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The MRE11–ATM–SOG1 DNA damage signaling pathway confers rice immunity to Xanthomonas oryzae

Plant Communications 2024年第4期5卷 194-207页

作者： Zhan Xu Mingnan Qu Chuanlin Shi Hong Zhang Wu Chen hongge qian Zhipeng Zhang Jiehua Qiu qian qian Lianguang Shang Guangzhou City Academy of Agricultural Sciences Key Laboratory of BiologyGenetics and BreedingGuangzhou 510000China 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 SciencesShenzhen 518120China Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding College of AgricultureYangzhou UniversityYangzhou 225009China State Key Laboratory of Rice Biology China National Rice Research InstituteHangzhou 311400China Yazhouwan National Laboratory No.8 Huanjin RoadYazhou DistrictSanya CityHainan Province 572024China These authors contributed equally to this article

Plants are constantly exposed to microbial pathogens in the *** branch of innate plant immunity is mediated by cell-membrane-localized receptors,but less is known about associations between DNA damage and plant immune ***,we show that rice(Oryza sativa)mesophyll cells are prone to DNA double-stranded breaks(DSBs)in response to ZJ173,a strain of Xanthomonas oryzae ***(Xoo).The DSB signal transducer ataxia telangiectasia mutated(ATM),but not the ATM and Rad3-related branch,confers resistance against ***,the MRE11–ATM module phosphorylates suppressor of gamma response 1(SOG1),which activates several phenylpropanoid pathway genes and prompts downstream phytoalexin biosynthesis during Xoo ***,overexpression of the topoisomerase gene TOP6A3 causes a switch from the classic non-homologous end joining(NHEJ)pathway to the alternative NHEJ and homologous recombination pathways atXoo-induced *** enhanced ATM signaling of the alternative NHEJ pathway strengthens the SOG1-regulated phenylpropanoid pathway and thereby boosts Xoo-induced phytoalexin biosynthesis in TOP6A3-OE1 overexpression ***,the MRE11–ATM–SOG1 pathway serves as a prime example of plant–pathogen interactions that occur via host non-specific recogni*** function of TOP6-facilitated ATM signaling in the defense response makes it a promising target for breeding of rice germplasm that exhibits resistance to bacterial blight disease without a growth penalty.

关键词： Oryza sativa Xanthomonas oryzae pv.oryzae DSBs phytoalexins MRE11–ATM–SOG1 TOP6 complex

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BTA2 regulates tiller angle and the shoot gravity response through controlling auxin content and distribution in rice

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Journal of Integrative Plant Biology 2024年第9期66卷 1966-1982页

作者： Zhen Li Junhua Ye Qiaoling Yuan Mengchen Zhang Xingyu Wang Jing Wang Tianyi Wang hongge qian Xinghua Wei Yaolong Yang Lianguang Shang Yue Feng China National Center for Rice Improvement State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhou 310006China 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 SciencesShenzhen 518124China National Nanfan Research Institute(Sanya) Chinese Academy of Agricultural SciencesSanya 572024China

Tiller angle is a key agricultural trait that establishes plant architecture,which in turn strongly affects grain yield by influencing planting density in *** shoot gravity response plays a crucial role in the regulation of tiller angle in rice,but the underlying molecular mechanism is largely ***,we report the identification of the BIG TILLER ANGLE2(BTA2),which regulates tiller angle by controlling the shoot gravity response in ***-of-function mutation of BTA2 dramatically reduced auxin content and affected auxin distribution in rice shoot base,leading to impaired gravitropism and therefore a big tiller ***2 interacted with AUXIN RESPONSE FACTOR7(ARF7)to modulate rice tiller angle through the gravity signaling *** BTA2 protein was highly conserved during *** variation in the BTA2 promoter of indica cultivars harboring a less expressed BTA2 allele caused lower BTA2 expression in shoot base and thus wide tiller angle during rice *** of BTA2 significantly increased grain yield in the elite rice cultivar Huanghuazhan under appropriate dense planting *** findings thus uncovered the BTA2-ARF7 module that regulates tiller angle by mediating the shoot gravity *** work offers a target for genetic manipulation of plant architecture and valuable information for crop improvement by producing the ideal plant type.

关键词： auxin domestication gravity response rice tiller angle

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Identification of natural allelic variation in TTL1 controlling thermotolerance and grain size by a rice super pan-genome∞

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Journal of Integrative Plant Biology 2023年第12期65卷 2541-2551页

作者： Yarong Lin Yiwang Zhu Yuchao Cui hongge qian Qiaoling Yuan Rui Chen Yan Lin Jianmin Chen Xishi Zhou Chuanlin Shi Huiying He Taijiao Hu Chenbo Gu Xiaoman Yu Xiying Zhu Yuexing Wang qian qian Cuijun Zhang Feng Wang Lianguang Shang Institute of Biotechnology Fujian Academy of Agricultural Sciences/Fujian Provincial Key Laboratory of Genetic Engineering for AgricultureFuzhou 350003China 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 SciencesShenzhen 518124China Xiamen Key Laboratory for Plant Genetics School of Life SciencesXiamen UniversityXiamen 361102China College of Bioscience and Biotechnology Hunan Agricultural UniversityChangsha 410128China State Key Laboratory of Rice Biology China National Rice Research InstituteHangzhou 311401China Yazhouwan National Laboratory Sanya City 572024China

Continuously increasing global temperatures present great challenges to food *** size,one of the critical components determining grain yield in rice(Oryza sativa L.),is a prime target for genetic ***,there is an immediate need for genetic improvement in rice to maintain grain yield under heat ***,quantitative trait loci(QTLs)endowing heat stress tolerance and grain size in rice are extremely ***,we identified a novel negative regulator with pleiotropic effects,Thermo‐Tolerance and grain Length 1(TTL1),from the super pan‐genomic and transcriptomic ***‐of‐function mutations in TTL1 enhanced heat tolerance,and caused an increase in grain size by coordinating cell expansion and ***1 was shown to function as a transcriptional regulator and localized to the nucleus and cell ***,haplotype analysis showed that hapL and hapS of TTL1 were obviously correlated with variations of thermotolerance and grain size in a core collection of *** evolution analysis of available rice germplasms suggested that TTL1 was selected during domestication of the indica and japonica rice subspecies,but still had much breeding potential for increasing grain length and *** findings provide insights into TTL1 as a novel potential target for the development of high‐yield and thermotolerant rice varieties.

关键词： domestication grain size heat tolerance pan‐genome natural variation

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A pan-TE map highlights transposable elements underlying domestication and agronomic traits in Asian rice

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National Science Review 2024年第6期11卷 105-118页

作者： Xiaoxia Li Xiaofan Dai Huiying He Yang Lv Longbo Yang Wenchuang He Congcong Liu Hua Wei Xiangpei Liu Qiaoling Yuan Xianmeng Wang Tianyi Wang Bintao Zhang Hong Zhang Wu Chen Yue Leng Xiaoman Yu hongge qian Bin Zhang Mingliang Guo Zhipeng Zhang Chuanlin Shi qianqian Zhang Yan Cui qiang Xu Xinglan Cao Dandan Chen Yongfeng Zhou 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 Rice Research Institute Shenyang Agricultural University Yazhouwan National Laboratory State Key Laboratory of Rice Biology China National Rice Research Institute National Key Laboratory of Tropical Crop Breeding Tropical Crops Genetic Resources InstituteChinese Academy of Tropical Agricultural Sciences

Transposable elements(TEs) are ubiquitous genomic components and hard to study due to being highly repetitive. Here we assembled 232 chromosome-level genomes based on long-read sequencing *** the 232 genomes with 15 existing assemblies, we developed a pan-TE map comprising both cultivated and wild Asian rice. We detected 177 084 high-quality TE variations and inferred their derived state using outgroups. We found TEs were one source of phenotypic variation during rice domestication and differentiation. We identified 1246 genes whose expression variation was associated with TEs but not single-nucleotide polymorphisms(SNPs), such as Os Rboh B, and validated Os Rboh B's relative expression activity using a dual-Luciferase(LUC) reporter assays system. Our pan-TE map allowed us to detect multiple novel loci associated with agronomic traits. Collectively, our findings highlight the contributions of TEs to domestication, differentiation and agronomic traits in rice, and there is massive potential for gene cloning and molecular breeding by the high-quality Asian pan-TE map we generated.

关键词： transposable element super pan-genome pan-TE rice

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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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A centromere map based on super pan-genome highlights the structure and function of rice centromeres

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Journal of Integrative Plant Biology 2024年第2期66卷 196-207页

作者： Yang Lv Congcong Liu Xiaoxia Li Yueying Wang Huiying He Wenchuang He Wu Chen Longbo Yang Xiaofan Dai Xinglan Cao Xiaoman Yu Jiajia Liu Bin Zhang Hua Wei Hong Zhang hongge qian Chuanlin Shi Yue Leng Xiangpei Liu Mingliang Guo Xianmeng Wang Zhipeng Zhang Tianyi Wang Bintao Zhang qiang Xu Yan Cui qianqian Zhang Qiaoling Yuan Noushin Jahan Jie Ma Xiaoming Zheng Yongfeng Zhou qian qian Longbiao Guo Lianguang Shang State Key Laboratory of Rice Biology China National Rice Research InstituteHangzhou 310006China 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 SciencesShenzhen 518120China Yazhouwan National Laboratory No.8 Huanjin RoadYazhou DistrictSanya City 572024China National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijing 100081China

Rice(Oryza sativa)is a significant crop worldwide with a genome shaped by various evolutionary *** centromeres are crucial for chromosome segregation,and contain some unreported *** to the diverse and complex centromere region,a comprehensive understanding of rice centromere structure and function at the population level is *** constructed a high-quality centromere map based on the rice super pangenome consisting of a 251-accession panel comprising both cultivated and wild species of Asian and African *** showed that rice centromeres have diverse satellite repeat CentO,which vary across chromosomes and subpopulations,reflecting their distinct evolutionary *** also revealed that long terminal repeats(LTRs),especially young Gypsy-type LTRs,are abundant in the peripheral CentO-enriched regions and drive rice centromere expansion and ***,high-quality genome assembly and complete telomere-to-telomere(T2T)reference genome enable us to obtain more centromeric genome information despite mapping and cloning of centromere genes being *** investigated the association between structural variations and gene expression in the rice centromere.A centromere gene,OsMAB,which positively regulates rice tiller number,was further confirmed by expression quantitative trait loci,haplotype analysis and clustered regularly interspaced palindromic repeats(CRISPR)/CRISPR-associated protein9 *** revealing the new insights into the evolutionary patterns and biological roles of rice centromeres,our finding will facilitate future research on centromere biology and crop improvement.

关键词： centromere super pan-genome CentoO satellite repeat rice

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A complete assembly of the rice Nipponbare reference genome

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Molecular Plant 2023年第8期16卷 1232-1236页

作者： Lianguang Shang Wenchuang He Tianyi Wang Yingxue Yang qiang Xu Xianjia Zhao Longbo Yang Hong Zhang Xiaoxia Li Yang Lv Wu Chen Shuo Cao Xianmeng Wang Bin Zhang Xiangpei Liu Xiaoman Yu Huiying He Hua Wei Yue Leng Chuanlin Shi Mingliang Guo Zhipeng Zhang Bintao Zhang Qiaoling Yuan hongge qian Xinglan Cao Yan Cui qianqian Zhang Xiaofan Dai Congcong Liu Longbiao Guo Yongfeng Zhou Xiaoming Zheng Jue Ruan Zhukuan Cheng Weihua Pan qian qian 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 SciencesShenzhen 518120China Yazhouwan National Laboratory No.8 Huanjin RoadYazhou DistrictSanya CityHainan Province 572024China State Key Laboratory of Rice Biology China National Rice Research InstituteHangzhou 310006China National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijing 100081China Key Laboratory of Plant Functional Genomics of the Ministry of Education Jiangsu Co-Innovation Center for Modern Production Technology of Grain CropsYangzhou UniversityYangzhou 225009China

Dear Editor,In 2005,the current commonly used rice reference genome(Oryza sativa *** ***)was initially released by the International Rice Genome Sequencing Project(International Rice Genome Sequencing Project,2005).Thereafter,the reference genome was further updated in 2013 with improved genome assembly(IRGSP-1.0)and gene annotations(MSU7,RAP-DB)(Kawahara et al.,2013;Sakai et al.,2013).In the past 10 years,this reference has been serving as one of the most important genetic resources for subsequent rice functional genomics *** several rice genomes had been assembled into gapless chromosomes with only 2–5 telomeres absent(Li et al.,2021;Song et al.,2021;Zhang et al.,2022),the IRGSP1.0 and its annotations still performed as the most widely used ***,limitations of sequencing technology and intricate genomic organization led to an under-representation of complex regions in this reference,leaving a total of 72 major gaps(including 19 telomeres),167 minor gaps,and 779 unknown bases(Kawahara et al.,2013),with an estimated length of3%of the genome unsolved.

关键词： Sakai bases assembly

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江苏省常州市武进区昆虫多样性及区系特征分析

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内蒙古林业调查设计 2022年第1期45卷 52-57,85页

作者：王倩钱宏革苏日娜白晓拴内蒙古师范大学生命科学与技术学院内蒙古呼和浩特010022 湖南农业大学生物科学技术学院湖南长沙410125

2018年7月28日至8月22日,2019年4月18~24日在江苏省常州市武进区选取42条样线进行了昆虫调查。经统计,在科级、属级、种级水平上,半翅目昆虫的数目(21科52属57种)都是最多的,鞘翅目昆虫(19科43属49种)次之,而蜚蠊目和革翅目昆虫(1科1属1... 详细信息

2018年7月28日至8月22日,2019年4月18~24日在江苏省常州市武进区选取42条样线进行了昆虫调查。经统计,在科级、属级、种级水平上,半翅目昆虫的数目(21科52属57种)都是最多的,鞘翅目昆虫(19科43属49种)次之,而蜚蠊目和革翅目昆虫(1科1属1种)最少。物种多样性指数分析表明,武进区半翅目昆虫的多样性指数(4.0132)和均匀度指数(0.9926)最高,优势度指数(0.0248)最低;鞘翅目昆虫的丰富度指数(8.4555)最高。武进区不同生境中昆虫多样性指数和丰富度指数均表现为草地灌木>森林>水域>耕地>居民地;优势度指数表现为居民地>耕地>水域>森林>草地灌木;均匀度指数表现为森林>草地灌木>水域>耕地>居民地。武进区昆虫在世界动物地理分布中具有典型的东洋界分布类型,与古北界关系密切;在中国动物地理分布中,武进区昆虫分布组成以全国、华中区、华中区—华南区、华中区—华南区—西南区、华中区—华南区—西南区—华北区5种分布型为主。

关键词：昆虫多样性群落生境类型区系特征江苏

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褐背施蝗Schmidtiacris schmidti雄成虫染色体核型分析

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植物保护学报 2021年第1期48卷 239-240页

作者：钱宏革林晨王宁王树森温苏雅勒图李媛媛内蒙古师范大学生命科学与技术学院呼和浩特010022 中国农业科学院草原研究所呼和浩特010010 内蒙古农业大学沙漠治理学院呼和浩特010018 乌拉特后旗林业局内蒙古巴彦诺尔015500 内蒙古民族大学农学院通辽028000

蝗灾一直是世界性的难题,几乎所有国家都曾经或正在遭受蝗灾为害(于红妍和石旺鹏,2020)。随着监测和防控技术的发展以及人们环保意识的进一步加强和绿色治理技术的广泛应用,蝗灾将被可持续控制(赵紫华等,2020)。作为生物遗传物质的载体... 详细信息

蝗灾一直是世界性的难题,几乎所有国家都曾经或正在遭受蝗灾为害(于红妍和石旺鹏,2020)。随着监测和防控技术的发展以及人们环保意识的进一步加强和绿色治理技术的广泛应用,蝗灾将被可持续控制(赵紫华等,2020)。作为生物遗传物质的载体,染色体在各个物种细胞内的数量是一定的,但对于不同物种来说,其染色体数目、相对长度、着丝粒位置会有所不同。对染色体特征进行研究和分析,可以为昆虫近缘种的鉴别、物种演化及亲缘关系分析提供参考和依据。

关键词：亲缘关系分析防控技术染色体核型分析可持续控制蝗灾物种演化相对长度绿色治理

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樟子松嫩枝嫁接成活率的影响因素

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西北农业学报 2014年第7期23卷 191-196页

作者：杨涛刘喜东王强郭瑾梅栗大海钱红格陕西省治沙研究所陕西榆林719000 重庆市南川区森防站重庆南川408400 重庆市南川区大观镇重庆南川408415

采用不同种源地接穗,即内蒙古呼伦贝尔市红花尔基天然林、辽宁省昌图县傅家林场樟子松林木良种基地和陕西省榆林市樟子松种子园的接穗,通过嫩枝嫁接技术进行试验研究,分析不同种源地接穗亲和力、接穗保存时间和不同规格接穗3个因素对嫩... 详细信息

采用不同种源地接穗,即内蒙古呼伦贝尔市红花尔基天然林、辽宁省昌图县傅家林场樟子松林木良种基地和陕西省榆林市樟子松种子园的接穗,通过嫩枝嫁接技术进行试验研究,分析不同种源地接穗亲和力、接穗保存时间和不同规格接穗3个因素对嫩枝嫁接成活率的影响。结果表明:不同种源地采集的樟子松优良接穗嫁接成活率具有明显的差异,采自榆林市樟子松种子园的11个无性系接穗嫁接成活率达到98.7%,辽宁省昌图县樟子松林木良种基地的30个无性系和内蒙古红花尔基樟子松天然林的34个无性系成活率分别是72.7%和61.3%。接穗低温保存第9天后对嫁接成活率具有显著影响;不同规格的接穗其嫁接成活率也有差异。

关键词：樟子松种源地嫩枝嫁接成活率影响因素

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