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Cryptic divergences and repeated hybridizations within the endangered “living fossil” dove tree(Davidia involucrata) revealed by whole genome resequencing

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Plant Diversity 2024年第2期46卷 169-180页

作者： Yumeng Ren Lushui Zhang Xuchen Yang Hao Lin Yupeng Sang Landi Feng Jianquan Liu Minghui Kang key laboratory of Bio-resource and Eco-environment of Ministry of Education College of Life SciencesSichuan UniversityChengdu 610065China State key laboratory of Herbage Improvement and Grassland Agro-ecosystem College of EcologyLanzhou UniversityLanzhou 730000China Guangdong Provincial key laboratory of Plant Adaptation and molecular Design Guangzhou Key Laboratory of Crop Gene EditingInnovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhou 510006China

The identification and understanding of cryptic intraspecific evolutionary units(lineages) are crucial for planning effective conservation strategies aimed at preserving genetic diversity in endangered ***, the factors driving the evolution and maintenance of these intraspecific lineages in most endangered species remain poorly understood. In this study, we conducted resequencing of 77 individuals from 22 natural populations of Davidia involucrata, a “living fossil” dove tree endemic to central and southwest China. Our analysis revealed the presence of three distinct local lineages within this endangered species, which emerged approximately 3.09 and 0.32 million years ago. These divergence events align well with the geographic and climatic oscillations that occurred across the distributional ***, we observed frequent hybridization events between the three lineages, resulting in the formation of hybrid populations in their adjacent as well as disjunct regions. These hybridizations likely arose from climate-driven population expansion and/or long-distance gene flow. Furthermore, we identified numerous environment-correlated gene variants across the total and many other genes that exhibited signals of positive evolution during the maintenance of two major local lineages. Our findings shed light on the highly dynamic evolution underlying the remarkably similar phenotype of this endangered species. Importantly, these results not only provide guidance for the development of conservation plans but also enhance our understanding of evolutionary past for this and other endangered species with similar histories.

关键词： Davidia involucrata Cryptic lineage Hybridization Population genomics Positive evolution

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The gene encoding flavonol synthase contributes to lesion mimic in wheat

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The Crop Journal 2024年第3期12卷 814-825页

作者： Tingting Dong Hongchun Xiong Huijun Guo Yongdun Xie Linshu Zhao Jiayu Gu Huiyuan Li Shirong Zhao Yuping Ding Xiyun Song Luxiang Liu college of life sciences Key Laboratory of Major Crop Germplasm Innovation and Application in QingdaoQingdao Agricultural UniversityQingdao 266109ShandongChina State key laboratory of Crop gene resources and Breeding/National Engineering laboratory of Crop molecular Breeding/CAEA Research and development Centre on Nuclear Technology Applications for Irradiation Mutation Breeding Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China

Lesion mimic often exhibits leaf disease-like symptoms even in the absence of pathogen infection,and is characterized by a hypersensitive-response(HR)that closely linked to plant disease *** this,only a few lesion mimic genes have been identified in *** this investigation,a lesion mimic wheat mutant named je0297 was discovered,showing no alteration in yield components when compared to the wild type(WT).Segregation ratio analysis of the F_(2)individuals resulting from the cross between the WT and the mutant revealed that the lesion mimic was governed by a single recessive gene in *** Bulked segregant analysis(BSA)and exome capture sequencing,we mapped the lesion mimic gene designated as lm6 to chromosome *** gene fine mapping using 3315 F_(2)individuals delimited the lm6 within a 1.18 Mb *** this region,we identified 16 high-confidence genes,with only two displaying mutations in ***,one of the two genes,responsible for encoding flavonol synthase,exhibited altered expression *** phenotype analysis of TILLING mutants confirmed that the gene encoding flavonol synthase was indeed the causal gene for *** sequencing analysis revealed that the DEGs between the WT and mutant were significantly enriched in KEGG pathways related to flavonoid biosynthesis,including flavone and flavonol biosynthesis,isoflavonoid biosynthesis,and flavonoid biosynthesis ***,more than 30 pathogen infection-related(PR)genes exhibited upregulation in the *** to this expression pattern,the flavonoid content in je0297 showed a significant decrease in the 4^(th)leaf,accompanied by a notable accumulation of reactive oxygen,which likely contributed to the development of lesion mimic in the *** investigation enhances our comprehension of cell death signaling pathways and provides a valuable gene resource for the breeding of disease-resistant wheat.

关键词： Lesion mimic mutant Wheat gene mapping Flavonol synthase gene Flavonoid

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Phosphorylation of ZmAL14 by ZmSnRK2.2 regulates drought resistance through derepressing ZmROP8 expression

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Journal of Integrative Plant Biology 2024年第7期66卷 1334-1350页

作者： Yalin Wang Jinkui Cheng Yazhen Guo Zhen Li Shuhua Yang Yu Wang Zhizhong Gong State key laboratory of Plant Environmental Resilience Frontiers Science Center for Molecular Design BreedingCollege of Biological SciencesChina Agricultural UniversityBeijing 100193China Center for Crop Functional Genomics and molecular Breeding China Agricultural UniversityBeijing 100193China college of life sciences Institute of Life Science and Green DevelopmentHebei UniversityBaoding 071002China

Drought stress has negative effects on crop growth and *** of transcription factors that regulate the expression of drought-responsive genes is critical for understanding the transcriptional regulatory networks in response to drought,which facilitates the improvement of crop drought ***,we identified an Alfin-like(AL)family gene ZmAL14 that negatively regulates drought *** of ZmAL14 exhibits susceptibility to drought while mutation of ZmAL14 enhances drought *** abscisic acid(ABA)-activated protein kinase ZmSnRK2.2 interacts and phosphorylates ZmAL14 at T38 *** of ZmSnRK2.2 gene decreases drought resistance of maize.A dehydration-induced Rho-like small guanosine triphosphatase gene ZmROP8 is directly targeted and repressed by *** of ZmAL14 by ZmSnRK2.2 prevents its binding to the ZmROP8 promoter,thereby releasing the repression of ZmROP8 *** of ZmROP8 stimulates peroxidase activity and reduces hydrogen peroxide accumulation after drought ***,our study indicates that ZmAL14 is a negative regulator of drought resistance,which can be phosphorylated by ZmSnRK2.2 through the ABA signaling pathway,thus preventing its suppression on ZmROP8 transcription during drought stress response.

关键词： ZmAL14 drought tolerance transcription factor maize

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Antimicrobial resistance characteristics and phylogenetic relationships of pleuromutilin-resistant Enterococcus isolates from different environmental samples along a laying hen production chain

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Journal of Environmental sciences 2024年第3期137卷 195-205页

作者： Cong Lin Yuxuan Feng Xianjun Xie Haoyu Zhang Jie Wu Yixiao Zhu Jing Yu Jingyi Feng Wen Su Shanming Lai Anyun Zhang Animal Disease Prevention and Food Safety key laboratory of Sichuan Province Key Laboratory of Bio-Resource and Eco-Environment of Ministry of EducationCollege of Life SciencesSichuan UniversityChengdu 610065China

Antimicrobial resistance in the laying hen production industry has become a serious public health *** antimicrobial resistance and phylogenetic relationships of the common conditional pathogen Enterococcus along the laying hen production chain have not been systematically clarified.105 Enterococcus isolates were obtained from 115 environmental samples (air,dust,feces,fies,sewage,and soil) collected along the laying hen production chain (breeding chicken,chick,young chicken,and commercial laying hen).These Enterococcus isolates exhibited resistance to some clinically relevant antibiotics,such as tetracycline (92.4%),streptomycin (92.4%),and erythromycin (91.4%),and all strains had multidrug resistance *** genome sequencing characterized 29 acquired antibiotic resistance genes (ARGs) that conferred resistance to 11 classes of antibiotics in 51pleuromutilin-resistant Enterococcus isolates,and lsa(E),which mediates resistance to pleuromutilins,always co-occurred with lnu(B).Alignments with the Mobile genetic Elements database identified four transposons (Tn554,Tn558,Tn6261,and Tn6674) with several ARGs(erm(A),ant(9)-la,fex(A),and optrA) that mediated resistance to many clinically important ***,we identified two new transposons that carried ARGs in the Tn554 family designated as Tn7508 and Tn7492.A complementary approach based on conventional multi-locus sequence typing and whole genome single nucleotide polymorphism analysis showed that phylogenetically related pleuromutilin-resistant Enterococcus isolates were widely distributed in various environments on different production *** results indicate that environmental contamination by antimicrobial-resistant Enterococcus requires greater attention,and they highlight the risk of pleuromutilin-resistant Enterococcus and ARGs disseminating along the laying hen production chain,thereby warranting effective disinfection.

关键词： Antimicrobial resistance Enterococcus Laying hen production chain Pleuromutilin

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Increased long-distance and homo-trans interactions related to H3K27me3 in Arabidopsis hybrids

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Journal of Integrative Plant Biology 2024年第2期66卷 208-227页

作者： Zhaoxu Gao Yanning Su Le Chang Guanzhong Jiao Yang Ou Mei Yang Chao Xu Pengtao Liu Zejia Wang Zewen Qi Wenwen Liu Linhua Sun Guangming He Xing Wang Deng Hang He School of Advanced Agriculture sciences and School of life sciences State Key Laboratory of Protein and Plant Gene ResearchPeking UniversityBeijing 100871China college of Grassland Science Beijing Forestry UniversityBeijing 100083China Peking University Institute of Advanced Agricultural sciences Shandong Laboratory of Advanced Agricultural Sciences in WeifangWeifang 261325China

In plants,the genome structure of hybrids changes compared with their parents,but the effects of these changes in hybrids remain *** reciprocal crosses between Col×C24 and C24×Col in Arabidopsis using high-throughput chromosome conformation capture assay(Hi-C)analysis,we found that hybrid three-dimensional(3D)chromatin organization had more long-distance interactions relative to parents,and this was mainly located in promoter regions and enriched in genes with heterosis-related *** interactions between euchromatin and heterochromatin were increased,and the compartment strength decreased in *** compartment domain(CD)boundaries,the distal interactions were more in hybrids than their *** the hybrids of CURLY LEAF(clf)mutants clfCol×clfC24and clfC24×clfCol,the heterosis phenotype was damaged,and the long-distance interactions in hybrids were fewer than in their parents with lower ***-seq data revealed higher levels of H3K27me3 in the region adjacent to the CD boundary and the same interactional homo-trans sites in the wild-type(WT)hybrids,which may have led to more long-distance *** addition,the differentially expressed genes(DEGs)located in the boundaries of CDs and loop regions changed obviously in WT,and the functional enrichment for DEGs was different between WT and clf in the longdistance interactions and loop *** findings may therefore propose a new epigenetic explanation of heterosis in the Arabidopsis hybrids and provide new insights into crop breeding and yield increase.

关键词： 3D chromatin organization H3K27me3 homo-trans hybrids long-distanceinteractions

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Dt1 inhibits SWEET-mediated sucrose transport to regulate photoperiod-dependent seed weight in soybean

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molecular Plant 2024年第3期17卷 496-508页

作者： Xiaoming Li Zhonghui Chen Haiyang Li Lin Yue Cuirong Tan Hongjie Liu Yilong Hu Yuhua Yang Xiani Yao Lingping Kong Xiang Huangi Bin Yu Chunyu Zhang Yuefeng Guan Baohui Liu Fanjiang Kong Xingliang Hou Guangdong Provincial key laboratory of Applied Botany&State key laboratory of Plant Diversity and Specialty Crops South China Botanical GardenChinese Academyof SciencesGuangzhou510650China Guangdong Provincial key laboratory of Plant Adaptation and molecular Design Guangzhou Key Laboratory of Crop Gene EditingInnovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhou 510006China University of Chinese Academy of sciences Beijing 100049China college of Agronomy and Biotechnology China Agricultural UniversityBeijing 100193China

Soybean is a photoperiod-sensitive short-day crop whose reproductive period and yield are markedly affected by day-length *** weight is one of the key traits determining the soybean yield;how-ever,the prominent genes that control the final seed weight of soybean and the mechanisms underlying the photoperiod's effect on this trait remain poorly *** this study,we identify SwW19 as a major locus controlling soybean seed weight by QTL mapping and determine Dt1,an orthologous gene of Arabidopsis TFL1 that is known to govern the soybean growth habit,as the causal gene of the SW19 *** showed that Dt1 is highly expressed in developing seeds and regulates photoperiod-dependent seed weight in *** analyses revealed that the Dt1 protein physically interacts with the sucrose transporter GmSWEET10a to negatively regulate the import of sucrose from seed coat to the embryo,thus modulating seed weight under long ***,Dt1 does not function in seed development under short days due to its very low ***,we discovered a novel natural allelic variant of Dt1(H4 haplotype)that decouples its pleiotropic effects on seed size and growth habit;i.e.,this variant remains functional in seed development but fails to regulate the stem growth habit of ***,our findings provide new insights into how soybean seed development responds to photoperiod at different latitudes,offering an ideal genetic component for improving soybean's yield by manipulating its seed weightandgrowth habit.

关键词： soybean seed weight photoperiod dt1 sucrose transport

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DDX21 is a new player in co-transcriptional RNA modification and functions

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Science China(life sciences) 2024年第10期67卷 2291-2293页

作者： Chengqi Yi State key laboratory of Protein and Plant gene Research School of Life SciencesPeking UniversityBeijing 100871China Peking-Tsinghua Center for life sciences Peking UniversityBeijing 100871China Department of Chemical Biology and Synthetic and Functional Biomolecules Center College of Chemistry and Molecular EngineeringPeking UniversityBeijing 100871China beijing Advanced Center of RNA Biology(BEACON) Peking UniversityBeijing 100871China

Ever since the first discovery of chemical modifications of RNA in 1951,researchers have been captivated by the diverse types of modifications,their associated enzymes and proteins(writers,erasers,or readers),and their downstream functional implications(Song and Yi,2017).Among the over 170 distinct types of RNA modifications identified thus far,N^(6)-methyladenosine(m6A)stands out as the most prevalent internal modification on mammalian messenger RNA(mRNA)(Song and Yi,2017).

关键词： modification player stands

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Green light mediates atypical photomorphogenesis by dual modulation of Arabidopsis phytochromes B and A

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Journal of Integrative Plant Biology 2024年第9期66卷 1915-1933页

作者： Miqi Xu Yi‐Yuan Wang Yujie Wu Xiuhong Zhou Ziyan Shan Kunying Tao Kaiqiang Qian Xuncheng Wang Jian Li Qingqing Wu Xing Wang Deng Jun‐Jie Ling National Engineering laboratory of Crop Stress Resistance Breeding School of Life SciencesAnhui Agricultural UniversityHefei 230036China Province key laboratory of resource Insect Biology and Innovative Utilization School of Life SciencesAnhui Agricultural UniversityHefei 230036China Biotechnology Center State Key Laboratory of Tea Plant Biology and UtilizationSchool of Tea and Food Sciences and TechnologyAnhui Agricultural UniversityHefei 230036China beijing key laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China Institute of Plant and Environment ProtectionBeijing Academy of Agriculture and Forestry SciencesBeijing 100097China college of life sciences Nanjing Normal UniversityNanjing 210023China State key laboratory of Protein and Plant gene Research Peking–Tsinghua Center for Life SciencesSchool of Advanced Agriculture Sciencesand School of Life SciencesPeking UniversityBeijing 100871China State key laboratory of Wheat Improvement Shandong Laboratory of Advanced Agricultural Sciences at WeifangPeking University Institute of Advanced Agricultural SciencesWeifang 261000China

Although green light(GL)is located in the middle of the visible light spectrum and regulates a series of plant developmental processes,the mechanism by which it regulates seedling development is largely *** this study,we demonstrated that GL promotes atypical photomorphogenesis in Arabidopsis thaliana via the dual regulations of phytochrome B(phyB)and *** the Pr-to-Pfr conversion rates of phyB and phyA under GL were lower than those under red light(RL)in a fluence rate-dependent and time-dependent manner,long-term treatment with GL induced high Pfr/Pr ratios of phyB and ***,GL induced the formation of numerous small phyB photobodies in the nucleus,resulting in atypical photomorphogenesis,with smaller cotyledon opening angles and longer hypocotyls in seedlings compared to *** abundance of phyA significantly decreased after short-and long-term GL *** determined that four major PHYTOCHROME-INTERACTING FACTORs(PIFs:PIF1,PIF3,PIF4,and PIF5)act downstream of phyB in GL-mediated cotyledon *** addition,GL plays opposite roles in regulating different *** example,under continuous GL,the protein levels of all PIFs decreased,whereas the transcript levels of PIF4 and PIF5 strongly increased compared with dark *** together,our work provides a detailed molecular framework for understanding the role of the antagonistic regulations of phyB and phyA in GL-mediated atypical photomorphogenesis.

关键词： cotyledon development green light photobody phytochrome PIF3

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TabHLH27 orchestrates root growth and drought tolerance to enhance water use efficiency in wheat

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Journal of Integrative Plant Biology 2024年第7期66卷 1295-1312页

作者： Dongzhi Wang Xiuxiu Zhang Yuan Cao Aamana Batool Yongxin Xu Yunzhou Qiao Yongpeng Li Hao Wang Xuelei Lin Xiaomin Bie Xiansheng Zhang Ruilian Jing Baodi Dong Yiping Tong Wan Teng Xigang Liu Jun Xiao key laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of sciences Beijing 100049China Center for Agricultural resources Research Institute of Genetics and Developmental BiologyChinese Academy of SciencesShijiazhuang 050022China key laboratory of Crop Biology College of Life SciencesShandong Agricultural UniversityTai'an 271018China State key laboratory of Crop gene resources and Breeding Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China Ministry of Education key laboratory of molecular and Cellular Biology Hebei Research Center of the Basic Discipline of Cell BiologyHebei Collaboration Innovation Center for Cell Signaling and Environmental AdaptationHebei Key Laboratory of Molecular and Cellular BiologyCollege of Life SciencesHebei Normal UniversityShijiazhuang 050024China Centre of Excellence for Plant and Microbial Science(CEPAMS) JIC‐CASBeijing 100101China

Cultivating high-yield wheat under limited water resources is crucial for sustainable agriculture in semiarid *** water scarcity,plants activate drought response signaling,yet the delicate balance between drought tolerance and development remains *** genome-wide association studies and transcriptome profiling,we identified a wheat atypical basic helix-loop-helix(b HLH)transcription factor(TF),Tab HLH27-A1,as a promising quantitative trait locus candidate for both relative root dry weight and spikelet number per spike in *** HLH27-A1/B1/D1 knockout reduced wheat drought tolerance,yield,and water use efficiency(WUE).Tab HLH27-A1 exhibited rapid induction with polyethylene glycol(PEG)treatment,gradually declining over *** activated stress response genes such as Ta CBL8-B1 and Ta CPI2-A1 while inhibiting root growth genes like Ta SH15-B1 and Ta WRKY70-B1 under short-term PEG *** distinct transcriptional regulation of Tab HLH27-A1 involved diverse interacting factors such as Ta ABI3-D1 and Tab *** variations of Tab HLH27-A1influence its transcriptional responses to drought stress,with Tab HLH27-A1^(Hap-II)associated with stronger drought tolerance,larger root system,more spikelets,and higher WUE in ***,the excellent Tab HLH27-A1^(Hap-II)was selected during the breeding process in China,and introgression of Tab HLH27-A1^(Hap-II)allele improved drought tolerance and grain yield,especially under water-limited *** study highlights Tab HLH27-A1's role in balancing root growth and drought tolerance,providing a genetic manipulation locus for enhancing WUE in wheat.

关键词： drought tolerance GWAS root growth wheat WUE

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Post-transcriptional regulation of grain weight and shape by the RBP-A-J-K complex in rice

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Journal of Integrative Plant Biology 2024年第1期66卷 66-85页

作者： Ding Ren Hui Liu Xuejun Sun Fan Zhang Ling Jiang Ying Wang Ning Jiang Peiwen Yan Jinhao Cui Jinshui Yang Zhikang Li Pingli Lu Xiaojin Luo State key laboratory of genetic Engineering and MOE Engineering Research Center of gene Technology School of Life SciencesFudan UniversityShanghai 200438China State key laboratory of Crop Stress Adaptation and Improvement School of Life SciencesHenan UniversityKaifeng 475004China MOE key laboratory of Crop Physiology Ecology and Genetic Breeding College of AgronomyJiangxi Agricultural UniversityNanchang 330045China State key laboratory of Crop gene resources and Breeding Institute of Crop SciencesChinese Academy of Agricultural Sciences(CAAS)Beijing 100081China college of Agronomy Anhui Agricultural UniversityHefei 230036China

RNA-binding proteins(RBPs)are components of the post-transcriptional regulatory system,but their regulatory effects on complex traits remain *** an integrated strategy involving map-based cloning,functional characterizations,and transcriptomic and population genomic analyses,we revealed that RBP-K(LOC_Os08g23120),RBP-A(LOC_Os11g41890),and RBP-J(LOC_Os10g33230)encode proteins that form an RBP-A-J-K complex that negatively regulates rice yield-related *** of the RBP-A-J-K complex indicated RBP-K functions as a relatively non-specific RBP chaperone that enables RBP-A and RBP-J to function ***,RBP-J most likely affects GA pathways,resulting in considerable increases in grain and panicle lengths,but decreases in grain width and *** contrast,RBP-A negatively regulates the expression of genes most likely involved in auxin-regulated pathways controlling cell wall elongation and carbohydrate transport,with substantial effects on the rice grain filling process as well as grain length and ***,RBP-K is relatively ancient and highly conserved,whereas RBP-J and RBP-A are more ***,the RBP-A-J-K complex may represent a typical functional model for many RBPs and protein complexes that function at transcriptional and post-transcriptional levels in plants and animals for increased functional consistency,efficiency,and versatility,as well as increased evolutionary *** results clearly demonstrate the importance of RBP-mediated post-transcriptional regulation for the diversity of complex ***,rice grain yield and quality may be enhanced by introducing various complete or partial loss-of-function mutations to specific RBP genes using clustered regularly interspaced palindromic repeats(CRISPR)/CRISPR-associated protein 9 technology and by exploiting desirable natural tri-genic allelic combinations at the loci encoding the components of the RBP-A-J-K complex through marker-assisted select

关键词： GL11 grain weight and shape post-transcriptional regulation RNA-binding proteins

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