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Physiological,transcriptome and gene functional analysis provide novel sights into cadmium accumulation and tolerance mechanisms in kenaf

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Journal of Environmental Sciences 2024年第3期137卷 500-514页

作者： Shan Cao Meng Wang Jiao Pan Dengjie Luo Samavia Mubeen Caijin Wang Jiao Yue Xia Wu Qijing Wu Hui Zhang Canni Chen Muzammal Rehman Sichen Xie Ru Li Peng Chen Guangxi key laboratory of Agro-environment and Agric-products safety Key Laboratory of Plant Genetics and BreedingCollege of AgricultureGuangxi UniversityNanning 530004China state key laboratory for Conservation and Utilization of Subtropical Agro-bioresources College of Life Science and TechnologyGuangxi UniversityNanning 530004China

Kenaf is considered to have great potential for remediation of heavy metals in ***,studies on molecular mechanisms of root Cd accumulation and tolerance are still *** this study,two differently tolerant kenaf cultivars were selected as materials and the physiological and transcriptomic effects were evaluated under Cd *** study showed that 200μmol/L CdCl_(2) treatment triggered the reactive oxygen species(ROS)explosion and membrane lipid *** with the Cd-sensitive cultivar‘Z',the Cd-tolerant cultivar‘F'was able to resist oxidative stress in cells by producing higher antioxidant enzyme activities and increasing the contents of ascorbic acid(AsA)and glutathione(GSH).The root cell wall of‘F'exhibited higher polysaccharide contents under Cd treatment,providing more Cd-binding *** were 3,439 differentially expressed genes(DEGs)that were co-regulated by Cd treatment in two *** biosynthesis and plant hormone signal transduction pathways were significantly enriched by functional annotation *** associated with pectin,cellulose,and hemi-cellulose metabolism were involved in Cd chelation of root cell wall;V-ATPases,ABCC3 and Narmp3 could participated in vacuolar compartmentalization of Cd;PDR1 was responsible for Cd effux;the organic acid transporters contributed to the absorption of Cd in *** genes might have played key roles in kenaf Cd tolerance and Cd ***,HcZIP2 was identified to be involved in Cd uptake and transport in *** findings provide a deeper understanding of the molecular pathways underlying Cd accumulation and detoxification mechanisms in kenaf.

关键词： Kenaf Cd stress Physiological Transcriptome HcZIP2

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Genetic variation in a heat shock transcription factor modulates cold tolerance in maize

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Molecular plant 2024年第9期17卷 1423-1438页

作者： Lei Gao Lingling Pan Yiting Shi Rong Zeng Minze Li Zhuoyang Li Xuan Zhang Xiaoming Zhao Xinru Gong Wei Huang Xiaohong Yang Jinsheng Lai Jianru Zuo Zhizhong Gong Xiqing Wang Weiwei Jin Zhaobin Dong Shuhua Yang state key laboratory of plant Environmental Resilience Frontiers Science Center for Molecular Design BreedingCollege of Biological SciencesCenter for Crop Functional Genomics and Molecular BreedingChina Agricultural UniversityBeijing 100193China state key laboratory of Maize Bio-breeding National Maize Improvement CenterFrontiers Science Center for Molecular Design BreedingDepartment of Plant Geneticsand BreedingChinaAgricultural UniversityBeijingChina state key laboratory of plant Genomics and National plant Gene Research Center Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing100101China

Understanding how maize(Zea mays)responds to cold stress is crucial for facilitating breeding programs of cold-tolerant *** extensive utilization of the genome-wide association study(GWAs)approach for exploring favorable natural alleles associated with maize cold tolerance,few studies have successfully identified candidate genes that contribute to maize cold *** this study,we used a diverse panel of inbred maize lines collected from different germplasm sources to perform a GWAS on var-iations in the relative injured area of maize true leaves during cold stress-a trait very closely correlated with maize cold *** identified HsF21,which encodes a B-class heat shock transcription factor(HSF)that positively regulates cold tolerance at both the seedling and germination *** varia-tions in the promoter of the cold-tolerant HSF21Hap1 allele led to increased HSF21 expression under cold stress by inhibiting binding of the basic leucine zipper bziP68 transcription factor,a negative regulator of cold *** integrating transcriptome deep sequencing,DNA affinity purification sequencing,and targeted lipidomic analysis,we revealed the function of HsF21 in regulating lipid metabolism homeo-stasis to modulate cold tolerance in *** addition,we found that HsF21 confers maize cold tolerance without incurring yield ***,this study establishes HsF21 as a key regulator that en-hances cold tolerance in maize,providing valuable genetic resources for breeding of cold-tolerant maize varieties.

关键词： heat shock factor HSF21 cold tolerance natural variation bZiP68 lipid metabolism maize

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Identification and Transcriptional Regulation of CAMTA Genes in Liriodendron chinense

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Phyton-International Journal of Experimental Botany 2024年第3期93卷 413-425页

作者： Kaiyue Hong Yasmina Radani Teja Manda Jinhui Chen Liming Yang state key laboratory of Tree genetics and breeding College of Life SciencesNanjing Forestry UniversityNanjing210037China

This study explores CAMTA genes in the rare and endangered Chinese plant species,Liriodendron *** the completion of whole-genome sequencing,the roles of CAMTA genes in calcium regulation and stress responses in this species remain largely *** the *** genome,we identiﬁed two CAMTA genes,Lchi09764 and Lchi222536,characterized by four functional domains:CG-1,TIG,ANK repeats,and IQ *** analyses,including phylogenetic investigations,cis-regulatory element analyses,and chromosomal location studies,aim to elucidate the deﬁning features of CAMTA genes in *** Weighted Gene Co-Expression Network Analysis(WGCNA),we explored the impact of CAMTA genes on different organs and their regulation under abiotic stress *** identiﬁcation of signiﬁcant gene modules and the prediction of promoter binding sites revealed co-expressed genes associated with CAMTA transcription *** summary,this study provides initial insights into CAMTA genes in ***,laying the groundwork for future research on their evolution and biological *** knowledge enhancement contributes to a better understanding of plant responses to environmental stress—an essential aspect of plant biology.

关键词： Liriodendron chinense CAMTA genes abiotic stress WGCNA different organs

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OsbZIP53 Negatively Regulates Immunity Response by Involving in Reactive Oxygen Species and Salicylic Acid Metabolism in Rice

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Rice science 2024年第2期31卷 190-202,I0022-I0028页

作者： WU Lijuan HAN Cong WANG Huimei HE Yuchang LIN Hai WANG Lei CHEN Chen E Zhiguo state key laboratory of Rice Biology and breeding China National Rice Research InstituteHangzhou 310006China 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/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops Agricultural College of Yangzhou UniversityYangzhou 225009China

The basic region/leucine zipper(bZIP)transcription factors play important roles in plant development and responses to abiotic and biotic ***53 regulates resistance to Magnaporthe oryzae in rice by analyzing APIP5-RNAi transgenic *** further investigate the biological functions of OsbZIP53,we generated osbzip53 mutants using CRISPR/Cas9 editing and also constructed OsbZIP53 over-expression transgenic *** analysis of phenotypical,physiological,and transcriptional data showed that knocking-out OsbZIP53 not only improved disease resistance by inducing a hypersensitivity response in plants,but also regulated the immune response through the salicylic acid ***,disrupting OsbZIP53 increased H2O2 accumulation by promoting reactive oxygen species generation through up-regulation of several respiratory burst oxidase homologs(Osrboh genes)and weakened H2O2 degradation by directly targeting *** addition,the growth of osbzip53 mutants was seriously impaired,while OsbZIP53 over-expression lines displayed a similar phenotype to the wild type,suggesting that OsbZIP53 has a balancing effect on rice immune response and growth.

关键词： OsbZIP53 hypersensitive response reactive oxygen species metabolism rice immunity salicylic acid transcription factor

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Unveiling the distinctive traits of functional rye centromeres:minisatellites,retrotransposons,and R-loop formation

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Science China(Life Sciences) 2024年第9期67卷 1989-2002页

作者： Chang Liu Shulan Fu Congyang Yi Yang Liu Yuhong Huang Xianrui Guo Kaibiao Zhang Qian Liu James A.Birchler Fangpu Han state 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 key laboratory for plant genetics and breeding Sichuan Agricultural UniversityChengdu 611130China Division of Biological Science University of MissouriColumbia 65211-7400USA

Centromeres play a vital role in cellular division by facilitating kinetochore assembly and spindle *** their conserved functionality,centromeric DNA sequences exhibit rapid evolution,presenting diverse sizes and compositions across *** functional significance of rye centromeric DNA sequences,particularly in centromere identity,remains *** this study,we comprehensively characterized the sequence composition and organization of rye *** findings revealed that these centromeres are primarily composed of long terminal repeat retrotransposons(LTR-RTs)and interspersed *** systematically classified LTR-RTs into five categories,highlighting the prevalence of younger CRS1,CRS2,and CRS3 of CRSs(centromeric retrotransposons of Secale cereale)were primarily located in the core centromeres and exhibited a higher association with CENH3 *** minisatellites,mainly derived from retrotransposons,along with CRSs,played a pivotal role in establishing functional centromeres in ***,we observed the formation of R-loops at specific regions of CRS1,CRS2,and CRS3,with both rye pericentromeres and centromeres exhibiting enrichment in ***,these R-loops selectively formed at binding regions of the CENH3 nucleosome in rye centromeres,suggesting a potential role in mediating the precise loading of CENH3 to centromeres and contributing to centromere *** work provides insights into the DNA sequence composition,distribution,and potential function of R-loops in rye *** knowledge contributes valuable information to understanding the genetics and epigenetics of rye centromeres,offering implications for the development of synthetic centromeres in future plant modifications and beyond.

关键词： centromere LTR-RTs minisatellite rye R-loop

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Genetic and molecular mechanisms of reproductive isolation in the utilization of heterosis for breeding hybrid rice

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Journal of genetics and Genomics 2024年第6期51卷 583-593页

作者： Chaolong Wang Xiaowen Yu Jian Wang Zhigang Zhao Jianmin Wan state key laboratory for Crop genetics&Germplasm Enhancement and Utlization Nanjing Agricultural UniversityZhongshan Biological Breeding LaboratoryNanjingJiangsu210095China state key laboratory of Crop Gene Resources and breeding Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China

Heterosis,also known as hybrid vigor,is commonly observed in rice *** hybridization of rice species or subspecies exhibits robust hybrid vigor,however,the direct harnessing of this vigor is hindered by reproductive ***,we review recent advances in the understanding of the molecular mechanisms governing reproductive isolation in inter-subspecific and inter-specific *** review encompasses the genetic model of reproductive isolation within and among Oryza sativa species,emphasizing the essential role of mitochondria in this ***,we delve into the molecular intricacies governing the interaction between mitochondria and autophagosomes,elucidating their significant contribution to reproductive ***,our exploration extends to comprehending the evolutionary dynamics of reproductive isolation and speciation in *** on these advances,we offer a forward-looking perspective on how to overcome the challenges of reproductive isolation and facilitate the utilization of heterosis in future hybrid rice breeding endeavors.

关键词： Hybrid vigor Reproductive isolation Hybrid ricebreeding

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Transcriptomic and epigenomic landscapes of muscle growth during the postnatal period of broilers

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Journal of Animal Science and Biotechnology 2024年第5期15卷 1851-1865页

作者： Shuang Gu Qiang Huang Yuchen Jie Congjiao Sun Chaoliang Wen Ning Yang state key laboratory of Animal Biotech breeding and Frontier Science Center for Molecular Design breeding China Agricultural UniversityBeijing 100193China National Engineering laboratory for Animal breeding and key laboratory of Animal genetics Breeding and ReproductionMinistry of Agriculture and Rural AffairsDepartment of Animal Genetics and BreedingCollege of Animal Science and Technology China Agricultural UniversityBeijing 100193China. Sanya Institute of China Agricultural University Hainan 572025China

Background Broilers stand out as one of the fastest-growing livestock globally,making a substantial contribution to animal meat ***,the molecular and epigenetic mechanisms underlying the rapid growth and development of broiler chickens are still *** study aims to explore muscle development patterns and regulatory networks during the postnatal rapid growth phase of fast-growing *** measured the growth performance of Cornish(CC)and White Plymouth Rock(RR)over a 42-d *** muscle samples from both CC and RR were randomly collected at day 21 after hatching(D21)and D42 for RNA-seq and ATAC-seq library *** The consistent increase in body weight and pectoral muscle weight across both breeds was observed as they matured,with CC outpacing RR in terms of weight at each stage of *** expression analysis identified 398 and 1,129 genes in the two dimensions of breeds and ages,respectively.A total of 75,149 ATAC-seq peaks were annotated in promoter,exon,intron and intergenic regions,with a higher number of peaks in the promoter and intronic *** age-biased genes and breed-biased genes of RNA-seq were combined with the ATAC-seq data for subsequent *** results spotlighted the upregulation of ACTC1 and FDPS at D21,which were primarily associated with muscle structure development by gene cluster ***,a noteworthy upregulation of MUSTN1,FOS and TGFB3 was spotted in broiler chickens at D42,which were involved in cell differentiation and muscle regeneration after injury,suggesting a regulatory role of muscle growth and *** This work provided a regulatory network of postnatal broiler chickens and revealed ACTC1 and MUSTN1 as the key responsible for muscle development and *** findings highlight that rapid growth in broiler chickens triggers ongoing muscle damage and subsequent *** findings provide a foundation for future research to i

关键词： ATAC-seq Broiler Pectoral muscle development Rapid growth RNA-seq

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Integrating machine learning and genome editing for crop improvement

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aBIOTECH 2024年第2期5卷 262-277页

作者： Long Chen Guanqing Liu Tao Zhang Jiangsu key laboratory of Crop Genomics and Molecular breeding/Zhongshan Biological breeding laboratory/key laboratory of plant Functional Genomics of the Ministry of Education Agricultural College of Yangzhou UniversityYangzhou 225009China Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu key laboratory of Crop genetics and Physiology Yangzhou UniversityYangzhou 225009China

Genome editing is a promising technique that has been broadly utilized for basic gene function studies and trait ***,the exponential growth of computational power and big data now promote the application of machine learning for biological *** this regard,machine learning shows great potential in the refinement of genome editing systems and crop ***,we review the advances of machine learning to genome editing optimization,with emphasis placed on editing efficiency and specificity ***,we demonstrate how machine learning bridges genome editing and crop breeding,by accurate key site detection and guide RNA ***,we discuss the current challenges and prospects of these two techniques in crop *** integrating advanced genome editing techniques with machine learning,progress in crop breeding will be further accelerated in the future.

关键词： Machine learning Genome editing Crop improvement Molecular design breeding

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Synthesis of betanin by expression of the core betalain biosynthetic pathway in carrot

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Horticultural plant Journal 2024年第3期10卷 732-742页

作者： Bo Wang Yahui Wang Yuanjie Deng Quanhong Yao Aisheng Xiong state key laboratory of Crop genetics and Germplasm Enhancement College of HorticultureNanjing Agricultural UniversityNanjingJiangsu 210095China Shanghai key laboratory of Agricultural genetics and breeding Biotechnology Research Institute of Shanghai Academy of Agricultural ScienceShanghai 201106China

Betalain has received increased attention because of its high nutritional value and crucial physiological *** on the elucidation of its core biosynthetic pathway,betalain can be produced in additional plants by metabolic *** of betalain in carrot(Daucus carota L.)can improve its nutritional quality and economic value by extracting betalain from the fleshy root,non-edible part,and processing residue of *** this study,two different constructs,namely,pYB:mCD(AomelOS,BvCYP76AD1S,and BvDODA1S)and p YB:CDD(BvCYP76AD1S,BvDODA1S,and MjcDOPA5GTS),were introduced into carrot for betanin synthesis by Agrobacterium-mediated *** can be synthetized in both transgenic calli,and p YB:m CD-transgenic callus can be used to produce betacyanin by suspension ***,pYB:mCD-transgenic seedlings can synthetize betanin only by tyrosine *** p YB:CDD-transgenic lines can synthetize betanin in whole *** betanin content in fleshy root of pYB:CDD-transgenic carrot was(63.4±9)μg·g^(-1)fresh weight according to quantitative *** betanin-producing carrot plant materials can be used to synthesize betanin for industrial application or consumption as dietary sources.

关键词： Daucus carota L. Betanin Biosynthesis Metabolic engineering Biofortification

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Development of Machine Learning Methods for Accurate Prediction of plant Disease Resistance

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Engineering 2024年第9期40卷 100-110页

作者： Qi Liu Shi-min Zuo Shasha Peng Hao Zhang Ye Peng Wei Li Yehui Xiong Runmao Lin Zhiming Feng Huihui Li Jun Yang Guo-Liang Wang Houxiang Kang state key laboratory for Biology of plant Diseases and Insect Pests Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing 100193China Zhongshan Biological breeding laboratory&Jiangsu key laboratory of Crop Genomics and Molecular breeding Agricultural College of Yangzhou UniversityYangzhou 225009China Hunan Provincial key laboratory of Crop Germplasm Innovation and Utilization and College of Agronomy Hunan Agricultural UniversityChangsha 410128China state key laboratory of Crop Gene Resources and breeding Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China College of plant Protection Hunan Agricultural UniversityChangsha 410128China key laboratory of Green Prevention and Control of Tropical plant Diseases and Pests Ministry of Education College of Plant ProtectionHainan UniversityHaikou 570228China MARA key laboratory of Surveillance and Management for plant Quarantine Pests Department of Plant BiosecurityCollege of Plant ProtectionChina Agricultural UniversityBeijing 100193China Department of plant Pathology Ohio State UniversityColumbusOH 43210USA

The traditional method of screening plants for disease resistance phenotype is both time-consuming and *** selection offers a potential solution to improve efficiency,but accurately predicting plant disease resistance remains a *** this study,we evaluated eight different machine learning(ML)methods,including random forest classification(RFC),support vector classifier(SVC),light gradient boosting machine(lightGBM),random forest classification plus kinship(RFC_K),support vector classification plus kinship(SVC_K),light gradient boosting machine plus kinship(lightGBM_K),deep neural network genomic prediction(DNNGP),and densely connected convolutional networks(DenseNet),for predicting plant disease *** results demonstrate that the three plus kinship(K)methods developed in this study achieved high prediction ***,these methods achieved accuracies of up to 95%for rice blast(RB),85%for rice black-streaked dwarf virus(RBSDV),and 85%for rice sheath blight(RSB)when trained and applied to the rice diversity panel I(RDPI).Furthermore,the plus K models performed well in predicting wheat blast(WB)and wheat stripe rust(WSR)diseases,with mean accuracies of up to 90%and 93%,*** assess the generalizability of our models,we applied the trained plus K methods to predict RB disease resistance in an independent population,rice diversity panel II(RDPII).Concurrently,we evaluated the RB resistance of RDPII cultivars using spray *** the predictions with the spray inoculation results,we found that the accuracy of the plus K methods reached 91%.These findings highlight the effectiveness of the plus K methods(RFC_K,SVC_K,and lightGBM_K)in accurately predicting plant disease resistance for RB,RBSDV,RSB,WB,and *** methods developed in this study not only provide valuable strategies for predicting disease resistance,but also pave the way for using machine learning to streamline genome-based crop breeding.

关键词： Predicting plant disease resistance Genomic selection Machine learning Genome-wide association study

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