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.

Physiological Response and Resistance of Plants to Disease and Pest Stress

This paper outlines the physiological responses of plants to pathogenic microbial infection and pest feeding stress,as well as the resistance characteristics of plants to diseases and pests,and proposes new directions for future research on crop resistance to diseases and pests.The objective of this paper is to provide a reference framework for the breeding of crops with enhanced resistance to diseases and pests,the utilization of natural immunity in crops,and the efficient prevention and control of diseases and pests.This framework is intended to facilitate the healthy and sustainable development of the agricultural industry.

Breeding and Application Techniques of a New Rice Variety Liliang-you 3822 with High Yield and Disease Resistance

Liliangyou 3822 is a novel indica hybrid rice variety that exhibits disease resistance,high yield,lodging resistance,and late maturity.It employs a self-selected two-line sterile line,Li 38S,and a self-selected restorer line,R22.This variety was subjected to a regional test of indica late-maturing groups in the middle and lower reaches of the Yangtze River in 2020.The results demonstrated that the average yield of the variety was 9.95 t/hm 2,which was 10.67%higher than that of the control Fengliangyou 4,indicating a highly significant yield increase.In the continuous test in 2021,the average yield was 9.74 t/hm 2,representing a 6.52%increase over the control,which also exhibited a significant increase.Finally,the average yield of the two years regional test was 9.84 t/hm 2,which was 8.58%higher than that of the control.In the 2021 production test,the average yield of the variety was 9.32 t/hm 2,which was 12.19%higher than that of the control,indicating a remarkably significant yield increase.In 2022,the variety was validated by the National Crop Variety Approval Committee(GSD 20220143).

Breeding of a New Medium Indica Variety Liangyou 7968 with Good Quality and Disease Resistance

With global warming and frequent occurrence of severe weather,rice diseases are also on the rise.Therefore,the breeding of new rice varieties with disease resistance is still the breeding direction for rice breeding experts."Liangyou 7968"is a new hybrid rice combination with double resistance to bacterial blight and rice blast.This paper introduced the breeding process,characteristics,high-yielding cultivation techniques and high-yielding seed production technical regulations for Liangyou 7968.

Utilization of Changyun Jujube, a Cultivar with Resistance to Witches Broom Disease

In 2021,the Shanting District Fruit Industry Service Center conducted an application test of a treatment for jujube witches broom disease using Changyun jujube.The results demonstrated that when diseased Changhong jujube plants were grafted with Changyun jujube in the spring using bark or cleft grafting,the majority of the new shoots of Changyun jujube exhibited no symptoms of witches broom disease,while a few exhibited symptoms of the disease.With the growth of new shoots,the symptoms of witches broom disease gradually abated,returning to normal growth and development.Similarly,the symptoms of witches broom disease on the rootstock below the grafting mouth also gradually abated,returning to normal.The Changyun jujube rootstock was utilized as the intermediate rootstock to grafting the jujube cultivars Qiyuexian and Fucuimi.The two cultivars were subsequently affixed with branch bark from the witches broom disease.The two cultivars did not exhibit any symptoms of witches broom disease,thus providing an opportunity to investigate potential treatments for this disease in jujube.Finally,the cultivation techniques of the Changyun jujube were presented.

Analysis of Yield and Disease Resistance Traits of New Winter Rapeseed Varieties over the Past Twenty Years in China

Based on the results of the national regional trail for winter rapeseed in four groups,including the upper reaches,middle reaches and lower reaches of Yangtze River and Huang-Huai region in the past twenty years,new varieties of winter rapeseed showed upward trend in average yield,the yield level in Huang-huai group was higher than other groups.The changes of average effective pods per plant were not significant in any group,but the number of grain per pod and 1 000-grain weight showed increase trend.However,the increment of grains per pod in three Yangtze River groups was higher than that in Huang-Huai River group,while the increment of 1 000-grain weight was just opposite.The incidence rate of Sclerotinia sclerotiorum and viral disease in new varieties of winter rapeseed obviously decreased,and the incidence rate of S.sclerotiorum decreased lower than 5%.Genetic improvement for winter rapeseed should be focus on the number of grain per pod and 1 000-grain weight in the future,and yield level of new varieties in all four groups is expected to increase.

Cloning and Analysis of a Disease Resistance Gene Homolog from Soybean

Conserved domains e.g. nucleotide binding site (NBS) were found in several cloned plant disease resistance genes. Based on the NBS domain, resistance gene analogs (RGAs) have been isolated previously and were used as probes to screen a soybean (Glycine max L. Merr.) cDNA library. A full-length cDNA, KR3, was obtained by screening the library and rapid amplification of cDNA ends (RACE) method. Sequence analysis revealed that the cDNA is 2 353 bp in length and the open reading frame (ORF) codes for a polypeptide of 636 amino acids with a Toll-Interleukin-1 receptor (TIR) and a NBS domain. Sequence alignment showed that it was similar to N gene of tobacco. The phylogenetic tree analysis of R proteins with NBS from higher plants was performed. The KR3 gene has low copies in soybean genome and its expression was induced by exogenous salicylic acid (SA).

Expression of Exogenous Antimicrobial Peptide and Resistance to Stem Rot Disease of Houttuynia cordata Thunb.

[Objective] This study was to identify the expression of exogenous antimicrobial peptide in transgenic Houttuynia cordata Thunb. plants,and analyze their resistance to stem rot disease. [Methods] SDS-PAGE and Western blot analysis were employed to detect expression of exogenous antimicrobial peptide in transgenic H. cordata plants. Both wild type and transgenic H. cordata plants were inoculated with different concentrations of Rhizoctonia solani spores for detecting their resistance. [Results] The exogenous antimicrobial peptide was detected at translation level. The optimal parameters for detecting the resistance of transgenic H. cordata plants to R. solani was inoculation of spores at a concentration of 3×105 ind./ml and cultured for three days. The results showed that resistance of transgenic H. cordata plants to R. solani was enhanced in comparison with CKs. [Conclusion] Expression of exogenous antimicrobial peptide can enhance the resistance of transgenic H. cordata plants to stem rot disease.

Problems, challenges and future of plant disease management: from an ecological point of view

Plant disease management faces ever-growing challenges due to： （i） increasing demands for total, safe and diverse foods to support the booming global population and its improving living standards; （ii） reducing production potential in agriculture due to competition for land in fertile areas and exhaustion of marginal arable lands; （iii） deteriorating ecology of agro-ecosystems and depletion of natural resources; and （iv） increased risk of disease epidemics resulting from agricultural intensification and monocultures. Future plant disease management should aim to strengthen food security for a stable society while simultaneously safeguarding the health of associated ecosystems and reducing dependency on natural resources. To achieve these multiple functionalities, sustainable plant disease management should place emphases on rational adaptation of resistance, avoidance, elimination and remediation strategies individually and collectively, guided by traits of specific host-pathogen associations using evolutionary ecology principles to create environmental （biotic and abiotic） conditions favorable for host growth and development while adverse to pathogen reproduction and evolution.

Development of a 50K SNP Array for Japanese Flounder and Its Application in Genomic Selection for Disease Resistance

Single nucleotide polymorphism(SNP)armays are a powerful genotyping tool used in genetic research and genomic breeding programs.Japanese flounder(Paralichthys olivaceus)is an economically-important aquaculture flatfish in many countries.However,the lack of high-efficient genotyping tools has impeded the genomic breeding programs for Japanese flounder.We developed a 50K Japanese flounder SNP array,"Yuxin No.1,"and report its utility in genomic selection(GS)for disease resistance to bacterial pathogens.We screened more than 42,.2 million SNPs from the whole-genome resequencing data of 1099 individuals and selected 48697 SNPs that were evenly distributed across the genome to anchor the array with Affymetrix Axiom genotyping technology.Evaluation of the array performance with 168 fishs howed that 74.7%of the loci were successfully genotyped with high call rates(>98%)and that the poly-morphic SNPs had good cluster separations.More than 85%of the SNPs were concordant with SNPs obtained from the whole-genome resequencing data.To validate"Yuxin No.1"for GS,the arrayed geno-typing data of 27 individuals from a candidate population and 931 individuals from a reference popula-tion were used to calculate the genomic estimated breeding values(GEBVs)for disease resistance toEdwardsiella tarda.There was a 21.2%relative increase in the accuracy of GEBV using the weighted geno-mic best linear unpiased prediction(wGBLUJP),compared to traditional pedigree-based best linear unbi-ased prediction(ABLUP),suggesting good performance of the'Yuxin No.1"SNP array for GS.In summary,we developed the"Yuxin No.1"50K SNP array,which provides a useful platform for high-quality geno-typing that may be beneficial to the genomic selective breeding of Japanese flounder.

Genetic Improvement of Japonica Rice Variety Wuyujing 3 for Stripe Disease Resistance and Eating Quality by Pyramiding Stv-b^i and Wx-mq

Japonica rice variety Kanto 194 as the donor of resistance gene Stv-b^i and Iow-amylose content gene Wx-mq was used to improve the resistance and eating quality of Wuyujing 3 by the breeding strategy of backcross. In continuous backcross and selfcross generations, the related molecular markers with Stvobi and Wx-mq genes were utilized for genotypic detection by associated with resistance identification of rice stripe disease and agronomic traits selection. Finally, 10 improved lines with homozygous genotype Stv-b^i Stv-b^iWx-mqWx-mq were obtained from BC3F4 generation. The results of comparative analysis indicated that most characters of these lines were consistent with those of recipient parent Wuyujing 3, except for the improved resistance, appearance and eating quality. By evaluation of the comprehensive performance of them, two excellent lines K01 and K04 were selected for further experiments.

Transferring Translucent Endosperm Mutant Gene Wx-mq and Rice Stripe Disease Resistance Gene Stv-bi by Marker-Assisted Selection in Rice (Oryza sativa)

A high-yielding japonica rice variety, Wuyunjing 7, bred in Jiangsu Province, China as a female parent was crossed with a Japanese rice variety Kantou 194, which carries a rice stripe disease resistance gene Stv-b＇ and a translucent endosperm mutant gene Wx-mq. From F2 generations, a sequence characterized amplified region （SCAR） marker tightly linked with Stv-b＇ and a cleaved amplified polymorphic sequence （CAPS） marker for Wx-mq were used for marker-assisted selection. Finally, a new japonica rice line, Ning 9108, with excellent agronomic traits was obtained by multi-generational selection on stripe disease resistance and endosperm appearance. The utilization of the markers from genes related to rice quality and disease resistance was helpful not only for establishing a marker-assisted selection system of high-quality and disease resistance for rice but also for providing important intermediate materials and rapid selection method for good quality, disease resistance and high yield in rice breeding.

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.

Effects of Nano Chinese Herbal Medicine Feed Additive on Growth Performance,Meat Quality and Disease Resistance of Chickens

[Objectives]To explore the effects of nano compound Chinese herbal medicine feed additive on growth performance,meat quality and disease resistance of chickens.[Methods]Chickens were fed with nano compound Chinese herbal medicine feed additive developed by Hunan Polytechnic of Environment and Biology,including 120 chickens in the treatment group and 120 chickens in the control group(CK).The growth performance indices(body weight gain,feed to gain ratio and slaughter index),meat quality indices(pH value,color,drip loss,shear force)and disease resistance indices(morbidity and mortality)of the chickens in the treatment and CK groups were recorded and determined,respectively.[Results]The inclusion of 2%nano compound Chinese herbal medicine feed additive in the diet significantly increased the growth rate,reduced the feed-to-gain ratio and improved the meat quality of the chickens.Supplementing Chinese herbal medicine could increase the pH value and reduce the drip loss and shear force of chicken meat.At the same time,the body's immune function,antioxidant level and resistance against diseases of the chickens fed with nano compound Chinese herbal medicine feed additive were improved.[Conclusions]The inclusion of nano compound Chinese herbal medicine feed additive in the diet can improve the growth performance,meat quality and disease resistance of chickens.

Breeding of Selectable Marker-Free Transgenic Rice Lines Containing AP1 Gene with Enhanced Disease Resistance

In order to obtain marker-free transgenic rice with improved disease resistance, the AP1 gene of Capsicum annuum and hygromycin-resistance gene （HPT） were cloned into the two separate T-DNA regions of the binary vector pSB130, respectively, and introduced into the calli derived from the immature seeds of two elite japonica rice varieties, Guangling Xiangjing and Wuxiangjing 9, mediated by Agrobacterium-mediated transformation. Many cotransgenic rice lines containing both the AP1 gene and the marker gene were regenerated and the integration of both transgenes in the transgenic rice plants was confirmed by either PCR or Southern blotting technique. Several selectable marker-free transgenic rice plants were subsequently obtained from the progeny of the cotransformants, and confirmed by both PCR and Southern blotting analysis. These transgenic rice lines were tested in the field and their resistance to disease was carefully investigated, the results showed that after inoculation the resistance to either bacterial blight or sheath blight of the selected transgenic lines was improved when compared with those of wild type.

Marker-Assisted Breeding of Thermo-Sensitive Genic Male Sterile Line 1892S for Disease Resistance and Submergence Tolerance

Rice line 1892S is an elite thermo-sensitive genic male sterile(TGMS)line for two-line hybrid rice production.However,1892S is susceptible to rice blast,bacterial blight and submergence.Here we reported the introduction of blast resistance(R)gene Pi9,bacterial blight R gene Xa21 and submergence tolerance gene Sub1A into 1892S genetic background through backcrossing and marker-assisted selection.The improved TGMS line 31892S and its hybrids conferred disease resistance to rice blast and bacterial blight,and showed submergence tolerance for over 14 d without significant loss of viability.The sterility-fertility conversion of 31892S was similar to that of 1892S.31892S and its derived hybrid rice had similar agronomic traits and grain quality with 1892S and the control hybrid rice,respectively.The newly developed 31892S provided an improved TGMS line for two-line hybrid rice production with disease resistance to rice blast and bacterial blight,and submergence tolerance with no yield penalty or change in grain quality.

Research Progress on the Mechanism of Plant Disease Resistance Regulated by NPR1

NPR1 is an intersection of different disease resistance pathways and plays a key role in systemic-acquired resistance and induced systemic resistance. NPR1 regulates constitutive resistance and disease resistance determined by resistant genes. In this paper, the mechanism of disease resistance of NPR1 genes and its analogs were described. The research status and progress of NPR1 transgenic crops were systematically discussed. The application prospect of NPR1 transgenic crops was also forecasted.

Improvement of three popular Indian groundnut varieties for foliar disease resistance and high oleic acid using SSR markers and SNP array in marker-assisted backcrossing

Foliar fungal diseases(rust and late leaf spot)incur large yield losses,in addition to the deterioration of fodder quality in groundnut worldwide.High oleic acid has emerged as a key market trait in groundnut,as it increases the shelf life of the produce/products in addition to providing health benefits to consumers.Marker-assisted backcrossing(MABC)is the most successful approach to introgressing or pyramiding one or more traits using traitlinked markers.We used MABC to improve three popular Indian cultivars(GJG 9,GG 20,and GJGHPS 1)for foliar disease resistance(FDR)and high oleic acid content.A total of 22 BC3F4 and 30 BC2F4 introgression lines(ILs)for FDR and 46 BC3F4 and 41 BC2F4 ILs for high oleic acid were developed.Recurrent parent genome analysis using the 58 K Axiom_Arachis array identified several lines showing upto 94%of genome recovery among second and third backcross progenies.Phenotyping of these ILs revealed FDR scores comparable to the resistant parent,GPBD 4,and ILs with high(~80%)oleic acid in addition to high genome recovery.These ILs provide further opportunities for pyramiding FDR and high oleic acid in all three genetic backgrounds as well as for conducting multi-location yield trials for further evaluation and release for cultivation in target regions of India.

Bioinformatics Analysis of Disease Resistance Gene PR1 and Its Genetic Transformation in Soybeans and Cultivation of Multi-resistant Materials

In agricultural production,a single insect-resistant and disease-resistant variety can no longer meet the demand.In this study,the expression vector pCAMBIA-3301-PR1 containing the disease-resistant gene PR1 was constructed by means of genetic engineering,and the PR1 gene was genetically transformed to contain the PR1 gene through the pollen tube method.In CryAb-8Like transgenic high-generation T7 receptor soybean,a new material that is resistant to insects and diseases is obtained.For T2 transformed plants,routine PCR detection,Southern Blot hybridization,fluorescence quantitative PCR detection,indoor and outdoor pest resistance identification and indoor disease resistance identification were performed.The results showed that there were 9 positive plants in the routine PCR test of T2 generation.In Southern Blot hybridization,both PR1 and CryAb-8Like genes are integrated in soybeans in the form of single copies.Fluorescence quantitative PCR showed that the expression levels of PR1 and CryAb-8Like genes are different in different tissues.The average expression levels of PR1 gene in plant roots,stems,and leaves are 2.88,1.54,and 5.26,respectively.CryAb-8Like genes are found in roots,stems,and leaves.The average expression levels were 1.36,1.39,and 4.25,respectively.The insectivorous rate of the CryAb-8Like gene in outdoor plants with positive insect resistance identification was 3.78%.The disc partition method was used indoors for pest resistance identification,and the bud length of transformed plants increased significantly.The average mortality rate of untransformed plants in indoor disease resistance identification was as high as 56.66%,and the average mortality rate of plants transformed with PR1 gene was 10.00%,and disease resistance was significantly improved.Therefore,a new material with resistance to diseases and insects is obtained.

Diallel Crossing Analyses of Resistance to Main Diseases in Pepper(Capsicum annuum L.)

Fifteen capsicum combinations were made with 6 parents by （1/2）n（n-1） diallel crossing. Genetic parameters in the resistance to TMV, CMV, phytophthora blight, bacterial spot of these combinations were studied by Hayman. The results indicated that the resistance to TMV, CMV and bacterial spot conformed genetically to the “additive-dominant” model but the resistance to phytophthora blight did not and significant epistatic dominance effect existed in it. F1 hybrid＇s resistance to CMV was controlled by homozygous dominant gene （s）, but resistance to bacterial spot by heterozygous one （s）. There were little, or no sum of dominant effect and genomes controlling the dominant expression of F1 hybrids in its phytophthora blight resistance.