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

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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The Molecular Regulatory Mechanism of the Hydrophobic Protein TaHFB1 from Trichoderma in Promoting Lateral Root Growth and Inducing Disease Resistance in Tomato

The Molecular Regulatory Mechanism of the Hydrophobic Protei...

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中国植物病理学会2024年学术年会

作者：尹雅萍 WANG Rui lin runmao TANG Zhengbin SUN Meiying YU Xiaoli 刘铜 School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication) Hainan University Key Laboratory of Green Prevention and Control of Tropical Diseases and Pests Ministry of Education (School of Tropical Agriculture and Forestry)Hainan University School of Tropical Agriculture and Forestry (School of Agricultural and Rural School of Rural Revitalization)Hainan University School of Life and health Sciences Hainan University Hainan Green Agricultural Biological Agent Innovation Engineering Research Center Hainan University Engineering Center of Agricultural Microbial Preparation Research and Development of Hainan Hainan University

Trichoderma *** a beneficial fungus known for its role in enhancing root growth and improving plant resistance to diseases,thereby sustaining plant *** the interactions between Trichoderma and plants have been the subject of several studies,the specific molecular mechanisms by which it promotes lateral root development and triggers plant disease resistance still need to be fully *** the interaction between Trichoderma harzianum and tomato,significant up-regulation of the expressed gene TaHFB1(with an up-regulation of 155-fold compared to the control) was observed,which promotes tomato lateral root growth and induces disease *** expression of the TaHFB 1 protein and its application to plant roots confirmed its functions in promoting growth and inducing disease *** function validation was performed to determine its role in promoting growth and inducing disease ***-MS/MS technology was used to screen for plant receptors interacting with the hydrophobicprotein TaHFB1,and yeast two-hybrid,pull-down,and co-immunoprecipitation assays were employed to confirm the target proteins involved in plant *** co-expression techniques were used to study the molecular mechanisms and signal transduction pathways of protein-receptor *** research aims to thoroughly comprehend the regulatory mechanism of TaHFBl and provide a theoretical foundation for the development of new plant growth stimulants or immune inducers.

关键词： Trichoderma harzianum plant disease resistance lateral root development plant receptors hydrophobic protein

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An optimized protocol for detecting guard cell specific gene expression by in situ RT-PCR in Brassica rapa

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Horticultural Plant Journal 2022年第3期8卷 311-318页

作者： Yingying Song Xinlei Guo Jian Wu Jianli Liang runmao lin Zifu Yan Xiaowu Wang College of Horticulture Henan Agricultural UniversityZhengzhou 450002China Institute of Vegetables and Flowers Chinese Academy of Agricultural SciencesBeijing 100081China

It is important to detect specific genes expressed in the guard cells,which control gas exchange and play key roles in response to drought and salt *** to the genetic transformation of Chinese cabbage(Brassica rapa)has not been well developed,in situ RT-PCR is a valuable option for detecting guard cell specific *** reported an optimized protocol of in situ RT-PCR by using an FAMA homologous gene Bra001929 in Brassica *** in Arabidopsis has been verified to be specially expressed in guard *** designed specific RT-PCR primers and optimized the protocol in terms of the(a)reverse transcription time,(b)blocking time,(c)antigen-antibody incubation time,and(d)washing *** approach provides a sensitive and effective in situ RT-PCR method for locating expression in the guard cells in Brassica ***,we proved the guard cell specific expression of Bra001929 in the epidermis indicating its’applicability as a marker gene for guard cells of Brassica rapa.

关键词： Brassica rapa In situ RT-PCR Gene expression Bra001929 Protocol

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Development of InDel Markers for Brassica rapa Based on a High-resolution Melting Curve

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Horticultural Plant Journal 2021年第1期7卷 31-37页

作者： Rong Chen Lichun Chang Xu Cai JianWu Jianli Liang runmao lin Yong Song Xiaowu Wang College of Horticulture Hunan Agricultural UniversityChangsha 410128China Institute of Vegetables and Flowers Chinese Academy of Agricultural SciencesBeijing 100081China

Brassica rapa is one of the most important leafy vegetable crops with large cultivated area in *** increase the availability of DNA markers in ***,we developed insertion-deletion(InDel)markers utilizing high-resolution melting(HRM)curve *** designed primers for 252 InDels(≥3 bp)evenly distributed in the genome and tested gene polymorphisms with eight *** total,208 markers were specifically amplified,and 148 InDels with polymorphism were genotyped successfully using *** further analyzed the correlation with InDel size,GC number,and predicted the difference in Tm values(Tm)using 208 markers with specific *** found that the success rate of InDel markers was correlated with the GC number of InDel and the predicted-Tm,but not clearly correlated with the length of *** the GC number within InDel was≥8,the successful rate exceeded 90.0%.When the predicted-Tm reached 0.5°C,the success rate was greater than 90.0%,and when it was≥0.6°C,the rate climbed to 100.0%,indicating their role as the optimal parameter for successful development of an applicable InDel *** polymorphic InDel markers can be easily genotyped using *** are of great value in genetic analysis,construction of linkage map,and molecular marker-assisted selection in ***.

关键词： Brassica rapa InDel marker HRM genotyping

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Variation in Plant Morphology and Sinigrin Content in Ethiopian Mustard(Brassica carinata L.)

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Horticultural Plant Journal 2019年第5期5卷 205-212页

作者： Tesfay Teklehaymanot Haijing Wang Jianli Liang Jian Wu runmao lin Zhen Zhou Xu Cai Xiaowu Wang Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture Sino-Dutch Joint Laboratory of Horticultural GenomicsInstitute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing100081China Tigray Agricultural Research Institute MekelleTigrayEthiopia

Ethiopian mustard(Brassica carinata) is mainly grown as a leafy vegetable and oilseed crop. Sinigrin is predominant glucosinolate in the leaves of Ethiopian mustard. It is hydrolyzed by enzyme myrosinase to produce bioactive product specifically allyl-isothiocyanates. Due to sinigrin content, Ethiopian mustard has a mild flavor and it is a healthy addition to human diet. However, sinigrin concentration depends on *** variations of plant morphology and sinigrin content may be the first step for crop improvement. According to the analyses of various plant characteristics among ninety nine Ethiopian mustard accessions, we found significant differences in plant height, chlorophyll content, and petiole length. In addition, sinigrin content was determined using ultra-performance liquid chromatography tandem quadrupole mass spectrometers/tunable ultraviolet detector(UPLC-TQS/TUV). We found a significant difference in sinigrin content among leaves of 94 Ethiopian mustard accessions. Except for petiole length, the sinigrin content was negatively correlated with leaf area, leaf width, number of primary branches, and plant height. This information will help Ethiopian mustard breeders in screening breeding lines for new accessions.

关键词： Brassicaceae mustard sinigrin leafy vegetable glucosinolate metabolite

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Conserved noncoding sequences correlate with distant gene contacts in Arabidopsis and Brassica

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Journal of Integrative Plant Biology 2023年第6期65卷 1467-1478页

作者： Lei Zhang Jian Wu Jianli Liang runmao lin Chao Sun Qirui Dai Lupeng Zhang Huiling Guo Ranze Zhao Xiaowu Wang State Key Laboratory of Vegetable Biobreeding Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing 100081China Research Institute of Forestry Chinese Academy of ForestryBeijing 100091China

Physical contact between genes distant on chromosomes is a potentially important way for genes to coordinate their *** investigate the potential importance of distant contacts,we performed high-throughput chromatin conformation capture(Hi-C)experiments on leaf nuclei isolated from Brassica rapa and Brassica *** then combined our results with published Hi-C data from Arabidopsis *** found that distant genes come into physical contact and do so preferentially between the proximal promoter of one gene and the downstream region of another *** with higher numbers of conserved noncoding sequences(CNSs)nearby were more likely to have contact with distant *** more CNSs came higher numbers of transcription factor binding sites and more histone modifications associated with the *** addition,for the genes we studied,distant contacting genes with CNSs were more likely to be transcriptionally *** observations suggest that CNSs may enrich active histone modifications and recruit transcription factors,correlating with distant contacts to ensure coordinated *** study advances our knowledge of gene contacts and provides insights into the relationship between CNSs and distant gene contacts in plants.

关键词： Arabidopsis Brassica conserved noncoding sequences distant gene contacts Hi-C

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Divergence of three BRX homoeologs in Brassica rapa and its effect on leaf morphology

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Horticulture Research 2021年第1期8卷 954-966页

作者： Yuanyuan Zhang Jianli Liang Xu Cai Haixu Chen Jian Wu runmao lin Feng Cheng Xiaowu Wang Institute of Vegetables and Flowers Chinese Academy of Agricultural ScienceBeijingChina

The leafy head characteristic is a special phenotype of Chinese cabbage resulting from artificial selection during domestication and *** RADIX(BRX)has been suggested to control root elongation,shoot growth,and tiller angle in Arabidopsis and *** Brassica rapa,three BrBRX homoeologs have been identified,but only BrBRX.1 and BrBRX.2 were found to be under selection in leaf-heading accessions,indicating their functional diversification in leafy head ***,we show that these three BrBRX genes belong to a plant-specific BRX gene family but that they have significantly diverged from other BRX-like members on the basis of different phylogenetic classifications,motif compositions and expression ***,although the expression of these three BrBRX genes differed,compared with BrBRX.3,BrBRX.1,and BrBRX.2 displayed similar expression *** mutant complementation studies showed that only BrBRX.1 could rescue the brx root phenotype,whereas BrBRX.2 and BrBRX.3 could ***,overexpression of each of the three BrBRX genes in Arabidopsis resulted in similar pleiotropic leaf phenotypes,including epinastic leaf morphology,with an increase in leaf number and leaf petiole length and a reduction in leaf *** leaf traits are associated with leafy head *** testing of a SNP(T/C)in BrBRX.2 confirmed that this allele in the heading accessions was strongly associated with the leaf-heading trait of *** results revealed that all three BrBRX genes may be involved in the leaf-heading trait,but they may have functionally diverged on the basis of their differential expression.

关键词： expression. traits heading

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白菜基因组导入芥菜的远缘杂交及后代分离偏向性

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新疆农业科学 2021年第7期58卷 1306-1315页

作者：李祥升常立春陈海旭武剑梁建丽林润茂郭新磊高杰王晓武新疆农业大学林学与园艺学院乌鲁木齐830052 中国农业科学院蔬菜花卉研究所北京100081

【目的】研究远缘杂交将结球白菜的A基因组导入包心芥菜,利用高分辨率熔解曲线(high-resolution melting,HRM)结合InDel标记辅助选择技术,筛选出保留白菜基因较多的回交后代,改良包心芥的结球性,丰富包心芥菜的种质资源。【方法】利用... 详细信息

【目的】研究远缘杂交将结球白菜的A基因组导入包心芥菜,利用高分辨率熔解曲线(high-resolution melting,HRM)结合InDel标记辅助选择技术,筛选出保留白菜基因较多的回交后代,改良包心芥的结球性,丰富包心芥菜的种质资源。【方法】利用幼胚培养技术辅助6份包心芥菜与2份结球白菜进行远缘杂交和回交,选取20个InDel标记追踪白菜A基因组全部染色体,从192的BC1单株中筛选出白菜A基因组标记占比较高的单株。田间调查筛选结球性近似结球白菜的单株。【结果】远缘杂交结合幼胚培养获得了9个种间杂种组合和14个BC1群体。筛选并获得203个在全基因组分布均匀的可区分白菜与芥菜的HRM-InDel标记;利用20个InDel标记追踪192株BC1单株的白菜基因,分离群体偏向传递白菜基因组,有54棵单株标记含量超过90%。【结论】幼胚培养技术可提高白菜与芥菜远缘杂交后回交的结实率,并可加快育种进程;筛选出了白菜基因组占比较高的组合和单株;分离群体明显偏向于传递白菜基因。

关键词：结球白菜包心芥菜远缘杂交 InDel标记偏分离

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两种方法治疗股骨干粉碎性骨折的疗效观察

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中国当代医药 2010年第20期17卷 18-19页

作者：戴润茂林天杰李国燕广东省电白县人民医院广东电白525400

目的:观察两种不同方法治疗股骨干粉碎性骨折的临床疗效。方法:将2008年1月～2009年1月在本院住院治疗的股骨干粉碎性骨折患者60例,随机分为观察组和对照组,每组各30例。对照组给予加压钢板内固定治疗,观察组给予交锁髓内钉内固定治疗... 详细信息

目的:观察两种不同方法治疗股骨干粉碎性骨折的临床疗效。方法:将2008年1月～2009年1月在本院住院治疗的股骨干粉碎性骨折患者60例,随机分为观察组和对照组,每组各30例。对照组给予加压钢板内固定治疗,观察组给予交锁髓内钉内固定治疗。结果:观察组患者手术时间、骨折愈合时间明显少于对照组,两组比较差异有统计学意义(P<0.05)。观察组患者术中出血量明显少于对照组,两组比较差异有统计学意义(P<0.05)。观察组并发症发生率为6.67%,对照组为33.33%,两组比较差异有统计学意义(P<0.05)。结论:交锁髓内钉内固定治疗股骨干粉碎性骨折效果优于加压钢板内固定,值得临床应用。

关键词：股骨干粉碎性骨折交锁髓内钉加压钢板内固定

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Sequencing,annotation and comparative analysis of nine BACs of the giant panda(Ailuropoda melanoleuca)

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Science China(Life Sciences) 2010年第1期53卷 107-111页

作者： ZHENG Yang1,2,3,CAI Jing4,LI JianWen3,6,LI Bo3,lin runmao3,TIAN Feng3,WANG Xiaoling3 & WANG Jun3,5 1Beijing Institute of Genomics,Chinese Academy of Sciences(CAS),Beijing 100029,China 2College of Life Science,Graduate University of Chinese Academy of Sciences,Beijing 100049,China 3Beijing Genomics Institute at Shenzhen,Shenzhen 518083,China 4CAS-Max Planck Junior Research Group on Evolutionary Genomics,State Key Laboratory of Genetic Resources and Evolution,Kunming Institute of Zoology,Chinese Academy of Sciences(CAS),Kunming 650223,China 5Department of Biology,University of Copenhagen,Copenhagen DK-2200,Denmark 6School of Biological Science and Engineering,South China University of Technology,Guangzhou 510006,China Beijing Institute of Genomics Chinese Academy of Sciences (CAS) Beijing China College of Life Science Graduate University of Chinese Academy of Sciences Beijing China Beijing Genomics Institute at Shenzhen Shenzhen China CAS-Max Planck Junior Research Group on Evolutionary Genomics State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences (CAS) Kunming China School of Biological Science and Engineering South China University of Technology Guangzhou China Department of Biology University of Copenhagen Copenhagen Denmark

A 10-fold BAC library for the giant panda was constructed and nine BACs were selected to generate finish *** BACs could be used as a validation resource for the de novo assembly accuracy of the whole genome shotgun sequencing reads of the giant panda newly generated by Illumina GA sequencing *** Sanger sequencing,assembly,annotation and comparative analysis were carried out on the selected BACs of a joint length 878 *** search and de novo prediction methods were used to annotate genes and *** protein coding genes were predicted,seven of which could be functionally *** seven genes have an average gene size of about 41 kb,an average coding size of about 1.2 kb and an average exon number of 6 per ***,seven tRNA genes were *** 27 percent of the BAC sequence is composed of repeats.A phylogenetic tree was constructed using a neighbor-join algorithm across five species,including the giant panda,human,dog,cat and mouse,which reconfirms dog as the most closely related species to the giant *** results provide detailed sequence and structure information for new genes and repeats of the giant panda,which will be helpful for further studies about the giant panda.

关键词： giant panda BAC sequencing assembly annotation evolution

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