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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

Identification of a unique 312.nucleotides variant of Hop stunt viroid（HSVd） with a tandem 15 nucleotides repeat from plum

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Identification of a unique 312 nucleotides variant of Hop st...

The GmSTF1/2.GmBBX4 negative feedback loop acts downstream of blue-light photoreceptors to regulate isoflavonoid biosynthesis in soybean

中国植物保护学会2.07年学术年会

作者： Yuanai Yang~(1,2. Hongqing wang~2.Zujian WU~3 Zhuomin Cheng~1 Shifang Li~(1*) (1 State Key Laboratory for Biology of plant Diseases and Insect Pests,Institute of plant Protection,Chinese Academy of agricultural Sciences,Yuanmingyuan West No.2. beijing 100094,People''s Republic of china 2.department of Fruit Science, College of Agronomy and Biotechnology,china agricultural university,beijing, People''s Republic of china.3 Institute of plant Virology,Fujian Agriculture and Forestry university,Fuzhou 350002.china)

＜正＞Sixty-eight plum samples were collected from 12.different provinces of *** molecular weight RNAs were extracted and used for dot-blot,reverse transcription-polymerase chain reaction （RT-PCR）,return-polyacrylamide gel electrophoresis（R-PAGE）,and biological indexing using cucumber .Results showed that 15 of the 68 plum samples were positive for Hop stunt viroid（HSVd）.Four positive samples were selected for cloning and sequence *** indicated that most HSVd sequences from the plum in china had 1～3 nucleotides changes from the closest HSVd in *** addition,the sample PB2.（cv."Friar"） collected from Hebei province had one sequence with a 15 nt duplication （named HSVd D-15） at the 2.4/2.5 position in the lower central *** biological indexing,cucumber seedlings,an indicator {2. for HSVd,were inoculated with RNAs directly extracted from the original plum source（PB 2.,cv."Friar"）.Nucleotide sequencing analysis of the progeny showed that HSVd but not HSVd-D15,was recovered from inoculated *** very unlikely,the possibility that this extra sequence was the result of a PCR artifact cannot be completely ruled out.

关键词： Hop stunt viroid plum recombination sequence repeat

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plant Communications 2024年第2期5卷 198-214页

作者： Zhaoqing Song Fengyue Zhao Li Chu Huan lin Yuntao Xiao Zheng Fang Xuncheng wang Jie Dong Xiangguang Lyu Deyue Yu Bin Liu Junyi Gai Dongqing Xu National Center for Soybean Improvement State Key Laboratory of Crop Genetics&Germplasm Enhancement and UtilizationCollege of AgricultureNanjing Agricultural UniversityNanjing 210095China beijing Key Laboratory of Environmentally Friendly Management of Fruit Diseases and Pests in North china Institute of Plant and Environment ProtectionBeijing Academy of Agriculture and Forestry SciencesBeijing 100097China Institute of Crop Science College of Agriculture and BiotechnologyZhejiang UniversityHangzhou 310058China State Key Laboratory of Crop Gene Resources and Breeding Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijing 100081China

Isoflavonoids,secondary metabolites derived from the phenylalanine pathway,are predominantly bio-synthesized in legumes,especially soybean(Glycine max).They are not only essential for plant responses to biotic and abiotic stresses but also beneficial to human *** this study,we report that light signaling controls isoflavonoid biosynthesis in ***-light photoreceptors(GmCRY1s,GmCRY2.,GmPHOT1s,and GmPHOT2.)and the transcription factors GmSTF1 and GmSTF2.promote isoflavonoid accumulation,whereas the E3 ubiquitin ligase GmCOP1b negatively regulates isoflavonoid ***1s and GmPHOT2. stabilize GmSTF1/2.whereas GmCOP1b promotes the degradation of these two proteins in ***1/2.regulate the expression of approximately 2..9%of the genes involved in soybean isoflavonoid biosynthesis,including GmPAL{2.GmPAL2.3,and *** also repress the expression of GmBBX4,a negative regulator of isoflavonoid biosynthesis in *** addition,GmBBX4 physically interacts with GmSTF1 and GmSTF2.to inhibit their transcriptional activation activity toward target genes related to isoflavonoid ***,GmSTF1/2.and GmBBX4 form a negative feedback loop that acts downstream of photoreceptors in the regulation of isoflavonoid *** study provides novel insights into the control of isoflavonoid biosynthesis by light signaling in soybean and will contribute to the breeding of soybean cultivars with high isoflavonoid content through genetic and metabolic engineering.

关键词： photoreceptor light signaling isoflavonoid GmSTF GmBBX4 soybean

Plastid phylogenomics provides new insights into the systematics,diversification,and biogeography of Cymbidium(Orchidaceae)

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plant Diversity 2024年第4期46卷 448-461页

作者： Hai-Yao Chen Zhi-Rong Zhang Xin Yao Ji-Dong Ya Xiao-Hua Jin lin wang Lu Lu De-Zhu Li Jun-Bo Yang Wen-Bin Yu Center for Integrative Conservation&Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesMenglaYunnan 666303China university of Chinese Academy of Sciences Huairou DistrictBeijing 101408China plant Germplasm and Genomics Center Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunmingYunnan 650201China State Key Laboratory of plant Diversity and Specility Crops Institute of BotanyChinese Academy of SciencesHaidian DistrictBeijing 100093China School of Pharmaceutical Sciences Yunnan Key Laboratory of Pharmacology for Natural Productsand Yunnan College of Modern Biomedical IndustryKunming Medical UniversityKunmingYunnan 650500China Southeast Asia Biodiversity Research Institute Chinese Academy of SciencesYezinNay Pyi Taw 05282Myanmar

Cymbidium(Orchidaceae:Epidendroideae),with around 60 species,is widely-distributed across Southeast Asia,providing a nice system for studying the processes that underlie patterns of biodiversity in the ***,phylogenetic relationships of Cymbidium have not been well resolved,hampering investigations of species diversification and the biogeographical history of this *** this study,we construct a plastome phylogeny of 56 Cymbidium species,with four well-resolved major clades,which provides a framework for biogeographical and diversification rate *** dating and biogeographical analyses show that Cymbidium likely originated in the region spanning northern IndoBurma to the eastern Himalayas during the early Miocene(~2..10 Ma).It then rapidly diversified into four major clades in East Asia within approximately a million years during the middle *** *** to the adjacent regions(Borneo,Philippines,and Sulawesi)primarily occurred during the Pliocene-Pleistocene *** analyses indicate that the net diversification rate of Cymbidium has decreased since its origin,and is positively associated with changes in temperature and monsoon *** hydrothermal conditions brought by monsoon intensification in the early Miocene possibly contributed to the initial rapid diversification,after which the net diversification rate was reduced with the cooling climate after the middle *** transition from epiphytic to terrestrial habits may have enabled adaptation to cooler environments and colonization of northern niches,yet without a significant effect on diversification *** study provides new insights into how monsoon activity and temperature changes affected the diversification dynamics of plants in Southeast Asia.

关键词： Cymbidium East Asia Asian monsoons Climate change Biogeographical patterns

The MADS-box transcription factor GmFULc promotes GmZTL4 gene transcription to modulate maturity in soybean

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Journal of Integrative plant Biology 2024年第8期66卷 1603-1619页

作者： Jingzhe Sun Yucheng Liu Yuhong Zheng Yongguo Xue Yuhuan Fan Xiaofei Ma Yujia Ji Gaoyuan Liu Xiaoming Zhang Yang Li Shuming wang Zhixi Tian lin Zhao Key Laboratory of Soybean Biology of Ministry of Education china Northeast Agricultural UniversityHarbin 150030China Qingdao Institute of Bioenergy and Bioprocess Technology The Chinese Academy of SciencesQingdao 266101China State Key Laboratory of plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignThe Chinese Academy of SciencesBeijing 100101China Jilin Academy of agricultural Sciences China Agricultural Science and Technology Northeast Innovation CenterChangchun 130033China Institute of Soybean Research Heilongjiang Provincial Academy of Agricultural SciencesHarbin 150086China Depatment of Environmental and plant Biology Ohio UniversityAthensOhio 45701USA

Flowering time and maturity are crucial agronomic traits that affect the regional adaptability of soybean *** development of soybean cultivars with early maturity adapted to longer days and colder climates of high latitudes is very important for ensuring normal ripening before frost *** belongs to the MADS-box transcription factor family and has several duplicated members in *** this study,we observed that overexpression of GmFULc in the Dongnong 50 cultivar promoted soybean maturity,while GmFULc knockout mutants exhibited late *** immunoprecipitation sequencing(ChIP-seq)and RNA sequencing(RNA-seq)revealed that GmFULc could bind to the CArG,bHLH and homeobox *** investigation revealed that GmFULc could directly bind to the CArG motif in the promoters of the GmZTL3 and GmZTL4 *** of GmZTL4 promoted soybean maturity,whereas the ztl4 mutants exhibited delayed ***,we found that the cis element box 4 motif of the GmZTL4 promoter,a motif of light response elements,played an important role in controlling the growth *** of this motif shortened the growth period by increasing the expression levels of *** investigations revealed that short-day treatment promoted the binding of GmFULc to the promoter of GmZTL4 and inhibited the expression of E1 and E1Lb,ultimately resulting in the promotion of flowering and early *** together,these findings suggest a novel photoperiod regulatory pathway in which GmFULc directly activates GmZTL4 to promote earlier maturity in soybean.

关键词： flowering time GmFULc GmZTL4 maturity photoperiod

Hydrogen peroxide-mediated activation of mitogen-activated protein kinase 6 modulates nitric oxide biosynthesis and signal transduction in Arabidopsis thaliana

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Cloning and functional analysis of chloroplast division gene NtFtsZ2.l in Nicotiana tabacum

中国植物学会植物细胞生物学2.1.年学术年会

作者： Pengcheng wang~1,Yanyan Du~1,Yuan Li~2.Dongtao Ren~2.Chun-Peng Song~(1*) 1 Laboratory of plant Stress Biology,{2. of Biology,Henan university,Kaifeng 475001 2.State Key Laboratory of plant Physiology and Biochemistry,china agricultural university,beijing 100193

Nitric oxide(NO) is a bioactive molecule that functions in numerous physiological and developmental processes in plants,including lateral root *** this study,we used biochemical and genetic approaches to analyze the function of Arabidopsis mitogen-activated protein kinase 6(MPK6) in the regulation of NO synthesis in response to hydrogen peroxide(HO) during lateral root *** both mpk6 mutants studied,HO-induced NO synthesis and nitrate reductase(NR) activity were decreased ***,the NR isoform,NIA2.was required for the MPK6-mediated production of NO induced by ***,NIA2.interacted physically with MPK6 in vitro and in vivo,and also served as a substrate of *** 62. was the putative phosphorylation site of *** of NIA2.by MPK6 led to an increase in NR activity. Phenotypical analysis revealed that mpk6-2.and mpk6-3 seedlings produce more and longer lateral roots than that wild-type plants did after application of the NO donor sodium nitroprosside(SNP) or HO. These data support strongly a novel function of MPK6 in modulating NO production and signal transduction in response to HO during root development.

关键词：

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Progress in Natural Science:Materials International 2003年第5期 39-43页

作者： KONG Dongdong , JU Chuanli, wang Dong, HU Yong, ZHU Zhiqing, HE Yikun and SUN Jingsan (1. Key Laboratory of Photosynthesis and Enviromental Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, beijing 100093, {2. 2. department of Biology, Capital Normal university, beijing 100037, {2. 3. Laboratory of Agronomy and Biotechnology, china agricultural university, beijing 100037, {2. 4. College of Life Sciences, beijing Normal university, beijing 100875, {2.)

FtsZ protein plays an important role in the division of chloroplasts. With the finding and functional analysis of higher plant FtsZ proteins, people have deepened the understanding in the molecular mechanism of chloroplast division. Multiple ftsZ genes are diversified into two families in higher plants, ftsZ1 and ftsZ2.. On the basis of the research on ftsZl family, we analyzed the function of NtFtsZ2.l gene in Nicotiana tabacum . Microscopic analysis of the sense and antisense NtFtsZ2.l transgenic tobacco plants revealed that the chloroplasts were abnormal in size and also in number when compared with wild-type tobacco chloroplasts. Our investigations confirmed that the NtFtsZ2.l gene is involved in plant chloroplast division.

关键词： Nicotiana tabacum NtFtsZ2.l gene chloroplast division.

TOTAL SYNTHESIS OF SEX PHEROMONE COMPONENTS OF HYPHANTRIA CUNEA

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TOTAL SYNTHESIS OF SEX PHEROMONE COMPONENTS OF HYPHANTRIA CU...

AtHsfA2.modulates expression of stress responsive genes and enhances tolerance to heat and oxidative stress in Arabidopsis

The ⅩⅤth International plant Protection Congress

作者： CHE Chao1 ZHANG Zhong-ning1 wang Xin-xing2.and YAN Zheng-liang1 1Institute of Zoology Chinese Academy of Sciences beijing 100080 {2. 2.3} of Applied Chemistry {2. agricultural university beijing 100094 {2.

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Science china(Life Sciences) 2005年第6期48卷 540-550页

作者： LI Chunguang1,2. CHEN Qijun1, GAO Xinqi1,3, QI Bishu1, CHEN Naizhi1, XU Shouming1, CHEN Jia1 & wang Xuechen1 1. State Key Laboratory of plant Physiology and Biochemistry, College of Biological Sciences,{2., beijing 100094, china 2. department of Industry Engineering, Zhengzhou Institute of Aeronautic Industry Management, Zhengzhou 450015, china 3. College of Life Science, Qufu Normal university, Qufu Shandong 2.3165, china 1. State Key Laboratory of plant Physiology and Biochemistry College of Biological Sciences China Agricultural University 100094 Beijing China 2. department of Industry Engineering Zhengzhou Institute of Aeronautic Industry Management 450015 Zhengzhou China 3. College of Life Science Qufu Normal University 273165 Qufu Shandong China

There is increasing evidence for considerable interlinking between the responses to heat stress and oxidative stress, and recent researches suggest heat shock transcription factors (Hsfs) play an important role in linking heat shock with oxidative stress signals. In this paper, we present evidence that AtHsfA2.modulated expression of stress responsive genes and enhanced tolerance to heat and oxidative stress in Arabidopsis. Using Northern blot and quantitative RT-PCR analysis, we demonstrated that the expression of AtHsfA2.was induced by not only HS but also oxidative stress. By functional analysis of AtHsfA2.knockout mutants and AtHsfA2.overexpressing transgenic {2.s, we also demonstrated that the mutants displayed reduced the basal and acquired thermotolerance as well as oxidative stress tolerance but the overexpression lines displayed increased tolerance to these stress. The phenotypes correlated with the expres-sion of some Hsps and APX1, ion leakage, H2.2.level and degree of oxidative injuries. These results showed that, by modulated expression of stress responsive genes, AtHsfA2.enhanced tolerance to heat and oxidative stress in Arabidopsis. So we suggest that AtHsfA2.plays an im-portant role in linking heat shock with oxidative stress signals.

关键词： heat shock transcription factor, heat stress response, oxidative stress response, tolerance.