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Characterisation of manganese toxicity tolerance in Arabis paniculata

plant Diversity 2021年第2期43卷 163-172页

作者： Ting Tang Faqing Tao Weiqi Li School of Life Sciences Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated UtilizationKey Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted SoilsHunan University of Science and TechnologyXiangtan411201China plant Germplasm and Genomics center Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunming650201China

Manganese(Mn)contamination limits the production and quality of crops,and affects human health by disrupting the food *** paniculata is a pioneer species of Brassicaceae found in mining areas,and has the ability to accumulate heavy ***,little is known about the genetic mechanisms of Mn tolerance in *** this study,we found that Mn tolerance and ability to accumulate Mn were higher in *** than in Arabidopsis *** mechanisms underlying the response and recovery of *** to Mn toxicity were further investigated using transcriptome analysis.A total of 69,862,281 base pair clean reads were assembled into 61,627 high-quality unigenes,of which 41,591(67.5%)and 39,297(63.8%)were aligned in the Kyoto Encyclopedia of Genes and Genomes(KEGG)and Gene Ontology(GO),*** response to Mn toxicity,genes were expressed in twelve distinct patterns,which can be divided into four general categories:initial,stable,dose-dependent,and *** that were differentially expressed during Mn response and recovery belong to several dominant KEGG *** early response to Mn toxicity in *** includes the upregulation of genes involved in glutathione ***-binding cassette(ABC)transporter proteins were up-regulated during the entire response phase,and genes involved in glycerophospholipid metabolism were upregulated during the late phase of the Mn *** in the phenylpropanoid pathway were differentially expressed in the repair process after Mn *** findings reveal ideal material and genetic resources for phytoremediation in Mn-contaminated areas and highlight new knowledge and theoretical perspectives on the mechanisms of Mn tolerance.

关键词： Arabis paniculata Manganese toxicity Transcriptome Gene expression

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A wheat integrative regulatory network from large-scale complementary functional datasets enables trait-associated gene discovery for crop improvement

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Molecular plant 2023年第2期16卷 393-414页

作者： Yongming Chen Yiwen Guo Panfeng Guan Yongfa Wang Xiaobo Wang Zihao Wang Zhen Qin Shengwei Ma Mingming Xin Zhaorong Hu Yingyin Yao Zhongfu Ni Qixin Sun Weilong Guo Huiru Peng Frontiers Science center for Molecular Design Breeding Key Laboratory of Crop Heterosis and UtilizationBeijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing 100193China Hainan Yazhou Bay Seed Laboratory SanyaHainanChina State Key Laboratory of plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina

Gene regulation is central to all aspects of organism growth,and understanding it using large-scale functional datasets can provide a whole view of biological processes controlling complex phenotypic traits in ***,the connection between massive functional datasets and trait-associated gene discovery for crop improvement is still *** this study,we constructed a wheat integrative gene regulatory network(wGRN)by combining an updated genome annotation and diverse complementary functional datasets,including gene expression,sequence motif,transcription factor(TF)binding,chromatin accessibility,and evolutionarily conserved *** contains 7.2 million genome-wide interactions covering 5947 TFs and 127439 target genes,which were further verified using known regulatory relationships,condition-specific expression,gene functional information,and *** used wGRN to assign genome-wide genes to 3891 specific biological pathways and accurately prioritize candidate genes associated with complex phenotypic traits in genome-wide association *** addition,wGRN was used to enhance the interpretation of a spike temporal transcriptome dataset to construct high-resolution *** further unveiled novel regulators that enhance the power of spike phenotypic trait prediction using machine learning and contribute to the spike phenotypic differences among modern wheat ***,we developed an interactive webserver,wGRN(http://***/wGRN),for the community to explore gene regulation and discover trait-associated ***,this community resource establishes the foundation for using large-scale functional datasets to guide trait-associated gene discovery for crop improvement.

关键词： wheat integrative gene regulatory network functional gene discovery phenotype prediction crop improvement

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Use of genotype-environment interactions to elucidate the pattern of maize root plasticity to nitrogen deficiency

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Journal of Integrative plant Biology 2016年第3期58卷 242-253页

作者： Pengcheng Li Zhongjuan Zhuang Hongguang Cai Shuai Cheng Ayaz Ali Soomro Zhigang Liu Riliang Gu Guohua Mi Lixing Yuan Fanjun Chen Key Lab of plant-Soil Interaction MOECenter for ResourcesEnvironment and Food SecurityCollege Resources and Environmental SciencesChina Agricultural UniversityBeijing 100193China Jiangsu Key Laboratory of Crop genetics and Physiology/Co-Innovation center for Modern Production Technology of Grain Crops Key Laboratory of Plant Functional Genomics of the Ministry of EducationYangzhou UniversityYangzhou 225009China Leading Bio-agricultural Co. Ltd.Qinhuangdao 066000China Institute of Agricultural resource and Environment Jilin Academy of Agricultural SciencesChangchun 130033China

Maize（Zea mays L.） root morphology exhibits a high degree of phenotypic plasticity to nitrogen（N） de ficiency,but the underlying genetic architecture remains to be investigated Using an advanced BC_4F_3 population,we investigated the root growth plasticity under two contrasted N levels and identi fied the quantitative trait loci（QTLs） with QTL-environment（Q×E）interaction effects. Principal components analysis（PCA） on changes of root traits to N de ficiency（D LN-HN） showed that root length and biomass contributed for 45.8% in the same magnitude and direction on the first PC,while root traits scattered highly on PC_2 and PC_3. Hierarchical cluster analysis on traits for D LN-HN further assigned the BC_4F_3 lines into six groups,in which the special phenotypic responses to N de ficiency was presented These results revealed the complicated root plasticity of maize in response to N de ficiency that can be caused by genotype environment（G×E） interactions. Furthermore,QTL mapping using a multi-environment analysis identi fied 35 QTLs for root traits. Nine of these QTLs exhibited signi ficant Q×E interaction effects. Taken together,our findings contribute to understanding the phenotypic and genotypic pattern of root plasticity to N de ficiency,which will be useful for developing maize tolerance cultivars to N de ficiency.

关键词： Genotype-environment interactions nitrogen stress quantitative trait locus root morphology root plasticity Zea mays L

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The prevalence of deleterious mutations during the domestication and improvement of soybean

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The Crop Journal 2023年第2期11卷 523-530页

作者： Shichao Sun Yumin Wang He Wei David E.Hufnagel Ya Wang Shiyu Guo Yinghui Li Li Wang Li-juan Qiu Shenzhen Branch Guangdong Laboratory for Lingnan Modern Agriculture/Genome Analysis Laboratory of the Ministry of Agriculture/Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural SciencesShenzhen 518000GuangdongChina Soybean Research Institute Jilin Academy of Agricultural SciencesChangchun 130033JilinChina Henan Academy of Crops Molecular Breeding Henan Academy of Agricultural Sciences/National Centre for Plant BreedingZhengzhou 450002HenanChina Virus and Prion Research Unit National Animal Disease CenterThe Agricultural Research Service(ARS)of the United States Department of Agriculture(USDA)AmesIA 50010USA The national Key Facility for Crop Gene resources and genetic Improvement(NFCRI)/Key Laboratory of Crop Gene resource and Germplasm Enhancement(MOA)/Key Laboratory of Soybean Biology(Beijing)(MOA) Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China Kunpeng Institute of Modern Agriculture at Foshan Foshan 528200GuangdongChina

Soybean(Glycine max L.)is a protein and oil crop grown *** fitness may be reduced by deleterious mutations,whose identification and purging is desirable for crop *** the published whole-genome re-sequenced data of 2214 soybean accessions,including 221 wild soybean,1132 landrace cultivars and 861 improved soybean lines,we identified 115,275 deleterious single-nucleotide polymorphisms(SNPs).Numbers of deleterious alleles increased from wild soybeans to landraces and decreased from landraces to modern improved *** in selective-sweep regions showed fewer deleterious mutations than the remaining *** mutations explained 4.3%-48%more phenotypic variation than randomly selected SNPs for resistance to soybean cyst nematode race 2(SCN2),soybean cyst nematode race 3(SCN3)and soybean mosaic virus race 3(SMV3).These findings illustrate how mutation load has shifted during soybean domestication,expansion and improvement and provide candidate sites for breeding out deleterious mutations in soybean by genome editing and/or conventional breeding focused on the selection of progeny with fewer deleterious alleles.

关键词： Deleterious mutations Domestication cost Expansion load BAD_Mutations Soybean cyst nematode

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SSR Marker Analysis on indica-japonica Differentiation of Natural Population of Oryza rufipogon in Yuanjiang, Yunnan Province

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Rice science 2006年第1期13卷 71-74页

作者： LI Ya-li YANG Xiao-xi ZHAO Feng-ping Xu Ming-hui Kunming Institute of Botany Chinese Academy of Sciences Kunming 650204 China Yunnan Rare and Endangered plant Species Conservation center Kunming 650032 China Biotechnology and genetic resource Research Institute Yunnan Academy of Agricultural Sciences Kunming 650223 China

By using 19 pairs of primers that could identify two subspecies （indica and japonica） of cultivated rice （Oryza sativa L.）, the indica-japonica differentiation of 56 individuals from the natural population of common wild rice （Oryza rufipogon Griff.） in Yuanjiang was analyzed by SSR （microsatellite DNAs, or simple sequence repeat）. Of the 19 pairs of primers, 17 pairs （89.47%） could amplify only one kind of band type among all of the individuals, but primers RM251 and RM18 could amplify polymorphic band types. The bands amplified by 16 pairs of primers （84.21%） were identical to the indica-japonica diagnostic bands of relevant locus in cultivated rice, including 11 japonica-like loci and 4 indica-like loci. The bands amplified by the other three pairs of primers （RM18, RM202, RM205） were different from indica or japonica diagnostic bands of cultivated rice. The results showed that according to 19 loci analyzed, 84.21% of SSR loci in genomic DNA of common wild rice in Yuanjiang displayed indica-japonica differentiation and 13.79% of the loci still kept primitive, and most of the detected loci were homoaenetic in the natural population.

关键词： Oryza rufipogon indica-japonica differentiation simple sequence repeat population

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Multiple sgRNAs facilitate base editingmediated i-stop to induce complete and precise gene disruption

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Protein & Cell 2019年第11期10卷 832-839页

作者： Kun Jia Zongyang Lu Fei Zhou Zhiqi Xiong Rui Zhang Zhiwei Liu Yu'e Ma Lei He Cong Li Zhen Zhu Dejing Pan Zhengxing Lian Beijing Key Laboratory of Animal genetic Improvement China Agricultural UniversityBeijing 100094China Cambridge-Suda Genomic resource center and Jiangsu Key Laboratory of Neuropsychiatric Diseases Research Soochow UniversitySuzhou 215123China School of Life Science and Technology ShanghaiTech UniversityShanghai 201210China Key Laboratory of MEMS of Ministry of Education Southeast UniversityNanjing 210096China

Dear Editor,Gene editing is a process to introduce desired changes into targeted loci of genomic ***,type II clustered regularly in terspaced short palindromic repeats-associated Cas9 endonuclease(CRISPR/Cas9)system has been demonstrated as a versatile tool for engineering eukaryote genome(Hsu et al.,2014),such as in mice(Zuo et al.,2017).

关键词： CRISPR/Cas9 sgRNA versatile

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The Melastoma dodecandrum genome and the evolution of Myrtales

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Journal of genetics and Genomics 2022年第2期49卷 120-131页

作者： Yang Hao Yu-Zhen Zhou Bin Chen Gui-Zhen Chen Zhen-Ying Wen Diyang Zhang Wei-Hong Sun Ding-Kun Liu Jie Huang Jin-Liao Chen Xiao-Qin Zhou Wan-Lin Fan Wen-Chun Zhang Lin Luo Wen-Chao Han Yan Zheng Long Li Peng-Cheng Lu Yue Xing Shu-Ya Liu Jia-Ting Sun Ying-Hui Cao Yan-Ping Zhang Xiao-Ling Shi Sha-Sha Wu Ye Ai Jun-Wen Zhai Si-Ren Lan Zhong-Jian Liu Dong-Hui Peng Key Laboratory of national Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture Fujian Agriculture and Forestry UniversityFuzhou 350002China Innovation and Application Engineering Technology Research center of Ornamental plant Germplasm resources in Fujian Province Fuzhou 350002China

Melastomataceae has abundant morphological diversity with high economic and ornamental merit in Myrtales. The phylogenetic position of Myrtales is still contested. Here, we report the chromosome-level genome assembly of Melastoma dodecandrum in Melastomataceae. The assembled genome size is299.81 Mb with a contig N50 value of 3.00 Mb. Genome evolution analysis indicated that M. dodecandrum,Eucalyptus grandis, and Punica granatum were clustered into a clade of Myrtales and formed a sister group with the ancestor of fabids and malvids. We found that M. dodecandrum experienced four whole-genome polyploidization events: the ancient event was shared with most eudicots, one event was shared with Myrtales, and the other two events were unique to M. dodecandrum. Moreover, we identified MADS-box genes and found that the AP1-like genes expanded, and AP3-like genes might have undergone subfunctionalization. The SUAR63-like genes and AG-like genes showed different expression patterns in stamens, which may be associated with heteranthery. In addition, we found that LAZY1-like genes were involved in the negative regulation of stem branching development, which may be related to its creeping features. Our study sheds new light on the evolution of Melastomataceae and Myrtales, which provides a comprehensive genetic resource for future research.

关键词： Melastoma Genome evolution Flower development Heteranthery Flower color Creeping stem

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Cell type-specific proteomics uncovers a RAF15-SnRK2.6/OST1 kinase cascade in guard cells

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植物学报:英文版 2023年第9期65卷 2122-2137页

作者： Hongliang Wang Yubei Wang Tian Sang Zhen Lin Rongxia Li Weiwei Ren Xin Shen Bing Zhao Xiao Wang Xuebin Zhang Shaoqun Zhou Shaojun Dai Honghong Hu Chun-Peng Song Pengcheng Wang Shanghai center for plant Stress Biology CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai 200032China University of Chinese Academy of Sciences Beijing 100049China Institute of Advanced Biotechnology and School of Life Sciences Southern University of Science and TechnologyShenzhen 518055China Shanghai Bioprofile Technology Company Ltd Shanghai 200241China center of plant Germplasm resources College of Life SciencesShanghai Normal UniversityShanghai 200234China national Key Laboratory of Crop genetic Improvement College of Life Science and TechnologyHuazhong Agricultural UniversityWuhan 430070China State Key Laboratory of Crop Stress Adaptation and Improvement College of Life SciencesCollege of AgricultureAcademy for Advanced Interdisciplinary StudiesHenan UniversityKaifeng 475004China Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureKey Laboratory of Synthetic BiologyMinistry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China

Multicellular organisms such as plants contain various cell types with specialized *** the characteristics of each cell type reveals specific cell functions and enhances our understanding of organization and function at the organismal *** cells(GCs)are specialized epidermal cells that regulate the movement of the stomata and gaseous exchange,and provide a model genetic system for analyzing cell fate,signaling,and *** proteomics analyses of GC are available,but these are limited in *** we used enzymatic isolation and flow cytometry to enrich GC and mesophyll cell protoplasts and perform in-depth proteomics in these two major cell types in Arabidopsis *** identified approximately 3,000 proteins not previously found in the GC proteome and more than600 proteins that may be specific to *** depth of our proteomics enabled us to uncover a guard cell-specific kinase cascade whereby Raf15and Snf1-related kinase2.6(SnRK2.6)/OST1(open stomata 1)mediate abscisic acid(ABA)-induced stomatal ***15 directly phosphorylated SnRK2.6/OST1 at the conserved Ser175 residue in its activation loop and was sufficient to reactivate the inactive form of SnRK2.6/*** SnRK2.6/OST1 activation and stomatal closure was impaired in raf15 *** also showed enrichment of enzymes and flavone metabolism in GC,and consistent,dramatic accumulation of flavone *** study answers the long-standing question of how ABA activates SnRK2.6/OST1 in GCs and represents a resource potentially providing further insights into the molecular basis of GC and mesophyll cell development,metabolism,structure,and function.

关键词： abscisic acid guard cell metabolomics phosphorylation proteomics signaling

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Identification of QTL for adult-plant resistance to powdery mildew in Chinese wheat landrace Pingyuan 50

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The Crop Journal 2014年第5期2卷 308-314页

作者： Muhammad Azeem Asad Bin Bai Caixia Lan Jun Yan Xianchun Xia Yong Zhang Zhonghu He Institute of Crop Science National Wheat Improvement Center/The National Key Facility for Crop Gene Resources and Genetic ImprovementChinese Academy of Agricultural Sciences (CAAS) Wheat Research Institute Gansu Academy of Agricultural Sciences Cotton Research Institute Chinese Academy of Agricultural Sciences (CAAS) International Maize and Wheat Improvement center (CIMMYT) China Office c/o CAAS

Powdery mildew caused by Blumeria graminis f. sp. tritici is one of the major wheat diseases worldwide. The Chinese wheat landrace Pingyuan 50 has shown adult-plant resistance(APR)to powdery mildew in the field for over 60 years. To dissect the genetic basis of APR to powdery mildew in this cultivar, a mapping population of 137 double haploid(DH) lines derived from Pingyuan 50/Mingxian 169 was evaluated in replicated field trials for two years in Beijing(2009–2010 and 2010–2011) and one year in Anyang(2009–2010). A total of 540 polymorphic SSR markers were genotyped on the entire population for construction of a linkage map and QTL analysis. Three QTL were mapped on chromosomes 2BS(***-2BS.2), 3BS(***-3BS),and 5AL(***-5AL) with the resistance alleles contributed by Pingyuan 50 explaining 5.3%,10.2%, and 9.1% of the phenotypic variances, respectively, and one QTL on chromosome 3BL(***-3BL) derived from Mingxian 169 accounting for 18.1% of the phenotypic ***-3BS, ***-3BL, and ***-5AL appear to be new powdery mildew APR ***-2BS.2 and ***-5AL are possibly pleiotropic or closely linked resistance loci to stripe rust resistance QTL. Pingyuan 50 could be a potential genetic resource to facilitate breeding for improved APR to both powdery mildew and stripe rust.

关键词： Triticum aestivum L Blumeria graminis f.sp.tritici Disease resistance Quantitative trait loci

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Use of Selection Indices based on Multivariate Analysis for Improving Grain Yield in Rice

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Rice science 2008年第4期15卷 303-310页

作者： Hossein SABOURI Babak RABIEI Maryam FAZLALIPOUR Department of plant Production Gonbad High Education Center Gorgan University of Agricultural Sciences & Natural Resources Department of Agronomy and plant Breeding Giulan University

In order to study selection indices for improving rice grain yield, a cross was made between an Iranian traditional rice (Oryza sativa L.) variety, Tarommahalli and an improved indica rice variety, Khazar in 2006. The traits of the parents (30 plants), F1 (30 plants) and F2 generations (492 individuals) were evaluated at the Rice Research Institute of Iran (RRII) during 2007. Heritabilities of the number of panicles per plant, plant height, days to heading and panicle exsertion were greater than that of grain yield. The selection indices were developed using the results of multivariate analysis. To evaluate selection strategies to maximize grain yield, 14 selection indices were calculated based on two methods (optimum and base) and combinations of 12 traits with various economic weights. Results of selection indices showed that selection for grain weight, number of panicles per plant and panicle length by using their phenotypic and/or genotypic direct effects (path coefficient) as economic weights should serve as an effective selection criterion for using either the optimum or base index.

关键词： rice (Oryza sativa) optimum index base index path analysis heritability grain yield selection index

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