2O2 accumulation by promoting reactive oxygen species generation through up-regulation of several respiratory burst oxidase homologs(Osrboh genes)and weakened H2O2 degradation by directly targeting *** addition,the growth of osbzip53 mutants was seriously impaired,while OsbZIP53 over-expression lines displayed a similar phenotype to the wild type,suggesting that OsbZIP53 has a balancing effect on rice immune response and growth.

关键词： OsbZIP53 hypersensitive response reactive oxygen species metabolism rice immunity salicylic acid transcription factor

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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 ***,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 *** 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 *** 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

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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 *** there is a single H3K36 methyltransferase in yeast and higher eukaryotes,two H3K36 methyltransferases,Ash1 and Set2,were present in many filamentous ***,their roles in H3K36 methylation and transcriptional regulation remained *** 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 ***1 and Set2 distinguish genomic H3K36me2/3-marked regions and are differentially associated with repressed and activated transcription,***,Ash1-catalysed H3K36me2 was co-localized with H3K27me3 at the chromatin,and Ash1 was required for the enrichment and transcriptional silencing of H3K27me3-occupied *** 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 ***,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

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Carotenoid isomerase regulates rice tillering and grain productivity by its biosynthesis pathway

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Journal of Integrative Plant biology 2024年第2期66卷 172-175页

作者： Chaoqing Ding Zhengji Shao Yuping Yan Guangheng Zhang Dali Zeng Li Zhu Jiang Hu Zhenyu Gao Guojun Dong Qian Qian Deyong Ren State key laboratory of rice biology and Breeding ChinaNational Rice Research InstituteHangzhou 310006China

Tillers are unique inflorescence-like branches in grasses,and their number determines the panicle number,plant architecture,and yield(Shang et al.,2021).Tiller formation mainly undergoes axillary meristem(AM)initiation and tiller bud outgrowth(Wang et al.,2018;Yan et al.,2023).The rice(Oryza sativa)KNOX gene OSH1 is expressed in AMs,and an osh1 mutant produces fewer tillers(Tanaka et al.,2015).

关键词： sativa Oryza panicle

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