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Multi-omics analysis reveals the pivotal role of phytohormone homeostasis in regulating maize grain water content

The Crop Journal 2024年第4期12卷 1081-1092页

作者： Yuanliang Liu Manman Li Jianju Liu Suining Deng Yan Zhang Yuanfeng Xia Baoshen Liu Mingliang Xu State key laboratory of Plant Environmental Resilience/College of agronomy and biotechnology/National Maize Improvement Center/Center for Crop Functional Genomics and Molecular Breeding China Agricultural UniversityBeijing 100193China College of agronomy/State key laboratory of Crop Biology Shandong Agricultural UniversityTai’an 271018ShandongChina institute of agricultural biotechnology Jilin Academy of Agricultural SciencesGongzhuling 136100JilinChina Maize Research institute Jilin Academy of Agricultural SciencesGongzhuling 136100JilinChina

Grain water content(GWC)is a key determinant for mechanical harvesting of maize(Zea mays).In our previous research,we identified a quantitative trait locus,qGWC1,associated with GWC in ***,we examined near-isogenic lines(NILs)NILL and NILH that differed at the qGWC1 *** GWC in NILL was primarily attributed to reduced grain water weight(GWW)and smaller fresh grain size,rather than the accumulation of dry *** difference in GWC between the NILs became more pronounced approximately 35 d after pollination(DAP),arising from a faster dehydration rate in *** an integrated analysis of the transcriptome,proteome,and metabolome,coupled with an examination of hormones and their derivatives,we detected a marked decrease in JA,along with an increase in cytokinin,storage forms of IAA(IAA-Glu,IAA-ASP),and IAA precursor IPA in immature NILL *** kernel development,genes associated with sucrose synthases,starch biosynthesis,and zein production in NILL,exhibited an initial up-regulation followed by a gradual down-regulation,compared to those in *** discovery highlights the crucial role of phytohormone homeostasis and genes related to kernel development in balancing GWC and dry matter accumulation in maize kernels.

关键词： Grain water content Maize kernel Phytohormone homeostasis

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WRKY33 negatively regulates anthocyanin biosynthesis and cooperates with PHR1 to mediate acclimation to phosphate starvation

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Plant Communications 2024年第5期5卷 134-147页

作者： Han Tao Fei Gao Linying Li Yuqing He Xueying Zhang Mengyu Wang Jia Wei Yao Zhao Chi Zhang Qiaomei Wang Gaojie Hong State key laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of agro-products Key Laboratory of Biotechnology in Plant Protection of the MOA of China and Zhejiang ProvinceInstitute of Virology and BiotechnologyZhejiang Academy of Agricultural SciencesHangzhou 310021China State key laboratory of Subtropical Silviculture Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese MedicineZhejiang A&F UniversityHangzhou 311300China Department of Horticulture College of Agriculture and BiotechnologyZhejiang UniversityKey Laboratory of Horticultural Plant GrowthDevelopment and Quality ImprovementMinistry of AgricultureHangzhouZhejiangChina institute of Sericulture and Tea Zhejiang Academy of Agricultural SciencesHangzhou 310000China

Anthocyanin accumulation is acknowledged as a phenotypic indicator of phosphate(Pi)***,negative regulators of this process and their molecular mechanisms remain largely *** this study,we demonstrate that WRKY33 acts as a negative regulator of phosphorus-status-dependent anthocyanin ***33 regulates the expression of the gene encoding dihydroﬂavonol 4-reductase(DFR),a rate-limiting enzyme in anthocyanin production,both directly and ***33 binds directly to the DFR promoter to repress its expression and also interferes with the MBW complex through interacting with PAP1 to indirectly inﬂuence DFR transcriptional ***�Pi conditions,PHR1 interacts with WRKY33,and the protein level of WRKY33 decreases;the repression of DFR expression by WRKY33 is thus attenuated,leading to anthocyanin accumulation in *** genetic and biochemical assays suggest that PHR1 is also involved in regulating factors that affect WRKY33 protein *** together,ourfindings reveal that Pi starvation represses WRKY33,a repressor of anthocyanin biosynthesis,tofinely tune anthocyanin ***‘‘double-negative logic’’regulation of phosphorus-status-dependent anthocyanin biosynthesis is required for the mainte-nance of plant metabolic homeostasis during acclimation to Pi starvation.

关键词： WRKY33 phosphate signaling PHR1 Arabidopsis thaliana anthocyanins

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Improving error-correcting capability in DNA digital storage via soft-decision decoding

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National Science Review 2024年第2期11卷 135-144页

作者：丁璐璐伍世刚候志浩李阿伦许亚苹冯虎潘玮华阮珏 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 Guangdong provincial key laboratory of Plant Molecular Breeding State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesSouth China Agricultural University

Error-correcting codes(ECCs) employed in the state-of-the-art DNA digital storage(DDS) systems suffer from a trade-off between error-correcting capability and the proportion of redundancy. To address this issue, in this study, we introduce soft-decision decoding approach into DDS by proposing a DNA-specific error prediction model and a series of novel strategies. We demonstrate the effectiveness of our approach through a proof-of-concept DDS system based on Reed-Solomon(RS) code, named as Derrick. Derrick shows significant improvement in error-correcting capability without involving additional redundancy in both in vitro and in silico experiments, using various sequencing technologies such as Illumina, Pac Bio and Oxford Nanopore Technology(ONT). Notably, in vitro experiments using ONT sequencing at a depth of 7× reveal that Derrick, compared with the traditional hard-decision decoding strategy, doubles the error-correcting capability of RS code, decreases the proportion of matrices with decoding-failure by 229-fold, and amplifies the potential maximum storage volume by impressive 32 388-fold. Also, Derrick surpasses ‘state-of-the-art' DDS systems by comprehensively considering the information density and the minimum sequencing depth required for complete information recovery. Crucially, the soft-decision decoding strategy and key steps of Derrick are generalizable to other ECCs' decoding algorithms.

关键词： DNA digital storage (DDS) error-correcting code (ECC) soft-decision decoding error-correcting capability storage volume

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Protein Disulfide Isomerase and Its Potential Function on Endoplasmic Reticulum Quality Control in Diatom Phaeodactylum tricornutum

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Phyton-International Journal of Experimental Botany 2024年第1期93卷 137-150页

作者： Yanhuan Lin Hua Du Zhitao Ye Shuqi Wang Zhen Wang Xiaojuan Liu Zhangzhou institute of Technology ZhangzhouChina Guangdong provincial key laboratory of Marine biotechnology Guangdong Provincial Key Laboratory of Marine Disaster Prediction and PreventionCollege of SciencesShantou UniversityShantouChina

PDI is a molecular chaperone and plays an important role in Endoplasmic Reticulum quality control (ERQC).PDI participates in the refolding of the misfolded/unfolded proteins to maintain cellular homeostasis under differentstresses. However, bioinformatic characteristics and potential functions of PDIs in diatom Phaeodactylumtricornutum (Pt) are still unknown so far. Hence, the genome-wide characteristics of PtPDI proteins in P. tricornutumwere first studied via bioinformatic and transcriptomic methods. 42 PtPDI genes were identified from thegenome of P. tricornutum. The motif, protein structure, classification, number of introns, phylogenetic relationship,and the expression level of 42 PtPDI genes under the tunicamycin stress were analyzed. A pair of tandemduplicated genes (PtPDI15 and PtPDI18) was observed in P. tricornutum. The 42 PtPDIs with different genecharacteristics were divided into three independent clades, indicating different evolutional relationships and functionsof these PtPDIs. The 14 up-regulated PtPDI genes under the tunicamycin treatment might have a positiveeffect on the ER quality control of the unfolded/misfolded proteins, while the 7 down-regulated PtPDIs mightnegatively affect the ERQC. The characteristics of all 42 PtPDIs and their proposed working model here providea comprehensive understanding of the PtPDIs gene family. The differential expression of 21 PtPDIs will be usefulfor further functional study in the ERQC.

关键词： Protein disulfide isomerase gene family Endoplasmic Reticulum quality control Phaeodactylum tricornutum

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Underground communication:Long non-coding RNA signaling in the plant rhizosphere

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Plant Communications 2024年第7期5卷 28-51页

作者： Muhammad Fahad Leeza Tariq Sajid Muhammad Liang Wu Hainan institute Zhejiang UniversitySanyaHainan 572000China Zhejiang provincial key laboratory of Crop Genetic Resources College of Agriculture and BiotechnologyZhejiang UniversityHangzhouZhejiang 310058China National key laboratory for Rice Biology Institute of BiotechnologyZhejiang UniversityHangzhou 310058China

Long non-coding RNAs(lncRNAs)have emerged as integral gene-expression regulators underlying plant growth,development,and *** adapt to the heterogeneous and dynamic rhizosphere,plants use interconnected regulatory mechanisms to optimally fine-tune gene-expression-governing interactions with soil biota,as well as nutrient acquisition and heavy metal ***,high-throughput sequencing has enabled the identification of plant lncRNAs responsive to rhizosphere biotic and abiotic ***,we examine lncRNA biogenesis,classification,and mode of action,highlighting the functions of lncRNAs in mediating plant adaptation to diverse rhizosphere *** then discuss studies that reveal the significance and target genes of lncRNAs during developmental plasticity and stress responses at the rhizobium interface.A comprehensive understanding of specific lncRNAs,their regulatory targets,and the intricacies of their functional interaction networks will provide crucial insights into how these transcriptomic switches fine-tune responses to shifting rhizosphere *** ahead,we foresee that single-cell dissection of cell-type-specific lncRNA regulatory dynamics will enhance our understanding of the precise developmental modulation mechanisms that enable plant rhizosphere *** future challenges through multi-omics and genetic approaches will more fully reveal the integral roles of lncRNAs in governing plant adaptation to the belowground environment.

关键词： biotic and abiotic cues heavy metals long non-coding RNAs nutrients phytoremediation rhizosphere microbiome

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Effect of sample temperature on femtosecond laser ablation of copper

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Chinese Physics B 2024年第2期33卷 377-385页

作者：党伟杰陈雨桐陈安民金明星 institute of Atomic and Molecular Physics Jilin UniversityChangchun 130012China jilin provincial key laboratory of Applied Atomic and Molecular Spectroscopy Jilin UniversityChangchun 130012China

We conduct an experimental study supported by theoretical analysis of single laser ablating copper to investigate the interactions between laser and material at different sample temperatures,and predict the changes of ablation morphology and lattice *** investigating the effect of sample temperature on femtosecond laser processing,we conduct experiments on and simulate the thermal behavior of femtosecond laser irradiating copper by using a two-temperature *** simulation results show that both electron peak temperature and the relaxation time needed to reach equilibrium increase as initial sample temperature *** the sample temperature rises from 300 K to 600 K,the maximum lattice temperature of the copper surface increases by about 6500 K under femtosecond laser irradiation,and the ablation depth increases by 20%.The simulated ablation depths follow the same general trend as the experimental *** work provides some theoretical basis and technical support for developing femtosecond laser processing in the field of metal materials.

关键词： femtosecond laser two-temperature model sample temperature ablation depth

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Direct Observation on H-Elimination Enhancement from C_(2)H_(4) through Non-Adiabatic Process by Femtosecond Laser Induced Coulomb Explosion

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Chinese Physics Letters 2024年第5期41卷 17-22页

作者：金无维王春成赵晓戈杨译章任殿相刘泽槿李孝开罗嗣佐丁大军 institute of Atomic and Molecular Physics Jilin UniversityChangchun 130012China jilin provincial key laboratory of Applied Atomic and Molecular Spectroscopy Jilin UniversityChangchun 130012China

Ethylene, the simplest model of a carbon-carbon double bond system, is pivotal in numerous chemical and biological processes. By employing intense infrared laser pump-probe techniques alongside coincidence measurements, we investigate the ultrafast non-adiabatic dynamics involved in the breakage of carbon-carbon double bonds and hydrogen elimination in dissociation of ethylene. Our study entails analyzing the dynamic kinetic energy release spectra to assess three bond-breaking scenarios, movements of nuclei, and structural changes around the carbon atoms. This allows us to evaluate the relaxation dynamics and characteristics of various dissociative states. Notably, we observe a significant rise in the yield of fragments resulting from C–H bond breakage with the delay time extended, suggesting non-adiabatic coupling through conical intersections from C–C bond breakage as a probable cause.

关键词： pump Femto adiabatic

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A novel semi-dominant allele of the transmembrane NAC transcription factor ZmNTL2 reduces the size of multiple maize organs

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The Crop Journal 2024年第3期12卷 676-687页

作者： Chuan Li Yun Bai Yuwei Hou Siyu Wang Yue Xin Tao Yu Jing Wang Xiaowei Liu Hongyang Yi Chao Xia Hai Lan Moju Cao State key laboratory of Crop Gene Exploration and Utilization in Southwest China Maize Research InstituteSichuan Agricultural UniversityChengdu 611130SichuanChina jilin Engineering Research Center for Crop biotechnology Breeding College of Plant ScienceJilin UniversityChangchun 130012JilinChina

Maize plant architecture influences planting density and,in turn,grain *** of the plant architecture-related traits can be described as organ *** describe a miniature maize mutant,Tiny plant 4(Tip4),which exhibits reduced size of multiple organs and exhibits a semi-dominant monofactorial inheritance *** cloning confirmed that a 4-bp deletion in the NAC TF with transmembrane motif 1-Like(NTL)gene ZmNTL2,denoted as ZmNTL2^(Δ),confers the Tip4 ***-PCR showed that ZmNTL2 was expressed in all tested ***2 functions as a transcriptional activator and is located in both the nucleus and *** mutation does not affect the mRNA abundance of ZmNTL2 locus,but it does result in the loss of transmembrane domain and confines the ZmNTL2^(Δ)protein to the *** out ZmNTL2 has no effect on maize organ size development,indicating that the 4-bp deletion might be a gain-of-function mutation in organ size *** transcriptome sequencing with cytokinin and auxin content determination suggests that the decreased organ size may be possibly mediated by changes in hormone homeostasis.

关键词： Organ size c-ray mutagenesis Membrane-bound NAC TF Hormone homeostasis Maize

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The OsBZR1-OsSPX1/2 module fine-tunes the growth-immunity trade-off in adaptation to phosphate availability in rice

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Molecular Plant 2024年第2期17卷 258-276页

作者： Yuqing He Yao Zhao Jitao Hu Lanlan Wang Linying Li Xueying Zhang Zhongjing Zhou Lili Chen Hua Wangl Jiaoyu Wang Gaojie Hong State key laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of agro-Products Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang ProvinceInstitute of Virology and BiotechnologyZhejiang Academy of Agricultural SciencesHangzhou 310021P.R.China key laboratory of Traceability for agricultural Genetically Modified Organisms Ministry of Agriculture and Rural AffairsHangzhou 310021P.R.China College of Life Sciences Zhejiang Sci-Tech UniversityHangzhou 310018P.R.China State key laboratory for Managing Biotic and Chemical Threats to the Qualty and Safety of agro-products Zhejang Academy of Agricultural SciencesHangzhou 310021P.R.China State key laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of agro-Products Key Labory of Biotechnology in Plant Protection of MOA of China and Zhejiang ProvinceInstitute of Plant Protection and MicrobiologyZhejiang Academy of Agricultural SciencesHangzhou 310021P.R.China

The growth-promoting hormones brassinosteroids(BRs)and their key signaling component BZR1 play a vital role in balancing normal growth and defense ***,we discovered that BRs and OsBZR1 up-regulated sakuranetin accumulation and conferred basal defense against Magnaporthe oryzae infection under normal *** shortages,including phosphate(Pi)deficiency,potentially disrupt this growth-defense ***1 and OsSPX2 have been reported to sense Pi concentration and interact with the Pi signal mediator OsPHR2,thus regulating Pi starvation *** this study,we discovered that OsSPX1/2 interacts with OsBZR1 in both Pi-sufficient and Pi-deficient conditions,inhibit-ing BR-responsive *** Pi is sufficient,OsSPX1/2 is captured by OsPHR2,enabling most of OsBzR1 to promote plant growth and maintain basal *** response to Pi starvation,more OsSPX1/2 is released from OsPHR2 to inhibit OsBZR1 activity,resulting in slower ***,our study reveals that the OsBZR1-SPX1/2 module balances the plant growth-immunity trade-off in *** Y.,Zhao Y.,Hu J.,Wang L.,Li L.,Zhang X.,Zhou Z.,Chen L.,Wang H.,Wang J.,and Hong G.(2024).The OsBZR1-OsSPX1/2 module fine-tunes the growth-immunity trade-off in adaptation to phosphate availability in esponse to Pi availability.

关键词： immunity maintain adaptation

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Expansion and improvement of ChinaMu by MuT-seq and chromosome-level assembly of the Mu-starter genome

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Journal of Integrative Plant Biology 2024年第4期66卷 645-659页

作者： Lei Liang Yuancong Wang Yanbin Han Yicong Chen Mengfei Li Yibo Wu Zeyang Ma Han Zhao Rentao Song State key laboratory of Maize Bio-breeding Frontiers Science Center for Molecular Design BreedingJoint International Research Laboratory of Crop Molecular BreedingNational Maize Improvement CenterCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijing 100091China institute of Crop Germplasm and biotechnology Jiangsu Provincial Key Laboratory of AgrobiologyJiangsu Academy of Agricultural SciencesNanjing 210014China Sanya institute of China agricultural University Sanya 572025China Hainan Yazhou Bay Seed laboratory Sanya 572025China

ChinaMu is the largest sequence-indexed Mutator(Mu)transposon insertional library in maize(Zea mays).In this study,we made significant improvements to the size and quality of the ChinaMu *** developed a new Mu-tag isolation method Mu-Tn5-seq(MuT-seq).Compared to the previous method used by ChinaMu,MuT-seq recovered 1/3 more germinal insertions,while requiring only about 1/14 of the sequencing volume and 1/5 of the experimental *** MuT-seq,we identified 113,879 germinal insertions from 3,168 Mu-active F1 *** also assembled a high-quality genome for the Mu-active line Mu-starter,which harbors the initial active MuDR element and was used as the pollen donor for the mutation *** the Mu-starter genome,we recovered 33,662(15.6%)additional germinal insertions in 3,244(7.4%)genes in the Mu-starter *** Mu-starter genome also improved the assignment of 117,689(54.5%)germinal *** newly upgraded ChinaMu dataset currently contains 215,889 high-quality germinal *** insertions cover 32,224 pan-genes in the Mu-starter and B73Ref5 genomes,including 23,006(80.4%)core genes shared by the two *** a test model,we investigated Mu insertions in the pentatricopeptide repeat(PPR)superfamily,discovering insertions for 92%(449/487)of PPR genes in ChinaMu,demonstrating the usefulness of ChinaMu as a functional genomics resource for maize.

关键词： ChinaMu Mutator MuT-seq PPR gene Zea mays

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