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

The traditional method of screening plants for disease resistance phenotype is both time-consuming and costly.Genomic selection offers a potential solution to improve efficiency,but accurately predicting plant disease resistance remains a challenge.In 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 resistance.Our results demonstrate that the three plus kinship(K)methods developed in this study achieved high prediction accuracy.Specifically,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%,respectively.To 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 inoculation.Comparing 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 WSR.The 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.

Pathogenesis-related protein genes involved in race-specific allstage resistance and non-race specific high-temperature adultplant resistance to Puccinia striiformis f. sp. tritici in wheat

Interactions of the stripe rust pathogen （Puccinia striiformis f. sp responses. Among various genes involved in the plant-pathogen related （PR） protein genes determine different defense responses tritici） with wheat plants activate a w^ae range OT nost nteractions, the expressions of particular pathogenesis-Different types of resistance have been recognized and utilized for developing wheat cultivars for resistance to stripe rust. All-stage resistance can be detected in seedling stage and remains at high levels throughout the plant growth stages. This type of resistance is race-specific and not durable. In contrast, plants with only high-temperature adult-plant （HTAP） resistance are susceptible in seedling stage, but become resistant when plants grow older and the weather becomes warmer. HTAP resistance controlled by a single gene is partial, but usually non-race specific and durable. The objective of this study was to analyze the expression of PR protein genes involved in different types of wheat resistance to stripe rust. The expression levels of 8 PR protein genes （PR1, PRI.2, PR2, PR3, PR4, PR5, PR9 and PRIO） were quantitatively evaluated at 0, 1, 2, 7 and 14 days after inoculation in single resistance gene lines of wheat with all-stage resistance genes YrTrl, Yr76, YrSP and YrExp2 and lines carrying HTAP resistance genes Yr52, Yr59, Yr62 and Yr7B. Races PSTv-4 and PSTv-37 for compatible and incompatible interactions were used in evaluation of PR protein gene expression in wheat lines carrying all-stage resistance genes in the seedling- stage experiment while PSTv-37 was used in the HTAP experiment. Analysis of quantitative real-time polymerase chain reaction （qRT-PCR） revealed that all of the PR protein genes were involved in the different types of resistance controlled by different Yr genes. However, these genes were upregulated at different time points and at different levels during the infection process among the wheat lines with different Yr genes for either all-stage resistance or HTAP resistance. Some of the genes were also induced in compatible interactions, but the levels were almost always higher in the incompatible interaction than in the compatible interaction at the same time point for each Yr gene. These results indicate that both salicylic acid and jasmonate signaling pathways are involved in both race-specific all-stage resistance and non-race specific HTAP resistance. Although expressing at different stages of infection and at different levels, these PR protein genes work in concert for contribution to different types of resistance controlled by different Yr genes.

Plant Resistance to Pest and Research Progress of Its Genetic Improvement

Pest damage is a significant factor that cuts agricultural production, and cultivation of pest-resistant varieties is the most economic and effective approach of controlling pest damage. Plant pest resistance includes antixenosis, antibiosis, and tolerance. Current popular methods for the genetic improvement of crop pest resistance are traditional breeding method, transgenic breeding, and molecular mark-assisted breeding. This paper introduced major mechanisms and genetic bases of plant pest resistance, ＂and reviewed research progress of domestic and international genetic improvement of plant pest resistance, analyzed the problems and its de- velopment prospects.

Evaluation of cotton germplasm for morphological and biochemical host plant UPdates resistance traits against sucking insect pests complex

Background:Sucking insect pests cause severe damage to cotton crop production.The development of insect resistant cotton cultivars is one of the most effective measures in curtailing the yield losses.Considering the role of morphological and biochemical host plant resista nee(HPR)traits in plant defense,12 cotton genotypes/varieties were evaluated for leaf area,leaf glanding,total soluble sugars,total soluble proteins,total phenolics,tannin and total flavonoids against fluctuating populations of whitefly,thrips and jassid under field conditions.Results:The population of these insects fluctuated during the growing seas on and remained above threshold level(whitefly>5,thrips>(8-10)f or jassid>1 per leaf)during late June and early July.Strong and negative association of whitefly(r=-0.825)and jassid(r=-0.929)with seed cotton yield was observed.Mean population of insects were the highest in Glandless-1 followed by NIA-82 and NIA-M30.NIAB-Kiran followed by NI AB-878 and Sadori were the most resistant,with the mean population of 1.41,1.60,1.66(whitefly);2.24,232,2.53(thrips)and 037,0.31,036(jassid),respectively.The resistant variety NIAB-Kiran showed less soluble sugars(8.54 mg.g^(-1)),soluble proteins(27.11 mg.g^(-1))and more phenolic(36.56 mg.g^(-1))and flavonoids(13.10mg.g^(-1))as compared with the susceptible check Glandless-1.Moreover,all insect populations were positively correlated with total soluble sugars and proteins.Whitefly populations exhibited negative response to leaf gossypol glands,total phenolics,tannins and flavonoids.The thrips and jassid populations had a significant and negative correlation with these four biochemical HPR traits.Conclusion:The ide ntified resistant resources and HPR traits can be deployed against sucking in sect pests'complex in future breeding programs of developing insect resistant cotton varieties.

An extraction-assay system： Evaluation on flavonols in plant resistance to Pb and Cd by supercritical extraction-gas chromatography

In this research, supercritical carbon dioxide extraction （SFE） showed better extraction etlect when compared with Solid- liquid extraction （SLE）, Soxhlet extraction （SEt and Ultrasonic extraction （UE）, not only in the rate but also the time. The comparison among these three extraction modifiers, including acetone, ethanol and methanol demonstrated that ethanol was preferred to SFE due to its high extraction effect and low toxicology. In addition, parameter of SFE, influence of temperature and pressure were investigated, and the best extraction effect was achieved at the optima conditions, temperature of 40℃ and the pressure of 35 MPa. Thus, SFE is a highly effective method for flavonols extraction, requiring minimum energy and producing non-toxic byproduct. SFE-GC system is applied for the evaluation on flavonols that plays a key role in plant resistance to heavy metal, with its content and synthetase gene expression significantly increasing in plant when threatened by heavy metal. Besides, results indicated that flavonols can improve plant resistance to oxidative stress by quenching the redundant ROS in matrix.

The Resistance of Crops in Plant Protection

World crop production requires highly-productive varieties of agricultural crops,which are resistant to pest organisms.Such varieties are also of great importance for the Uzbekistan.Their

Characterization and screening of cotton(Gossypium hirsutum L.)germplasm for leafhopper(Amrasca biguttula biguttula(Ishida))resistance

Background Cotton(Gossypium hirsutum L.)is one of the most significant fibre and cash crops and plays an important role in Indian industrial and agricultural economies.However,over the years quantity and quality have been hampered by the pest leafhopper.Leafhopper alone has been shown to cause yield losses of up to 40%.In this study,screening and evaluation were performed to identify and categorize 100 cotton genotypes along with 5 checks as resistant,moderately resistant,sensitive and highly sensitive to leafhoppers.Results A total of hundred genotypes were evaluated along with five checks for leafhopper resistance.Based on the screening results,a total of 19 genotypes were resistant to leafhoppers,which was on par with the findings of the check KC 3.The contents of total soluble sugar,total soluble protein,and total free amino acids were significantly positively correlated with the mean grade,whereas total phenols content and trichome density were significantly negatively correlated with the susceptibility grade.However,based on screening and biochemical analysis,the genotypes KC 2,JR-23,Samaru-26-T,D 4,TCH 1728,RS 253,and B-61-1862 exhibited high resistance to leafhopper.Conclusion According to the findings of this study,choosing genotypes with high total phenolics content together with high trichome density and low contents of total soluble sugar,total soluble protein,and free amino acids may aid in the development of resistant genotypes.

Application of Real-time Fluorescent Quantitative PCR in Plant

Real-time fluorescent quantitative PCR （RQ-PCR） is a detection method by adding fluorescent dye or fluorescent probe into the PCR reaction system, using fluorescent signal accumulation to monitor amplification reactions of PCR reaction process, and finally the unknown template can be quantitatively analyzed through the standard curve. So the detection level of PCR has improved from the qualitative to the quantitative. In order to provide a theoretical reference for further application, the principle, classification, advantages and disadvantages of RQ-PCR were intro- duced, and its application and progress in plants in recent years were reviewed.

Evaluation of the Resistance of Different Tea Cultivars to Tea Aphids by EPG Technique

In order to investigate the resistance of tea plant to tea aphid, the feeding behavior of tea aphids on six different tea cultivars was monitored by （EPG） technique. The result showed that the duration of El, E2 as well as （E I＋E2） which was feeding waveforrns of Toxoptera aurantii （Boyer） in tea phloem was significantly different by variance analysis （P〈0.05） and so did the duration of the probing of T. aurantii in all the tea tissues. And the six tea cultivars were classified into three groups with cluster analysis, based on the six major parameters which were durations of np, C, El, E2, F, and G waveforms, then the six major parameters of these three groups were detected by variance analysis, and the rank of six different tea cultivars＇ resistance to T. aurantii from strong to weak was Zhongcha 108, Sucha 1, Anjibaicha, Longjing 43, Xicha 5, and Sucha 120. As this result was in accord with the investigation into the tea field, we concluded that EPG technique was one of the most important means to examine tea plant resistance to T. aurantii and the durations of waveform El, E2 and （El＋E2） were important parameters for evaluating resistance of tea plants to tea aphids.

NaPDR1 and NaPDR1-like are essential for the resistance of Nicotiana attenuata against fungal pathogen Alternaria alternata

Pleiotropic drug resistance(PDR) transporters are widely distributed membrane proteins catalyzing the export or import of a diverse array of molecules, and are involved in many plant responses to biotic and abiotic stresses. However, it is unclear whether PDRs are involved in Nicotiana attenuata resistance to the necrotic fungal pathogen Alternaria alternata. In this study, transcriptional levels of both NaPDR1 and NaPDR1-like were highly induced in N. attenuata leaves after A. alternata inoculation. Interestingly,silencing NaPDR1 or NaPDR1-like individually had little effect on N. attenuata resistance to A. alternata;however, when both genes were co-silenced plants became highly susceptible to the fungus, which was associated with elevated JA and ethylene responses. Neither NaPDR1 nor NaPDR1-like was significantly elicited by exogenous treatment with methyl jasmonate(MeJA), whereas both were highly induced by ethylene. The elicitation levels of both genes by A. alternata were significantly reduced in plants with impaired JA or ethylene signaling pathways. Thus, we conclude that both NaPDR1 and NaPDR1-like function redundantly to confer resistance against A. alternata in N. attenuata, and the elicitation of the transcripts of both genes by the fungus is partially dependent on ethylene and jasmonate signaling.

Identification of stably expressed QTL for resistance to black shank disease in tobacco(Nicotiana tabacum L.) line Beinhart 1000-1

Cigar line Beinhart 1000-1 has effective durable resistance to black shank(BS) and is considered one of the most resistant sources in tobacco(Nicotiana tabacum L.). To investigate the inheritance and identification of stable quantitative trait loci(QTL) for BS response, F2,BC1 F2 individuals and BC1 F2:3 lines were produced from a cross between Beinhart 1000-1 and Xiaohuangjin 1025. Two major quantitative trait loci(M-QTL) named qBS7 and qBS17 were repeatedly detected under different conditions. QTL qBS7 was mapped to the region between PT30174 and PT60621 and explained 17.40%–25.60% of the phenotypic variance under different conditions. The other QTL qBS17 in interval PT61564–PT61538 of linkage group 17 was detected in a BC1 F2 population in the field and in BC1 F2:3 in both the field and at the seedling stage, explaining 6.90% to 11.60% of the phenotypic variance. The results improve our understanding of the inheritance of resistance to BS and provide information that can be used in marker-assisted breeding.

The Mechanisms of Trichoderma Species to Reduce Drought and Salinity Stress in Plants

Environmental stresses caused by climate change have severely affected agriculture in the present century;Salinity and drought have challenged most forecasts for increased agricultural production in the past few decades,there-fore,different methods that reduce the effect of these stresses on plants have attracted scientists’attention.The effect of beneficial soil microorganisms on soil health and increasing plants’resistance to stresses is one of the solutions that researchers have paid attention to.This study investigated how Trichoderma species can be affected by the molecular and morphophysiological mechanisms of plants and improve their salt and drought resistance.This study also studied the different Trichoderma species’functions to get a better understanding of how they reduce salt and drought stresses.Furthermore,thefindings of this study provide a clear path for future research to focus on the unknown aspects of Trichoderma species andfind effective ways to boost crop production under environmental stresses.

山东茶树叶片解剖结构分析

本文描述了茶树叶片的形态及解剖结构研究意义和现状,比较了 51 个茶树品种、育种材料的解剖结构,分析比较了不同品种、育种材料以及不同地区间的抗寒性,为茶树的北方地区茶树引种栽培、新品种和抗寒类型的筛选提供了理论依据。

Advances on Rare Earth Application in Pollution Ecology

The use of rare earth for inducing plant resistance was reviewed. The important developments in recent years were described, and rare earth can alleviate the pollution of acid rain, ozone, pesticide, heavy metals etc. in environment. The authors suggest that the mechanism of rare earth to inducing plant resistance and reducing plant injury is to control biochemical metabolism web in plant cell, to adjust its protection system of free radical, to maintain its photosynthesis, to protect cell membrane system and to carry through its function on mineral metabolism. Meanwhile some problems in the field were discussed as well.

CRYPTOCHROME 1 Is Implicated in Promoting R Protein-Mediated Plant Resistance to Pseudomonas syringae in Arabiclopsis

Plants have evolved complex mechanisms to defend themselves against pathogens. It has been shown that several defense responses are influenced by light, and the red/far-red light photoreceptor phytochromes （PHY） modulate plant defense responses in Arabidopsis. Blue light receptor cryptochromes （CRY） work together with PHY to regulate many light-controlled responses, including photomorphogenesis, floral induction, and entrainment of the circadian clock. We report here that the Arabidopsis blue light photoreceptor CRY1 positively regulates inducible resistance to Pseudomonas syringae under continuous light conditions. By challenging plants with R syringae pv. tomato （Pst.） DC3000 carrying avrRpt2, we demonstrate that effector-triggered local resistance is down-regulated in the cry1 mutant, leading to more pathogen multiplication. In plants overexpressing CRY1 （CRYl-ovx）, however, local resistance is significantly up-regulated. We also show that systemic acquired resistance （SAR） is positively regulated by CRY1, and that salicylic acid （SA）-induced pathogenesis-related gene PR-1 expression is reduced in the cry1 mutant, but enhanced in CRYl-ovx plants. However, our results in- dicate that CRY1 only modestly influences SA accumulation and has no effect on hypersensitive cell death. These results suggest that CRY1 may positively regulate R protein-mediated resistance to P. syringae with increased PR gene expression.

Effects of silicon amendment on the occurrence of rice insect pests and diseases in a field test

Rice is one of the most important staple foods for the world population,but it is attacked by a number of destructive pests.While evidence from greenhouse and laboratory tests has shown that silicon（Si）amendment can confer enhanced resistance to pests in rice,few studies have directly demonstrated the Si-mediated protection from pests in a field situation.In this study,field plots with silicon amendments at 0,75,150 and 300 kg SiO2 ha-1 in early-and late-season rice were employed to evaluate the effects of silicon amendment on the occurrence of major insect pests and diseases and rice yield.Compared with the control plots without silicon amendment,plant damage by stem borer and leaf folder and population size of planthopper were significantly lower in three to five of the seven monitoring observations in each season in the plots amended with 300 kg SiO2 ha-1.The disease index of rice blast in the early-season rice was lower in the plots amended with Si at 300 kg SiO2 ha-1 than in the control plots,while Si protection from rice blast in the late-season rice and from rice sheath blight in the early-season rice were not apparent.An insignificant increase of rice yield by 16.4%（604 kg ha-1）was observed in the plots amended with 300 kg SiO2 ha-1 over the control plots.Our results indicate that Si amendment at 300kg SiO2 ha-1 can provide substantial protection from some of the rice pests under field conditions.These findings support the recommendation of silicon amendment as a key component of integrated management of rice pests.

Field Evaluation of the Asian Corn Borer Control in Hybrid of Transgenic Maize Event MON 810

In this study, a transgenic Bt maize hybrid (event MON 810 from Monsanto Company) expressing Cry1Ab protein derived from Bacillus thuringiensis (Bt) and its negative isoline hybrid were evaluated for control of the Asian corn borer, Ostrinia furnacalis (Guenée) (Lepidoptera: Pyralidae), in a field trial. Maize plants were artificially infested with neonate larvae of Asian corn borer at the mid-whorl (first-generation), pre-tassel (first- and/or second-generation), and silk (second-generation) growth stages. The transgenic Bt maize hybrid sustained significantly less leaf feeding damage (rating 1.0±0.0) than its negative isoline control (rating 7.3±0.1). With the Bt maize, 1.36.8% of plants were damaged by corn borer tunneling with <0.5 cm tunneling per stalk under different levels of infestation, compared with 100% of plants damaged with 9.325.0 cm tunneling per stalk for the negative isoline control. On average, transgenic Bt maize hybrids had only 0.010.05 tunnels per stalk and no stems were broken. In contrast, the negative isoline control had 3.118.36 tunnels per stalk and 31.273.9% of stems broken. Yields were significantly higher in transgenic Bt maize than in the control. These results demonstrate that transgenic Bt maize can significantly minimize yield losses caused by the Asian corn borer through resistance to the first- and second-generation larvae.

Alternaria toxin-induced resistance against rose aphids and olfactory response of aphids to toxin-induced volatiles of rose plants

The search for active toxins for managing weeds or plant diseases is believed to be a promising avenue of investigation. However, the effects of Alternaria toxins on insects have just begun to be investigated. Bioactivities of toxins from four strains of Altemaria alternata on Rosa chinensis and rose aphid Macrosiphum rosivorum were tested in the present study. At a concentration of 50.0 pg/ml, the crude extract （toxin） of strain 7484 was found not to be harmful to rose plants with excised leaf-puncture method （P≥0.079）, and rose plants showed enhanced resistance to rose aphids when this Altemaria toxin was sprayed on the plants （P≤0.001）. However, this toxin caused no detrimental effects on aphids in insecticidal bioassay at a concentration of 10.0 to 160.0 μg/ml （P≥0.096）. Therefore, the Alternaria toxin had significantly induced the resistance of rose plants against rose aphids, demonstrating that the resistance mechanism triggered by the Altemaria toxin in the rose plant may also be used by the plant to defend itself against insects. Further bioassays aimed to discover the olfactory responses of aphids to the toxin-induced volatiles of host plants. The aphids were significantly more attracted to both volatiles emitted and collected from control rose plants than to both volatiles emitted and collected from the toxin-treated rose plants （P≤0.014）. This result showed that the toxin-induced resistance related to the volatile changes of host plants.

Integrating flood depth and plant resistance with chlorantraniliprole seed treatments for management of rice water weevil, Lissorhoptrus oryzophilus （Coleoptera： Curculionidae）

Chlorantraniliprole seed treatments in rice provide effective suppression of rice water weevil populations in the United States; however, heavy reliance on prophylac- tic insecticide treatments as a sole strategy could destabilize management programs for this insect. The present research evaluated the compatibility of seed treatments with two other potential management tactics--plant resistance and shallow flooding-by conducting two split-plot experiments in 2009 and 2011. In both experiments, no substantial antago- nism was found among the 3 different tactics. Statistical interactions in these experiments arose from the strong and persistent effects of chlorantraniliprole on larval densities rather than incompatibility of tactics. In 2009, weevil densities differed among varieties and were significantly lower on the cultivar ＂Jefferson.＂ In 2011, weevil densities were reduced sig- nificantly in shallow-flooded plots compared to deep-flooded plots. Significant reductions in weevil numbers by chlorantraniliprole seed treatments, even at application rates 5 fold lower than commercially recommended rates, demonstrated the potential to reduce appli- cation rates of this highly potent larvicide. These latter results suggest that future studies on the relationship between chlorantraniliprole seed treatment rate and weevil fitness are warranted.

Genome-wide identification and expression analysis of GDSL esterase/lipase genes in tomato

The GDSL esterase/lipase family contains many functional genes that perform important biological functions in growth and development, morphogenesis, seed oil synthesis, and defense responses in plants. The expression of GDSL esterase/lipase genes can respond to biotic and abiotic stresses. Although GDSL esterase/lipase family genes have been identified and studied in other plants, they have not been identified and their functions remain unclear in tomato. This study is the first to identify 80 GDSL esterase/lipase family genes in tomato, which were named SlGELP1–80. These genes were mapped to their positions on the chromosomes and their physical and chemical properties, gene structure, phylogenetic relationships, collinear relationships, and cis-acting elements were analyzed. The spatiotemporal expression characteristics of the Sl GELP genes in tomato were diverse. In addition, RNA-seq analysis indicated that the expression patterns of the SlGELP genes in tomato differed before and after inoculation with Stemphylium lycopersici. qRT-PCR was used to analyze the expression of five Sl GELP genes after treatments with S. lycopersici, salicylic acid and jasmonic acid. Finally, this study was the first to identify and analyze GDSL esterase/lipase family genes in tomato via bioinformatics approaches, and these findings provide new insights for improving the study of plant disease resistance.