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OsPRMT6a-mediated arginine methylation of OsJAZ1 regulates jasmonate signaling and spikelet development in rice

Molecular Plant 2024年第6期17卷 900-919页

作者： Kun Dong Fuqing Wu Siqi Cheng Shuai Li Feng Zhang Xinxin Xing Xin Jin Sheng Luo Miao Feng Rong Miao Yanqi Chang Shuang Zhang Xiaoman You Peiran Wang Xin Zhang Cailin Lei Yulong Ren Shanshan Zhu Xiuping Guo Chuanyin Wu Dong-Lei Yang Qibing Lin Zhijun Cheng Jianmin Wan State key Laboratory of crop gene resources and Breeding National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China State key Laboratory for crop genetics and Germplasm Enhancement Nanjing Agricultural UniversityNanjing 210095China

Although both protein arginine methylation(PRMT)and jasmonate(JA)signaling are crucial for regulating plant development,the relationship between these processes in the control of spikelet development remains *** this study,we used the CRISPR/Cas9 technology to generate two OsPRMT6a loss-of-function mutants that exhibit various abnormal spikelet ***,we found that OsPRMT6a can methylate arginine residues in JA signal repressors OsJAZ1 and *** showed that arginine methylation of OsJAZ1 enhances the binding affinity of OsJAZ1 with the JA receptors OsCOI1a and OsCOI1b in the presence of JAs,thereby promoting the ubiquitination of OsJAZ1 by the SCF^(OsCOI1a/OsCOI1b) complex and degradation via the 26S *** process ultimately releases OsMYC2,a core transcriptional regulator in the JA signaling pathway,to activate or repress JA-responsive genes,thereby maintaining normal plant(spikelet)***,in the osprmt6a-1 mutant,reduced arginine methylation of OsJAZ1 impaires the interaction between OsJAZ1 and OsCOI1a/OsCOI1b in the presence of *** a result,OsJAZ1 proteins become more stable,repressing JA responses,thus causing the formation of abnormal spikelet ***,we discovered that JA signaling reduces the OsPRMT6a mRNA level in an OsMYC2-dependent manner,thereby establishing a negative feedback loop to balance JA *** further found that OsPRMT6a-mediated arginine methylation of OsJAZ1 likely serves as a switch to tune JA signaling to maintain normal spikelet development under harsh environmental conditions such as high ***,our study establishes a direct molecular link between arginine methylation and JA signaling in rice.

关键词： protein arginine methylation jasmonate signaling negative feedback loop spikelet development adaptation to heat stress rice

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Natural variation of GmFNSII-2 contributes to drought resistance by modulating enzyme activity in soybean

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The crop Journal 2024年第2期12卷 529-539页

作者： Huihui Gao Pengcheng Wei Yongzhe Gu Pengbin Tang Yifan Shen Lei Yang Linxin Dong Haowei Zheng Kuo Shu Mayamiko Masangano Bin Dong Long Miao Jiajia Li Lijuan Qiu Xiaobo Wang School of Agronomy Anhui Agricultural UniversityHefei 230036AnhuiChina State key Laboratory of crop gene resources and Breeding The National Key Facility for Crop Gene Resources and Genetic Improvement(NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement(MOA)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China

As an essential crop that provides vegetable oil and protein,soybean(Glycine max(L.)Merr.)is widely planted all over the ***,the scarcity of water resources worldwide has seriously impacted on the quality and yield of *** address this,exploring excellent genes for improving drought resistance in soybean is *** this study,we identified natural variations of GmFNSII-2(flavone synthase II)significantly affect the drought resistance of *** sequence analysis of GmFNSII-2 in 632 cultivated and 44 wild soybeans nine haplotypes were *** full-length allele GmFNSII-2^(C),but not the truncated allele GmFNSII-2^(A) possessing a nonsense nucleotide variation,increased enzyme *** research found that GmDREB3,known to increase soybean drought resistance,bound to the promoter region of GmFNSII-2^(C).GmDREB3 positively regulated the expression of GmFNSII-2^(C),increased flavone synthase abundance and improved the drought ***,a singlebase mutation in the GmFNSII-2^(C) promoter generated an additional drought response element(CCCCT),which had stronger interaction strength with GmDREB3 and increased its transcriptional activity under drought *** frequency of drought-resistant soybean varieties with Hap 1(Pro:GmFNSII-2^(C))has increased,suggesting that this haplotype may be selected during soybean *** summary,GmFNSII-2^(C) could be used for molecular breeding of drought-tolerant soybean.

关键词： Drought stress Flavone synthase GmFNSII-2 Natural variation Drought response element

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Genome-wide association study of seedling nitrogen-use efficiency-associated traits in common wheat(Triticum aestivum L.)

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The crop Journal 2024年第1期12卷 222-231页

作者： Huawei Shi Weichong Wang Lifeng Gao Jirong Wu Chengmei Hu Huishu Yan Yugang Shi Ning Li Youzhi Ma Yongbin Zhou Zhaoshi Xu Jun Chen Wensi Tang Kai Chen Daizhen Sun Yuxiang Wu Ming Chen College of Agriculture Shanxi Agricultural UniversityJinzhong 030801ShanxiChina national key facility for crop gene resources and genetic improvement Key Laboratory of Biology and Genetic Improvement of Triticeae CropsMinistry of AgricultureInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China

Nitrogen(N)fertilizer application is essential for crop-plant growth and *** genetic loci associated with N-use efficiency(NUE)could increase wheat yields and reduce environmental pollution caused by *** subjected a panel of 389 wheat accessions to N and chlorate(a nitrate analog)treatments to identify quantitative trait loci(QTL)controlling NUE-associated traits at the wheat seedling *** the panel with a 660K single-nucleotide polymorphism(SNP)array,we identified 397 SNPs associated with N-sensitivity index and chlorate inhibition *** SNPs were merged into 49 QTL,of which eight were multi-environment stable QTL and 27 were located near previously reported QTL.A set of 135 candidate genes near the 49 QTL included TaBOX(F-box family protein)and TaERF(ethylene-responsive transcription factor).A Tabox mutant was more sensitive to low-N stress than the wild-type *** developed two functional markers for Hap 1,the favorable allele of TaBOX.

关键词： Wheat NUE Genome-wide association study Nitrogen sensitive index Chlorate inhibition rate

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The ABA synthesis enzyme allele OsNCED2^(T)promotes dryland adaptation in upland rice

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The crop Journal 2024年第1期12卷 68-78页

作者： Liyu Huang Yachong Bao Shiwen Qin Min Ning Qinyan Li Qingmao Li Shilai Zhang Guangfu Huang Jing Zhang Wensheng Wang Binying Fu Fengyi Hu key Laboratory of Biology and Germplasm Innovation of Perennial Rice from Ministry of Agriculture and Rural Affairs School of AgricultureYunnan UniversityKunming 650091YunnanChina national key facility for crop gene resources and genetic improvement Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China

Upland rice shows dryland adaptation in the form of a deeper and denser root system and greater drought resistance than its counterpart,irrigated *** previous study revealed a difference in the frequency of the OsNCED2 gene between upland and irrigated populations.A nonsynonymous mutation(C to T,from irrigated to upland rice)may have led to functional variation fixed by artificial selection,but the exact biological function in dryland adaptation is *** this study,transgenic and association analysis indicated that the domesticated fixed mutation caused functional variation in OsNCED2,increasing ABA levels,root development,and drought tolerance in upland rice under dryland ***2-overexpressing rice showed increased reactive oxygen species-scavenging abilities and transcription levels of many genes functioning in stress response and development that may regulate root development and drought ***2^(T)-NILs showed a denser root system and drought resistance,promoting the yield of rice under dryland ***2^(T)may confer dryland adaptation in upland rice and may find use in breeding dryland-adapted,water-saving rice.

关键词： Upland rice Dryland adaptation ABA Root development Drought tolerance

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A telomere-to-telomere genome assembly of Zhonghuang 13,a widely-grown soybean variety from the original center of Glycine max

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The crop Journal 2024年第1期12卷 142-153页

作者： Anqi Zhang Tangchao Kong Baiquan Sun Shizheng Qiu Jiahe Guo Shuyong Ruan Yu Guo Jirui Guo Zhishuai Zhang Yue Liu Zheng Hu Tao Jiang Yadong Liu Shuqi Cao Shi Sun Tingting Wu Huilong Hong Bingjun Jiang Maoxiang Yang Xiangyu Yao Yang Hu Bo Liu Tianfu Han Yadong Wang Center for Bioinformatics School of Computer Science and TechnologyHarbin Institute of TechnologyHarbin 150001HeilongjiangChina Ministry of Agriculture key Laboratory of Soybean Biology(Beijing) Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China national key facility for crop gene resources and genetic improvement Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China

Soybean(Glycine max)stands as a globally significant agricultural crop,and the comprehensive assembly of its genome is of paramount importance for unraveling its biological characteristics and evolutionary ***,previous soybean genome assemblies have harbored gaps and incompleteness,which have constrained in-depth investigations into ***,we present Telomere-to-Telomere(T2T)assembly of the Chinese soybean cultivar Zhonghuang 13(ZH13)genome,termed ZH13-T2T,utilizing PacBio Hifi and ONT ultralong *** employed a multi-assembler approach,integrating Hifiasm,NextDenovo,and Canu,to minimize biases and enhance assembly *** assembly spans 1,015,024,879 bp,effectively resolving all 393 gaps that previously plagued the reference *** annotation efforts identified 50,564 high-confidence protein-coding genes,707 of which are ***13-T2T revealed longer chromosomes,421 not-aligned regions(NARs),112 structure variations(SVs),and a substantial expansion of repetitive element compared to earlier ***,we identified 25.67 Mb of tandem repeats,an enrichment of 5S and 48S rDNAs,and characterized their genotypic *** summary,we deliver the first complete Chinese soybean cultivar T2T *** comprehensive annotation,along with precise centromere and telomere characterization,as well as insights into structural variations,further enhance our understanding of soybean genetics and evolution.

关键词： Soybean Telomere-to-Telomere assembly Zhonghuang 13 Structure variations

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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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Development and identification of two novel wheat-rye 6R derivative lines with adult-plant resistance to powdery mildew and high-yielding potential

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The crop Journal 2024年第1期12卷 308-313页

作者： Guohao Han Jing Wang Hanwen Yan Tiantian Gu Lijun Cao Shiyu Liu Xiuquan Li Yilin Zhou Jieru Fan Zhipeng Shi Hong Liu Lihui Li Diaoguo An Center for Agricultural resources Research Institute of Genetics and Developmental BiologyChinese Academy of SciencesShijiazhuang 050021HebeiChina The national key facility for crop gene resources and genetic improvement Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China The State key Laboratory for Biology of Plant Disease and Insect Pests Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing 100193China

Powdery mildew,caused by Blumeria graminis ***(Bgt),is a devastating disease that seriously threatens wheat yield and *** control this disease,host resistance is the most effective *** with the resistance genes from common wheat,alien resistance genes can better withstand infection of this highly variable *** of elite alien germplasm resources with powdery mildew resistance and other key breeding traits is an attractive strategy in wheat *** this study,three wheat-rye germplasm lines YT4-1,YT4-2,and YT4-3 were developed through hybridization between octoploid triticale and common wheat,out of which the lines YT4-1 and YT4-2 conferred adult-plant resistance(APR)to powdery mildew while the line YT4-3 was susceptible to powdery mildew during all of its growth *** genomic in situ hybridization,multi-color fluorescence in situ hybridization,multi-color GISH,and molecular marker analysis,YT4-1,YT4-2,and YT4-3 were shown to be cytogenetically stable wheat-rye 6R addition and T1RS.1BL translocation line,6RL ditelosomic addition and T1RS.1BL translocation line,and T1RS.1BL translocation line,*** with previously reported wheat-rye derivative lines carrying chromosome 6R,YT4-1 and YT4-2 showed stable APR without undesirable pleiotropic effects on agronomic ***,these novel wheat-rye 6R derivative lines are expected to be promising bridge resources in wheat disease breeding.

关键词： Powdery mildew Secale cereale Triticum aestivum Wheat-rye 6R derivatives Agronomic performance

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A k-mer-based pangenome approach for cataloging seed-storage-protein genes in wheat to facilitate genotype-to-phenotype prediction and improvement of end-use quality

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Molecular Plant 2024年第7期17卷 1038-1053页

作者： Zhaoheng Zhang Dan Liu Binyong Li Wenxi Wang Jize Zhang Mingming Xin Zhaorong Hu Jie Liu Jinkun Du Huiru Peng Chenyang Hao Xueyong Zhang Zhongfu Ni Qixin Sun Weilong Guo Yingyin Yao Frontiers Science Center for Molecular Design Breeding Key Laboratory of Crop Heterosis and Utilization(MOE)and Bejing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China key Laboratory of crop gene resources and Breeding Institute of Crop ScienceChinese Academy of Agricultural SciencesBejingChina

Wheat is a staple foodfor more than 35%of the world's population,with wheatflourused to make hundreds of baked *** end-use quality is a major breeding target;however,improving it is especially time-consuming and ***,genes encoding seed-storage proteins(ssPs)form multigene families and are repetitive,with gaps commonplace in several genome *** overcome these barriers and efficiently identify superior wheat SSP alleles,we developed"PanSK"(Pan-SSP k-mer)for genotype-to-phenotype prediction based on an SsP-based pangenome *** uses 29-mer sequences that represent each ssP gene at the pangenomic level to reveal untapped diversity across landraces and modern ***-wide association studies with k-mers identified 23 Ssp genes associated with end-use quality that represent novel targets for *** evaluated the effect of rye secalin genes on end-use quality and found that removal of w-secalins from 1BL/1RS wheat translocation lines is associated with enhanced end-use ***,using machine-learning-based prediction inspired by PanSK,we predicted the quality phenotypes with high accuracy from genotypes *** study provides an effective approach for genome design based on ssP genes,enabling the breeding of wheat varieties with superior processing capabilities and improved end-use quality.

关键词： wheat seed-storage protein end-use quality k-mer pangenome genomic prediction

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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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Proteomics analysis of coronary atherosclerotic heart disease with different Traditional Chinese Medicine syndrome types before and after percutaneous coronary intervention

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Journal of Traditional Chinese Medicine 2024年第3期44卷 554-563页

作者： WANG Zhibo LI Ying WANG Daoping MA Bo MIAO Lan REN Junguo LIU Jinghua LIU Jianxun Beijing key Laboratory of Pharmacology of Chinese Materia Region Institute of Basic Medical SciencesXiyuan HospitalChina Academy of Chinese Medical SciencesNational Clinical Research Center of Cardiovascular Disease of Traditional Chinese Medicine the national key facility for crop gene resources and genetic improvement Institute of Crop ScienceChinese Academy of Agricultural Science Department of Cardiology Beijing Anzhen HospitalCapital Medical University

OBJECTIVE: To investigate the underlying protein molecular mechanisms of "Qi stagnation and blood stasis syndrome"(QS) and "Qi deficiency and blood stasis syndrome"(QD), as two subtypes of coronary artery disease(CAD) in Traditional Chinese Medicine(TCM),following percutaneous coronary intervention(PCI).METHODS: In this study, a total of 227 CAD patients with QS and 211 CAD patients with QD were enrolled; all participants underwent PCI. Label-free quantification proteomics were employed to analyze the changes in serum in two subtypes of CAD patients before and 6 months after PCI, aiming to elucidate the intervention mechanism of PCI in treating CAD characterized by two different TCM ***: Biochemical analysis revealed significant changes in tumor necrosis factor-α, high density lipoprotein cholesterol, blood stasis clinical symptoms observation, and Gensini levels in both patient groups post-PCI; Proteomic analysis identified 79 and 95 differentially expressed proteins in the QS and QD patient groups, respectively, compared to their control *** C8 alpha chain, complement factor H,apolipoprotein H, apolipoprotein B, plasminogen,carbonic anhydrase 2, and complement factor Ⅰ were altered in both comparison groups. Furthermore,enrichment analysis demonstrated that cell adhesion and connectivity-related processes underwent changes in QS patients post-PCI, whereas lipid metabolism-related pathways, including the peroxisome proliferator-activated receptor signaling pathway and extracellular matrix receptor interaction, underwent changes in the QD *** protein-protein interaction network analysis further enriched 52 node proteins, including apolipoprotein B,lipoprotein(a), complement C5, apolipoprotein A4,complement C8 alpha chain, complement C8 beta chain,complement C8 gamma chain, apolipoprotein H,apolipoprotein A-Ⅱ, albumin, complement C4-B,apolipoprotein C3, among others. The functional network of these proteins is posited to contribute t

关键词： Traditional Chinese Medicine syndrome coronary atherosclerotic heart disease peptide mapping percutaneous coronary intervention proteomics

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