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Dynamics and genetic regulation of macronutrient concentrations during grain development in maize

Journal of Integrative Agriculture 2024年第3期23卷 781-794页

作者： Pengcheng Li Shuangyi Yin Yunyun wang Tianze Zhu Xinjie Zhu minggang Ji wenye Rui Houmiao wang Chenwu Xu Zefeng Yang Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant functional genomics Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Agricultural CollegeYangzhou UniversityYangzhou 225009China Jiangsu Co-lnnovation center for modern Production Technology of Grain Crops Yangzhou UniversityYangzhou 225009China

Nitrogen(N), phosphorus(P), and potassium(K) are essential macronutrients that are crucial not only for maize growth and development, but also for crop yield and quality. The genetic basis of macronutrient dynamics and accumulation during grain filling in maize remains largely unknown. In this study, we evaluated grain N, P, and K concentrations in 206 recombinant inbred lines generated from a cross of DH1m and T877 at six time points after pollination. we then calculated conditional phenotypic values at different time intervals to explore the dynamic characteristics of the N, P, and K concentrations. Abundant phenotypic variations were observed in the concentrations and net changes of these nutrients. Unconditional quantitative trait locus(QTL) mapping revealed 41 non-redundant QTLs, including 17, 16, and 14 for the N, P, and K concentrations, respectively. Conditional QTL mapping uncovered 39 non-redundant QTLs related to net changes in the N, P, and K concentrations. By combining QTL, gene expression, co-expression analysis, and comparative genomic data, we identified 44, 36, and 44 candidate genes for the N, P, and K concentrations, respectively, including GRmZm2G371058 encoding a Doftype zinc finger DNA-binding family protein, which was associated with the N concentration, and GRmZm2G113967encoding a CBL-interacting protein kinase, which was related to the K concentration. The results deepen our understanding of the genetic factors controlling N, P, and K accumulation during maize grain development and provide valuable genes for the genetic improvement of nutrient concentrations in maize.

关键词： maize nutrient concentration unconditional QTL mapping conditional QTL mapping dynamic trait

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Combining QTL mapping and multi-Omics Identify Candidate Genes for Nutritional Quality Traits during Grain Filling Stage in maize

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Phyton-International Journal of Experimental Botany 2024年第7期93卷 1441-1453页

作者： Pengcheng Li Tianze Zhu Yunyun wang Shuangyi Yin Xinjie Zhu minggang Ji wenye Rui Houmiao wang Zefeng Yang Chenwu Xu Jiangsu Key Laboratory of Crop Genetics and Physiology Key Laboratory of Plant Functional Genomics of the Ministry of EducationJiangsu Key Laboratory of Crop Genomics and Molecular BreedingAgricultural College of Yangzhou UniversityYangzhou225009China Jiangsu Co-Innovation center for modern Production Technology of Grain Crops Yangzhou UniversityYangzhou225009China

The nutritional composition and overall quality of maize kernels are largely determined by the key chemical com-ponents:protein,oil,and ***,the genetic basis underlying these nutritional quality traits during grainﬁlling remains poorly *** this study,the concentrations of protein,oil,and starch were studied in 204 recombinant inbred lines resulting from a cross between DH1m and T877 at four different stages *** the traits exhibited considerable phenotypic *** the grain-ﬁlling stage,the levels of protein and starch content generally increased,whereas oil content decreased,with signiﬁcant changes observed between 30 and 40 days after *** trait locus(QTL)mapping was conducted and a total of 32 QTLs,comprising 14,12,and 6 QTLs for grain protein,oil,and starch content were detected,*** QTLs were consistently detectable across different time *** integrating QTL analysis,glo-bal gene expression proﬁling,and comparative genomics,we identiﬁed 157,86,and 54 differentially expressed genes harboring nonsynonymous substitutions between the parental lines for grain protein,oil,and starch con-tent,*** gene function annotation prioritized 15 candidate genes potentially involved in reg-ulating grain quality traits,including those encoding transcription factors(NAC,mADS-box,bZIP,and mYB),cell wall invertase,cellulose-synthase-like protein,cell division cycle protein,trehalase,auxin-responsive factor,and phloem protein *** study offers signiﬁcant insights into the genetic architecture of maize kernel nutritional quality and identiﬁes promising QTLs and candidate genes,which are crucial for the genetic enhance-ment of these traits in maize breeding programs.

关键词： maize protein oil starch QTL mapping candidate genes

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Human ESC-derived vascular cells promote vascular regeneration in a HIF-1α dependent manner

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Protein & Cell 2024年第1期15卷 36-51页

作者： Jinghui Lei Xiaoyu Jiang Daoyuan Huang Ying Jing Shanshan Yang Lingling Geng Yupeng Yan Fangshuo Zheng Fang Cheng weiqi Zhang Juan Carlos Izpisua Belmonte Guang-Hui Liu Si wang Jing Qu Advanced Innovation center for Human Brain Protection National Clinical Research Center for Geriatric DisordersXuanwu Hospital Capital Medical UniversityBeijing 100053China State Key Laboratory of membrane Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China State Key Laboratory of Stem Cell and Reproductive Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China Aging Translational medicine center Intermational Center for Aging and CancerBeijing Municipal Geriatric Medical Research CenterXuanwu HospitalCapital Medical UniversityBeijing 100053China University of Chinese Academy of Sciences Beijing 100049China Institute for Stem Cell and Regeneration CASBeijing 100101China The Fifth People's Hospital of Chongqing Chongqing 400062China Beijing Institute for Stem Cell and Regenerative medicine Beijing 100101China National Laboratory of Biomacromolecules CAs Center for Excellence in BiomacromoleculesInstitute of BiophysicsBeijing 100101China CAS Key Laboratory of Genomic and Precision medicine Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China China National center for Bioinformation Beijing 100101China Sino-Danish College University of Chinese Academy of SciencesBeijing 101408China Sino-Danish center for Education and Research Beijing 101408China Aging Biomarker Consortium China Altos Labs San DiegoCA 92121United State

Hypoxia-inducible factor(HIF-1α),a core transcription factor responding to changes in cellular oxygen levels,is closely associated with a wide range of physiological and pathological ***,its differential impacts on vascular cell types and molecular programs modulating human vascular homeostasis and regeneration remain largely ***,we applied CRISPR/Cas9-mediated gene editing of human embryonic stem cells and directed differentiation to generate HIF-ia-deficient human vascular cells including vascular endothelial cells,vascular smooth muscle cells,and mesenchymal stem cells(msCs),as a platform for discovering cell type-specific hypox-ia-induced response *** comparative molecular profiling across cell types under normoxic and hypoxic conditions,we provide insight into the indispensable role of HIF-1αin the promotion of ischemic vascular *** found human mSCs to be the vascular cell type most susceptible to HIF-1a deficiency,and that transcriptional inactivation of ANKZF1,an effector of HIF-1a,impaired pro-angiogenic ***,our findings deepen the understanding of HIF-ia in human angiogenesis and support further explorations of novel therapeutic strategies of vascular regeneration against ischemic damage.

关键词： HIF-1 human ESC vascular cell regeneration

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Comparisons of Graph-structure Clustering methods for Gene Expression Data

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Acta Biochimica et Biophysica Sinica 2006年第6期38卷 379-384页

作者： Zhuo FANG~1,Lei LIU~(2,4),Jiong YANG~3,Qing-ming LUO~(1*),and Yi-Xue LI~(2*) ~1 Hubei Bioinformatics and molecular Imaging Key Laboratory,College of Life Science and Technology, Huazhong University of Science and Technology,wuhan 430074,China ~2 Shanghai center for Bioinformatics Technology,Shanghai 200235,China ~3 Department of EECS,Case western Reserve University,Cleveland 44106,USA ~4 w.m.keck center for comparative and functional genomics,University of Illinois at Urbana-Champaign,Urbana 61801,USA Hubei Bioinformatics and molecular Imaging Key Laboratory College of Life Science and Technology Huazhong University of Science and TechnologyWuhan 430074 China Shanghai center for Bioinformatics TechnologyShanghai 200235 China w.m. keck center for comparative and functional genomics University of Illinois at Urbana-ChampaignUrbana 61801 USA Department of EECS Case Western Reserve UniversityCleveland 44106 USA

Although many numerical clustering algorithms have been applied to gene expression dataanalysis,the essential step is still biological interpretation by manual *** correlation betweengenetic co-regulation and affiliation to a common biological process is what biologists ***,weintroduce some clustering algorithms that are based on graph structure constituted by biological *** applying a widely used dataset,we compared the result clusters of two of these algorithms in terms ofthe homogeneity of clusters and coherence of annotation and matching *** results show that theclusters of knowledge-guided analysis are the kernel parts of the clusters of Gene Ontology (GO)-Clustersoftware,which contains the genes that are most expression correlative and most consistent with ***,knowledge-guided analysis seems much more applicable than GO-Cluster in a largerdataset.

关键词： clustering expression pattern biological function

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CRL2^(APPBP2)-mediated TSPYL2 degradation counteracts human mesenchymal stem cell senescence

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Science China(Life Sciences) 2024年第3期67卷 460-474页

作者： Daoyuan Huang Qian Zhao Kuan Yang Jinghui Lei Ying Jing Hongyu Li Chen Zhang Shuai ma Shuhui Sun Yusheng Cai Guibin wang Jing Qu weiqi Zhang Si wang Guang-Hui Liu Advanced Innovation centerfor Human Brain Protection National Clinical Research Centerfor Geriatric DisordersXuanwu Hospital Capital Medical UniversityBeijing 100053China State Key Laboratory of Stem Cell and Reproductive Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China Aging Translational medicinecenter International Centerfor Aging and CancerBejing Municipal GeriatricMedical Research CenterXuanwu HospitalCapital Medical UniversityBeijing 100053China State Key Laboratory of membrane Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Beijing Institute for Stem Cell and Regenerative medicine Beijing100101China CAS Key Laboratory of Genomic and Precision medicine Bejing Institute of Genomics and China National Center for BioinformationChinese Academy of SciencesBeijing 100101China Institute for Stem Cell and Regeneration CASBeijing 100101China The Fifth People's Hospital of Chongqing Chongqing 400062China Sino-Danish Cllege University of Chinese Academy of SciencesBeijing101408China National Laboratory of Biomacromolecules CAS Center for Excelence in BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing100101China State Key Laboratory of Proteomics Beijing Proteome Research CenterNational Center for Protein Sciences(Beijing)Beijing Institute of LifeomicsBeijing 102206China

Cullin-RING E3 ubiquitin ligases(CRLs),the largest family of multi-subunit E3 ubiquitin ligases in eukaryotic cells,represent core cellular machinery for executing protein degradation and maintaining ***,we asked what roles Cullin proteins play in human mesenchymal stem cell(hmSC)homeostasis and *** this end,we conducted a comparative aging phenotype analysis by individually knocking down Cullin members in three senescence models:replicative senescent hmSCs,Hutchinson-Gilford Progeria Syndrome hmSCs,and werner syndrome *** all family members,we found that CUL2 deficiency rendered hmSCs the most susceptible to *** investigate CUL2-specific underlying mechanisms,we then applied CRISPR/Cas9-mediated gene editing technology to generate CUL2-deficient human embryonic stem cells(hESCs).when we differentiated these into h mSCs,we found that CUL2 deletion markedly accelerates hmSC ***,we identified that CUL2 targets and promotes ubiquitin proteasome-mediated degradation of TSPYL2(a known negative regulator of proliferation)through the substrate receptor protein APPBP2,which in turn downregulates one of the canonical aging marker-P21^(waf1/cip1),and thereby delays *** work provides important insights into how CRL2^(APPBP2)-mediated TSPYL2 degradation counteracts hmSC senescence,providing a molecular basis for directing intervention strategies against aging and aging-related diseases.

关键词： Cullins stem cell senescence aging proteostasis ubiquitination APPBP2 TSPYL2

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Identification and fine mapping of a fertility restorer gene for wild abortive cytoplasmic male sterility in the elite indica rice non-restorer line 9311

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The Crop Journal 2023年第3期11卷 887-894页

作者： Zuopeng Xu Yuanyue Du Xixu Li Ruixuan wang Zhi'ai Chen Xiangqiang Zhao Qiaoquan Liu Shuzhu Tang Honggen Zhang 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 Agricultural CollegeYangzhou UniversityYangzhou 225009JiangsuChina Jiangsu Co-Innovation center for modern Production Technology of Grain Crops Yangzhou UniversityYangzhou 225009JiangsuChina School of Life Sciences Nantong UniversityNantong 226019JiangsuChina

The wild abortive(wA)-type cytoplasmic male sterility(CmS)derived from the wild rice species Oryza rufipogon *** used widely in three-line indica *** identification and mapping of restorer of fertility(Rf)genes aided in the development of wA-type *** we report that testcross F1 plants from the wA-type CmS line and 9311 exhibited stainable pollen grains with no seed set,indicating that 9311 carries minor-effect Rfs for wA-type *** developed an advanced backcross population consisting of plants harboring small regions of donor chromosomal segments from 9311 in the wATianfeng A genetic background with moderate seed setting *** analysis showed that the pollen fertility levels of the backcross individuals are governed by a single gene from 9311 that we named Rf19(t).By use of the RICE 40 K gene chip,three introduced segments were identified in the fertile lines,and a candidate region spanning 4.37–8.29 mb on chromosome 1 was identified for Rf19(t).Finally,Rf19(t)was fine-mapped to a region of 90 kb between the DNA marker loci STS1-163 and STS1-183,in which eight ORFs were ***,using relative expression analyses,comparative sequence analyses and functional domain analyses,we identified LOC_Os01g10530 as the most likely candidate gene for Rf19(t).Furthermore,Rf19(t)was found to function in fertility restoration,most probably by regulating the degradation of m RNA transcribed from the mitochondrial gene *** results increase our knowledge of fertility restoration in wA-type CmS lines and will facilitate the development of high-quality pairs of wAtype CmS and maintainer lines.

关键词： Rice wA-type CmS Restorer of fertility(Rf)gene Gene mapping

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comparative transcriptome analysis between rhesus macaques(macaca mulatta) and crab-eating macaques(m. fascicularis)

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Zoological Research 2024年第2期45卷 299-310页

作者： Yu-Xiang mao Yamei Li Zikun Yang Ning Xu Shilong Zhang Xuankai wang Xiangyu Yang Qiang Sun Yafei mao Institute of Neuroscience State Key Laboratory of NeuroscienceCenter for Excellence in Brain Science&Intelligence TechnologyChinese Academy of SciencesShanghai 200031China Shanghai center for Brain Science and Brain-Inspired Intelligence Technology Shanghai 201210China University of Chinese Academy of Sciences Beijing 100049China Key Laboratory of Genetic Evolution&Animal models Chinese Academy of SciencesKunmingYunnan 650201China Bio-X Institutes Key Laboratory for the Genetics of Developmental and Neuropsychiatric DisordersMinistry of EducationShanghai Jiao Tong UniversityShanghai 200030China Zhiyuan College Shanghai Jiao Tong UniversityShanghai 200240China center for Genomic Research International Institutes of MedicineFourth Affiliated HospitalZhejiang UniversityYiwuZhejiang 322000China

Understanding gene expression variations between species is pivotal for deciphering the evolutionary diversity in phenotypes. Rhesus macaques(macaca mulatta, mmU)and crab-eating macaques(m. fascicularis, mFA) serve as crucial nonhuman primate biomedical models with different phenotypes. To date, however, large-scale comparative transcriptome research between these two species has not yet been fully explored. Here, we conducted systematic comparisons utilizing newly sequenced RNA-seq data from84 samples(41 mFA samples and 43 mmU samples)encompassing 14 common tissues. Our findings revealed a small fraction of genes(3.7%) with differential expression between the two species, as well as 36.5% of genes with tissue-specific expression in both macaques. Comparison of gene expression between macaques and humans indicated that 22.6% of orthologous genes displayed differential expression in at least two tissues. moreover,19.41% of genes that overlapped with macaque-specific structural variants showed differential expression between humans and macaques. Of these, the FAm220A gene exhibited elevated expression in humans compared to macaques due to lineage-specific duplication. In summary,this study presents a large-scale transcriptomic comparison between mmU and mFA and between macaques and humans. The discovery of gene expression variations not only enhances the biomedical utility of macaque models but also contributes to the wider field of primate genomics.

关键词： Crab-eating macaques Rhesus macaques comparative transcriptomics Biomedical models Nonhuman primates RNA-seq Duplicated genes

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Coordinated transcriptional and post-transcriptional epigenetic regulation during skeletal muscle development and growth in pigs

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Journal of Animal Science and Biotechnology 2023年第2期14卷 564-577页

作者： Du Zhang Shumei wu Xinxin Zhang Shuqiang Ren Zhonglin Tang Fei Gao Genome Analysis Laboratory of the ministry of Agriculture Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518000China College of Animal Sciences South China Agricultural UniversityGuangdong Provincial Key Lab of Agro-animal Genomics and Molecular BreedingNational Engineering Research Center for Breeding Swine IndustryGuangzhou 510642China Kunpeng Institute of modern Agriculture at Foshan Chinese Academy of Agricultural SciencesFoshan 528226China GuangXi Engineering Centre for Resource Development of Bama Xiang Pig Bama 547500China comparative Pediatrics and Nutrition Department of Veterinary and Animal SciencesFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark.

Background:N6-methyladenosine(m^(6)A)and DNA 5-methylcytosine(5mC)methylation plays crucial roles in diverse biological processes,including skeletal muscle development and *** studies unveiled a potential link between these two systems,implicating the potential mechanism of coordinated transcriptional and post-transcrip-tional regulation in porcine prenatal myogenesis and postnatal skeletal muscle ***:Immunofluorescence and co-IP assays were carried out between the 5mC writers and m^(6)A writers to investigate the molecular basis ***-scale in-house transcriptomic data were compiled for applying weighted correlation network analysis(wGCNA)to identify the co-expression patterns of m^(6)A and 5mC regulators and their potential role in pig ***-genome bisulfite sequencing(wGBS)and methylated RNA immu-noprecipitation sequencing(meRIP-seq)were performed on the skeletal muscle samples from Landrace pigs at four postnatal growth stages(days 30,60,120 and 180).Results:Significantly correlated expression between 5mC writers and m^(6)A writers and co-occurrence of 5mC and m^(6)A modification were revealed from public datasets of C2C12 *** protein-protein interactions between the DNA methylase and the m^(6)A methylase were observed in mouse myoblast ***,by analyzing tran-scriptome data comprising 81 pig skeletal muscle samples across 27 developmental stages,we identified a 5mC/m^(6)A epigenetic module eigengene and decoded its potential functions in pre-or post-transcriptional regulation in postnatal skeletal muscle development and growth of *** integrative multi-omics analyses on the wGBS methylome data and meRIP-seq data for both m^(6)A and gene expression profiles revealed a genome/transcriptome-wide correlated dynamics and co-occurrence of 5mC and m^(6)A modifications as a consequence of 5mC/m^(6)A crosstalk in the postnatal myogenesis progress of ***,we identified a group of myogenesis-relat

关键词： DNA methylation Epigenetic modification Epigenomic analysis 5mC regulators m^(6)A methylation m^(6)A regulators myogenesis

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YPED: An Integrated Bioinformatics Suite and Database for mass Spectrometry-based Proteomics Research

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genomics, Proteomics & Bioinformatics 2015年第1期13卷 25-35页

作者： Christopher m.Colangelo mark Shifman Kei-Hoi Cheung Kathryn L.Stone Nicholas J.Carriero Erol E.Gulcicek TuKiet T.Lam Terence wu Robert D.Bjornson Can Bruce Angus C.Nairn Jesse Rinehart Perry L.miller Kenneth R.williams w.m.keck Foundation Biotechnology Resource Laboratory School of Medicine Yale University Department of molecular Biophysics & Biochemistry Yale University Yale center for medical Informatics School of Medicine Yale University Department of Anesthesiology School of Medicine Yale University Department of Emergency medicine School of Medicine Yale University VA Connecticut Healthcare System w.m. keck Foundation Biotechnology Resource Laboratory School of Medicine Yale University Department of Computer Science Yale University Yale center for Genome Analysis West Campus Yale University Yale west Campus Analytical Core West Campus Yale University Yale Bioinformatics Resource School of Medicine Yale University Department of Psychiatry School of Medicine Yale University Department of Cellular & molecular Physiology School of Medicine Yale University Systems Biology Institute Yale University

we report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database（YPED） that is used by investigators at more than 300 institutions worldwide. YPED meets the data management, archival, and analysis needs of a high-throughput mass spectrometry-based proteomics research ranging from a singlelaboratory, group of laboratories within and beyond an institution, to the entire proteomics community. The current version is a significant improvement over the first version in that it contains new.m.dules for liquid chromatography–tandem mass spectrometry（LC–mS/mS） database search results, label and label-free quantitative proteomic analysis, and several scoring outputs for phosphopeptide site localization. In addition, we have added both peptide and protein comparative analysis tools to enable pairwise analysis of distinct peptides/proteins in each sample and of overlapping peptides/proteins between all samples in multiple datasets. we have also implemented a targeted proteomics module for automated multiple reaction monitoring（mRm）/selective reaction monitoring（SRm） assay development. we have linked YPED＇s database search results and both label-based and label-free fold-change analysis to the Skyline Panorama repository for online spectra visualization. In addition, we have built enhanced functionality to curate peptide identifications into an mS/mS peptide spectral library for all of our protein database search identification results.

关键词： Proteomics Database Bioinformatics mass spectrometry Repository Spectral library

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Root-derived long-distance signals trigger ABA synthesis and enhance drought resistance in Arabidopsis

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Journal of Genetics and genomics 2024年第7期51卷 749-761页

作者： Qian-Qian Liu Jin-Qiu Xia Jie wu Yi Han Gui-Quan Zhang Ping-Xia Zhao Cheng-Bin Xiang Division of Life Sciences and medicine Division of Molecular&Cell BiophysicsHefei National Science Center for Interdisciplinary Sciences at the MicroscaleUniversity of Science and Technology of ChinaThe Innovation Academy of Seed DesignChinese Academy of SciencesHefeiAnhui 230027China College of Life Sciences Anhui Agricultural UniversityHefeiAnhui 230036China College of Agronomy South China Agricultural UniversityGuangzhouGuangdong 510642China School of Biology and Basic medical Sciences Soochow UniversitySuzhouJiangsu 215123China

Vascular plants have evolved intricate long-distance signaling mechanisms to cope with environmental stress,with reactive oxygen species(ROS)emerging as pivotal systemic signals in plant stress ***,the exact role of ROS as root-to-shoot signals in the drought response has not been *** this study,we reveal that compared with wild-type plants,ferric reductase defective 3(frd3)mutants exhibit enhanced drought resistance concomitant with elevated NINE-CIS-EPOXYCAROTENOID DIOXYGENASE 3(NCED3)transcript levels and abscisic acid(ABA)contents in leaves as well as increased hydrogen peroxide(H_(2)O_(2))levels in roots and *** experiments distinctly illustrate that drought resistance can be conferred by the frd3 rootstock regardless of the scion genotype,indicating that long-distance signals originating from frd3 roots promote an increase in ABA levels in ***,the drought resistance conferred by the frd3 mutant rootstock is weakened by the CAT2-overexpressing scion,suggesting that H_(2)O_(2)may be involved in long-distance ***,the results of comparative transcriptome and proteome analyses support the drought resistance phenotype of the frd3 *** together,our findings substantiate the notion that frd3 root-derived long-distance signals trigger ABA synthesis in leaves and enhance drought resistance,providing new evidence for root-to-shoot long-distance signaling in the drought response of plants.

关键词： frd3 Drought resistance Root-to-shoot long-distance signals Reactive oxygen species(ROS) H_(2)O_(2) Iron ABA

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