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Why mosaic? Gene expression profiling of African cassava mosaic virus-infected cassava reveals the effect of chlorophyll degradation on symptom development

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Journal of Integrative plant Biology 2014年第2期56卷 122-132页

作者： Jiao Liu Jun Yang Huiping Bi Peng Zhang shanghai chenshan plant science research center the chinese academy of sciences Chenshan Botanical Garden National Key Laboratory of plant Molecular Genetics and National center for plant Gene research (shanghai) Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences the Chinese Academy of Science Key Laboratory of Systems Microbial Biotechnology Tianjin Institute of Industrial Biotechnology the Chinese Academy of Sciences Tianjin Airport Economic Park

Cassava mosaic disease, caused by cassava bego- moviruses, is the most serious disease for cassava in Africa. However, the pathogenesis of this disease is poorly under- stood. We employed high throughput digital gene expression profiling based on the Illumina Solexa sequencing technology to investigate the global transcriptional response of cassava to African cassava mosaic virus infection. We found that 3,21o genes were differentially expressed in virus-infected cassava leaves. Gene ontology term and Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated that genes implicated in photosynthesis were most affected, consistent with the chlorotic symptoms observed in infected leaves. The upregu- lation of chlorophyll degradation genes, including the genes encoding chlorophyUase, pheophytinase, and pheophorbide a oxygenase, and downregulation of genes encoding the major apoproteins in light-harvesting complex II were confirmed by qRT-PCR. These findings, together with the reduction of chlorophyll b content and fewer grana stacks in the infected leaf cells, reveal that the degradation of chlorophyll plays an important role in A^rican cassava mosaic virus symptom development. This study will provide a road map for future investigations into viral pathogenesis.

关键词： Afriican cassava mosaic virus cassava chlorophylldegradation digital gene expression mosaic symptom

plant latent defense response to microbial non-pathogenic factors antagonizes compatibility

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National science Review 2022年第8期9卷 26-34页

作者： Yu Yang Shenglan Chen Xiaoxuan Wu Li Peng Juan I.Vílchez Richa Kaushal Xiaomin Liu Sunil K.Singh Danxia He Fengtong Yuan Suhui Lv Rafael J.L.Morcillo Wei Wang Weichang Huang Mingguang Lei Jian-Kang Zhu Paul W.Paré Huiming Zhang shanghai center for plant Stress Biology Center for Excellence in Molecular Plant Sciences Chinese Academy of Sciences University of chinese academy of sciences shanghai chenshan Botanical Garden Department of Chemistry and Biochemistry Texas Tech University

Unlike microbe-associated molecular patterns(MAMPs) that are readily targeted by host immunity,microbial non-pathogenic factors(NPFs) appear negligible as they do not elicit defense. Little is known about whether and how NPFs may be monitored by hosts to control compatibility. Herein, a forward genetic screening isolated an Arabidopsis mutant with a loss of plant-rhizobacteria mutualism, leading to the disclosure of a plant latent defense response(LDR) to NPFs. The activation of LDR in the mutant,named rol1 for regulator of LDR 1, is triggered by several non-pathogenic volatile organic compounds and antagonizes plant compatibility with the beneficial bacterium Bacillus amyloliquefaciens GB03. The activation of LDR in rol1 is mediated through the prokaryotic pathway of chloroplastic lipid *** rol1 root microbiome showed a reduced proportion of the Bacillaceae family. We propose that, parallel to the forefront immunity to MAMPs, LDR to certain NPFs provides a hidden layer of defense for controlling compatibility with commensal or beneficial microbes.

关键词： microbial non-pathogenic factors latent defense response compatibility plant-beneficial bacteria chloroplastic lipid biosynthesis

Production of very-high-amylose cassava by post-transcriptional silencing of branching enzyme genes

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Journal of Integrative plant Biology 2020年第6期62卷 832-846页

作者： Wenzhi Zhou Shanshan Zhao Shutao He Qiuxiang Ma Xinlu Lu Xiaomeng Hao Hongxia Wang Jun Yang Peng Zhang National Key Laboratory of plant Molecular Genetics CAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and EcologyShanghai Institutes for Biological Sciencesthe Chinese Academy of SciencesShanghai 200032China shanghai Key Laboratory of plant Functional Genomics and Resources Shanghai Chenshan Plant Science Research CenterShanghai Chenshan Botanical Gardenthe Chinese Academy of SciencesShanghai 201602China University of chinese academy of sciences Beijing 100049China

High amylose starch can be produced by plants deficient in the function of branching enzymes(BEs).Here we report the production of transgenic cassava(Manihot esculenta Crantz)with starches containing up to 50%amylose due to the constitutive expression of hair-pin ds RNAs targeting the BE1 or BE2 *** BE1-RNAi plant lines(BE1i)and BE2-RNAi plant lines(BE2i)were grown up in the field,but with reduced total biomass *** high amylose content in the storage roots of BE2i plant lines was *** starch granules of BE1i and BE2i plants had similar morphology as wild type(WT),however,the size of BE1i starch granules were bigger than that of *** of amylograms and thermograms of all three sources of storage starches revealed dramatic changes to the pasting properties and a higher melting temperature for BE2i *** chain length distribution analysis showed a slight increase in chains of DP>36 in BE1i lines and a dramatic increase in glucan chains between DP 10-20 and DP>40 in BE2i ***,BE2i starches displayed a B-type X-ray diffraction pattern instead of the A-type pattern found in BE1i and WT ***,cassava BE1 and BE2 function differently in storage root starch biosynthesis.

关键词： chains branching pattern

Expression Profiling of Cassava Storage Roots Reveals an Active Process of Glycolysis/Gluconeogenesis

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Journal of Integrative plant Biology 2011年第3期53卷 193-211页

作者： Jun Yang Dong An Peng Zhang shanghai center for Cassava Biotechnology National Laboratory of Plant Molecular Genetics Institute of Plant Physiology & Ecology Shanghai Institutes for Biological Sciences the Chinese Academy of Sciences Shanghai 200032 China Key Laboratory of Synthetic Biology Institute of Plant Physiology & Ecology Shanghai Institutes for Biological Sciences the Chinese Academy of Sciences Shanghai 200032 China shanghai chenshan plant science research center the Chinese Academy of Sciences Chenshan Botanical Garden Shanghai 201602 China

Mechanisms related to the development of cassava storage roots and starch accumulation remain largely unknown. To evaluate genome-wide expression patterns during tuberization, a 60 mer oligonucleotide microarray representing 20 840 cassawl genes was designed to identify differentially expressed transcripts in fibrous roots, developing storage roots and mature storage roots. Using a random variance model and the traditional twofold change method for statistical analysis, 912 and 3 386 upregulated and downregulated genes related to the three developmental phases were identified. Among 25 significantly changed pathways identified, glycolysis/gluconeogenesis was the most evident one. Rate-limiting enzymes were identified from each individual pathway, for example, enolase, L-lactate dehydrogenase and aldehyde dehydrogenase for glycolysis/gluconeogenesis, and ADP-glucose pyrophosphorylase, starch branching enzyme and glucan phosphorylase for sucrose and starch metabolism. This study revealed that dynamic changes in at least 16% of the total transcripts, including transcription fac- tors, oxidoreductases/transferases/hydrolases, hormone-related genes, and effectors of homeostasis. The reliability of these differentially expressed genes was verified by quantitative real-time reverse transcription-polymerase chain reaction. Tlhese studies should facilitate our understanding of the storage root formation and cassava improvement.

关键词： CASSAVA ROOTS (Botany) -- Formation GLYCOLYSIS GLUCONEOGENESIS LACTATE dehydrogenase REVERSE transcriptase polymerase chain reaction plant gene expression OLIGONUCLEOTIDE arrays

A new high-quality genome sequence in soybean

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science China(Life sciences) 2018年第12期61卷 1604-1605页

作者： Jun Yang Xuehui Huang shanghai Key Laboratory of plant Functional Genomics and Resources Shanghai Chenshan Plant Science Research Center Chinese Academy of SciencesShanghai Chenshan Botanical GardenShanghai 201602China College of life sciences Shanghai Normal UniversityShanghai 200234China

In the 1940s,Nikolai Ivanovich Vavilov(Russian:Hиколай Иванович Вавилов)published his manuscript "The theory of origins of cultivated plants after Darwin(Russian:учение о происхожцении кулътурньIх растенийпосле дарвина)".Vavilov believed that among various crops,soybean(Glycine max)originated from China.

关键词： Nikolai Ivanovich Vavilov China

Spatio-temporal Variation of Soil Respiration and Its Driving Factors in Semi-arid Regions of North China

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chinese Geographical science 2018年第1期28卷 12-24页

作者： ZENG Xinhua SONG Yigang ZHANG Wanjun HE Shengbing College of Environmental science and Engineering Shanghai Jiaotong University Key Laboratory of Agricultural Water Resources Center for Agricultural Resources Research Institute of Genetics and Developmental Biology Chinese Academy of Sciences shanghai chenshan plant science research center Chinese Academy of Sciences

Soil respiration （SR） is the second-largest flux in ecosystem carbon cycling. Due to the large spatio-temporal variability of environmental factors, SR varied among different vegetation types, thereby impeding accurate estimation of CO2 emissions via SR. However, studies on spatio-temporal variation of SR are still scarce for semi-arid regions of North China. In this study, we conducted 12-month SR measurements in six land-use types, including two secondary forests （Populus tomentosa （PT） and Robinia pseudoacacia （RP））, three artificial plantations （Armeniaca sibirica （AS）, Punica granatum （PG） and Ziziphusjujuba （Z J）） and one natural grassland （GR）, to quantify spatio-temporal variation of SR and distinguish its controlling factors. Results indicated that SR exhibited distinct sea- sonal patterns for the six sites. Soil respiration peaked in August 2012 and bottomed in April 2013. The temporal coefficient of variation （CI0 of SR for the six sites ranged from 76.98% to 94.08%, while the spatial CV of SR ranged from 20.28% to 72.97% across the 12-month measurement. Soil temperature and soil moisture were the major controlling factors of temporal variation of SR in the six sites, while spatial variation in SR was mainly caused by the differences in soil total nitrogen （STN）, soil organic carbon （SOC）, net photosynthesis rate, and fine root biomass. Our results show that the annual average SR and Q10 （temperature sensitivity of soil respira- tion） values tended to decrease from secondary forests and grassland to plantations, indicating that the conversion of natural ecosystems to man-made ecosystems may reduce CO2 emissions and SR temperature sensitivity. Due to the high spatio-temporal variation of SR in our study area, care should be taken when converting secondary forests and grassland to plantations from the point view of accurately quantifying C02 emissions via SR at regional scales.

关键词： soil respiration spatio-temporal variation substrate availability temperature sensitivity global carbon cycle North China

Breeding Major Cereal Grains through the Lens o~ ~iutrition Sensitivity

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Molecular plant 2018年第1期11卷 23-30页

作者： Shu Yu Li Tian Department of plant sciences University of California Davis Davis CA 95616 USA shanghai chenshan plant science research center Chinese Academy of Sciences Shanghai 201602 China shanghai Key Laboratory of plant Functional Genomics and Resources Shanghai Chenshan Botanical Garden Shanghai 201602 China

Cereal grains are the common food staples that collectively provide over 50% of dietary calories and proteins for the world＇s population. Although the Green Revolution has greatly increased the yield of commercial cereal crops, they often lack nutrients essential for human health in the edible tissues. In developing nutrition-sensitive agriculture, the nutritional quality of cereal grains has been a major target for improvement using breeding and biotechnology approaches. This review examines recent progress on biofortification of micronutrients （provitamin A and folates） and an essential amino acid （lysine） in three major cereal grains, wheat, rice, and maize, through plant breeding. In addition, how natural variations, induced mutations, and the advanced genome-editing technologies can be applied to improving the nutrient content and stability in these cereal grains are discussed. High-yield cereal crops pyramided with improved （micro）nutrient contents hold great promise to meet the increasing demand of nutritionally limited popula- tions and to contribute to achieving sustainable nutrition security.

关键词： cereal grains nutrition sensitive plant breeding provitamin A lysine folates

Diversity and conservation of chinese wild begonias

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plant Diversity 2018年第3期40卷 75-90页

作者： Daike Tian Yan Xiao Yi Tong Naifeng Fu Qingqing Liu Chun Li shanghai chenshan plant science research center of chinese academy of sciences Shanghai Chenshan Botanical Garden Shanghai 201602 China shanghai Key Laboratory of plant Functional Genomics and Resources Shanghai 201602 China Lushan Forestry Bureau Ya'an 625600 Sichuan China

Begonia, one of the most diverse plant taxa and the fifth or sixth largest angiosperm genus, consists of over1800 accepted species. The number of species recognized within this genus has greatly increased over the past 20 years, rising from 80 to 200 species in China alone. Based on recent field surveys, the number of begonia species in China is predicted to be between 250 and 300. Given the large number of begonia species that still remain to be described, further taxonomical work is urgently required. This is especially true for chinese Begonia, in which there is a huge diversity of habitat, habit, plant size, leaf type, flower and fruit morphology, and most species are narrowly distributed in isolated habitats that are subject to negative disturbances from climate change, as well as agricultural and industrial activities. Although the conservation status for the majority of species has been evaluated using the standards of the International Union for Conservation of Nature, the results don't represent the truth in many species, and also about11.5% of which are data-absent. In addition, illegal collection and over-harvesting of wild begonias for ornamental or medicinal use has increased due to the rapid development of internet commerce. Far more often than predicted, these species should be categorized as rare and endangered and require immediate protection. Ex situ conservation of chinese begonias started in 1995 and over 60% of the total species have been so far introduced into cultivation by several major botanical gardens in China. However, only few research institutions, limited funds and human resources have been involved in Begonia conservation;moreover, no project has conducted reintroduction. Therefore, more conservation-based work remains to be done. Improved conservation of chinese begonias in the future depends on further field survey, an improved understanding of population diversity, and integrative approaches, including in situ and ex situ conservat

关键词： Begonia Germplasm Diversity Conservation Taxonomic status China

Effective genome editing and identification of a regiospecific gallic acid 4-O-glycosyltransferase in pomegranate(Punica granatum L.)

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Horticulture research 2019年第1期6卷 206-220页

作者： Lijing Chang Sheng Wu Li Tian shanghai Key Laboratory of plant Functional Genomics and Resources Shanghai Chenshan Botanical Garden201602 ShanghaiChina shanghai chenshan plant science research center Chinese Academy of Sciences201602 ShanghaiChina Department of plant sciences University of CaliforniaDavisCA 95616USA

Pomegranate(Punica granatum L.)trees are woody perennials that bear colorful and nutritious fruits rich in phenolic metabolites,e.g.,hydrolyzable tannins(HTs)and *** here report genome editing and gene discovery in pomegranate hairy roots using Clustered Regularly Interspaced Short Palindromic Repeats(CRISPR)/CRISPR-associated protein 9(Cas9)(CRISPR/Cas9),coupled with transcriptome and biochemical *** guide RNAs(sgRNAs)were designed to target two UDP-dependent glycosyltransferases(UGTs),PgUGT84A23 and PgUGT84A24,which possess overlapping activities inβ-glucogallin(a galloylglucose ester;biosynthetic precursor of HTs)biosynthesis.A unique accumulation of gallic acid 3-O-and 4-O-glucosides(galloylglucose ethers)was observed in the PgUGT84A23 and PgUGT84A24 dual CRISPR/Cas9-edited lines(i.e.,ugt84a23 ugt84a24)but not the control(empty vector)or PgUGT84A23/PgUGT84A24 single edited lines(ugt84a23 or ugt84a24).Transcriptome and real-time qPCR analyses identified 11 UGTs with increased expression in the ugt84a23 ugt84a24 hairy roots compared to the *** the 11 candidate UGTs,only PgUGT72BD1 used gallic acid as substrate and produced a regiospecific product gallic acid *** work demonstrates that the CRISPR/Cas9 method can facilitate functional genomics studies in pomegranate and shows promise for capitalizing on the metabolic potential of pomegranate for germplasm improvement.

关键词： roots specific phenolic