Classification Method of Rape Root Swelling Disease Based on Convolution Neural Network

Abstract Both the seedling stage and the adult plant stage of rape can be infected with root edema, and the damaged roots swell to form tumors of different sizes and shapes. The incidence of rape root swelling at the seedling stage reached 17%, and the average incidence at the adult plant stage was 15%, resulting in a 10.2% reduction in rape production. The average plant height, number of siliques, number of kernels per horn, 1000-seed weight and yield per plant of healthy plants were significantly higher than those of diseased plants. Grading root lesions can help trace the root causes of root lesions. However, the method of grading is often performed manually by professionals at present, which has the problems of low speed and low efficiency. In order to solve this problem, a method for grading rape root swelling based on deep convolutional neural network is proposed in this paper. Firstly, a rape root swelling model based on convolutional neural network and regional candidate network was established, and then implement it on the deep learning Tensorflow framework Model, and finally compare and analyze the results. The rape root swelling model uses the VGG16 network to extract the characteristics of the rape root swelling image. The regional candidate network generates the preliminary position candidate frame of the rape root swelling, and Fast-RCNN realizes the classification and positioning of the candidate frame. The results show that this method can achieve rapid and accurate detection of healthy, first-level tumors, second-level tumors, and third-level tumors of four-level rape root swelling, with an average accuracy rate of 84.12%. The experimental results show that the accuracy rate can reach more than 90%.

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RNA-seq reveals few differences in resistant and susceptible responses of barley to infection by the spot blotch pathogenBipolaris sorokiniana

10.1101/384529 ◽

2018 ◽

Cited By ~ 1

Author(s):

Matthew Haas ◽

Martin Mascher ◽

Claudia Castell-Miller ◽

Brian J. Steffenson

Keyword(s):

Expression Profiles ◽

Durable Resistance ◽

Defense Responses ◽

Spot Blotch ◽

Seedling Stage ◽

Differentially Expressed ◽

Adult Plant ◽

Rna Seq ◽

Adult Plant Stage ◽

Plant Stage

AbstractSpot blotch, caused byBipolaris sorokiniana(Sacc.) Shoem., is an economically important disease affecting barley (Hordeum vulgareL.). The disease has largely been controlled in the Upper Midwest region of the USA through a suite of quantitative trait loci (QTL) termed the Midwest Six-rowed Durable Resistance Haplotype (MSDRH). These QTL have been bred into all six-rowed Midwest barley cultivars, including the widely used cultivar Morex. We identified a gamma ray- induced Morex mutant (MUT) that exhibits spot blotch susceptibility at the seedling stage. This mutant also spontaneously develops extremely large necrotic lesions in the absence of the pathogen at the adult plant stage. Spot blotch susceptibility at the seedling stage and necrotic lesion formation at the adult plant stage are highly correlated. To start dissecting the molecular responses underlying the observed symptoms at the seedling stage, we conducted a time course RNA-seq experiment comparing the wild type (WT) and the mutant (MUT) Morex at 12, 24 and 36 h afterB. sorokinianainoculation. Mock-inoculated controls were also included. A total of 10,772 and 11,530 genes were differentially expressed between treatments for WT and MUT genotypes, respectively, while 277 and 195 genes were differentially expressed between fungal and mock-inoculated genotypes, respectively. The transcript expression profiles of WT and MUT Morex samples were similar for most treatments. Two genes whose expression was putatively knocked out in the MUT were identified: HORVU3Hr1G019920 (glycine-rich protein) and HORVU5Hr1G120850 (Long- chain-fatty-acid—CoA ligase 1). The latter appears to be genetically intact, but not expressed. Collectively, these data suggest that MUT susceptibility toB. sorokinianais a result of minor, rather than major, differences in the defense responses.

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ADULT PLANT RESISTANCE OF SOME OAT VARIETIES TO PHYSIOLOGIC RACES OF CROWN RUST

Canadian Journal of Research ◽

10.1139/cjr44c-025 ◽

1944 ◽

Vol 22c (6) ◽

pp. 287-289 ◽

Cited By ~ 6

Author(s):

B. Peturson

Keyword(s):

Plant Resistance ◽

Adult Plant Resistance ◽

Crown Rust ◽

Seedling Stage ◽

Puccinia Coronata ◽

Adult Plant ◽

Adult Plant Stage ◽

Plant Stage ◽

Physiologic Races ◽

Generalized Type

The reactions of five varieties of oats in the seedling and adult plant stages to seven physiologic races of crown rust, Puccinia coronata Corda var. Avenae Erikss. & Henn. were determined.All five varieties were completely susceptible in the seedling stage to all the races. Two varieties, Erban and Ajax, were resistant in the adult plant stage to some of the races and susceptible or moderately susceptible to others. Two other varieties, R.L. No. 1370 and R.L. No. 1510 were resistant in the adult plant stage to all the races used in this test, and apparently possess a generalized type of adult plant resistance to crown rust.

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DANGEROUS NEW RACES OF OAT STEM RUST AND SOURCES OF RESISTANCE TO THEM

Canadian Journal of Plant Science ◽

10.4141/cjps64-082 ◽

1964 ◽

Vol 44 (5) ◽

pp. 418-426 ◽

Cited By ~ 4

Author(s):

G. J. Green ◽

R. I. H. McKenzie

Keyword(s):

Resistance Genes ◽

Stem Rust ◽

Seedling Stage ◽

Adult Plant ◽

Santa Fe ◽

Sources Of Resistance ◽

Adult Plant Stage ◽

Plant Stage ◽

New Races ◽

Moderately Resistant

New races of oat stem rust that can attack varieties carrying all identified resistance genes were found in Canada between 1957 and 1963. Varieties moderately resistant to some of these races have been found, but they are susceptible to other less-prevalent races. Some of the sources of resistance are: Ukraine, C.I. 3259; Ark. 674(2)-39-F, C.I. 4529; C.I. 4673; C.I. 5109; Santa Fe Selection, C.I. 5844; C.I. 6792; Silva No. 1729-49-1, C.I. 6849; and Rosen’s Mutant. White Russian (gene D) and Sevnothree (gene E) were resistant in the adult plant stage to one culture of race 6AF, although susceptible in the seedling stage.

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A Genome-Wide Association Study of Resistance to Puccinia striiformis f. sp. hordei and P. graminis f. sp. tritici in Barley and Development of Resistant Germplasm

Phytopathology ◽

10.1094/phyto-11-19-0415-r ◽

2020 ◽

Vol 110 (5) ◽

pp. 1082-1092 ◽

Cited By ~ 1

Author(s):

Javier Hernandez ◽

Alicia del Blanco ◽

Tanya Filichkin ◽

Scott Fisk ◽

Lynn Gallagher ◽

...

Keyword(s):

Stripe Rust ◽

Stem Rust ◽

Rust Resistance ◽

Puccinia Striiformis ◽

Seedling Stage ◽

Stripe Rust Resistance ◽

Adult Plant ◽

Adult Plant Stage ◽

A Genome ◽

Plant Stage

Stripe rust (incited by Puccinia striiformis f. sp. hordei) and stem rust (incited by P. graminis f. sp. tritici) are two of the most important diseases affecting barley. Building on prior work involving the introgression of the resistance genes rpg4/Rpg5 into diverse genetic backgrounds and the discovery of additional quantitative trait locus (QTLs) for stem rust resistance, we generated an array of germplasm in which we mapped resistance to stripe rust and stem rust. Stem rust races TTKSK and QCCJB were used for resistance mapping at the seedling and adult plant stages, respectively. Resistance to stripe rust, at the adult plant stage, was determined by QTLs on chromosomes 1H, 4H, and 5H that were previously reported in the literature. The rpg4/Rpg5 complex was validated as a source of resistance to stem rust at the seedling stage. Some parental germplasm, selected as potentially resistant to stem rust or susceptible but having other positive attributes, showed resistance at the seedling stage, which appears to be allelic to rpg4/Rpg5. The rpg4/Rpg5 complex, and this new allele, were not sufficient for adult plant resistance to stem rust in one environment. A QTL on 5H, distinct from Rpg5 and a previously reported resistance QTL, was required for resistance at the adult plant stage in all environments. This QTL is coincident with the QTL for stripe rust resistance. Germplasm with mapped genes/QTLs conferring resistance to stripe and stem rust was identified and is available as a resource to the research and breeding communities.

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Molecular Mapping of Loci Conferring Resistance to Different Pathotypes of the Spot Blotch Pathogen in Barley

Phytopathology ◽

10.1094/phyto-96-0699 ◽

2006 ◽

Vol 96 (7) ◽

pp. 699-708 ◽

Cited By ~ 30

Author(s):

H. Bilgic ◽

B. J. Steffenson ◽

P. M. Hayes

Keyword(s):

Quantitative Analysis ◽

Qualitative Analysis ◽

Spot Blotch ◽

Seedling Stage ◽

Chromosome 3 ◽

Adult Plant ◽

Chromosome 2 ◽

Chromosome 4 ◽

Adult Plant Stage ◽

Plant Stage

Spot blotch, caused by Cochliobolus sativus, is an important disease of barley in many production areas and is best controlled through the deployment of resistant cultivars. Information on the genetics of resistance in various sources can be useful in developing effective breeding strategies. Parents of the doubled haploid mapping population Calicuchima-sib/ Bowman-BC (C/B) exhibit a differential reaction to pathotypes 1 and 2 of C. sativus. To elucidate the genetics of spot blotch resistance in this population, C/B progeny were evaluated with both pathotypes at the seedling stage in the greenhouse and at the adult plant stage in the field. At the seedling stage, progeny segregated 84 resistant to 26 susceptible based on the qualitative analysis of infection response (IR) data to pathotype 1. This fit best to a 3:1 ratio, indicating that two genes were involved in conferring resistance. Quantitative analysis of the raw IR data to pathotype 1 revealed a single quantitative trait locus (QTL) on chromosome 4(4H) explaining 14% of the phenotypic variance. Adult plant resistance to pathotype 1 was conferred by QTL on chromosome 2(2H) and chromosome 3(3H), explaining 21 and 32% of the phenotypic variation, respectively. Bowman contributed the resistance alleles on chromosome 3(3H) and chromosome 4(4H), whereas Calicuchima-sib contributed the resistance allele on chromosome 2(2H). Resistance to pathotype 2 was conferred by a single gene (designated Rcs6) on chromosome 5(1H) based on qualitative analysis of data. Rcs6 was effective at both the seedling and adult plant stages and was contributed by Calicuchima-sib. This result was corroborated in the quantitative analysis of raw IR (seedling stage) and disease severity (adult plant stage) data as a single major effect (r2 = 0.93 and 0.88, respectively) QTL was identified on chromosome 5(1H). Progeny with resistance to both pathotypes were identified in the C/B population and may be useful in programs breeding for spot blotch resistance.

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Identification of Resistant Germplasm and Detection of Genes for Resistance to Powdery Mildew and Leaf Rust from 2,978 Wheat Accessions

Plant Disease ◽

10.1094/pdis-03-21-0532-re ◽

2021 ◽

Author(s):

Yuli Jin ◽

Fengyu Shi ◽

Weihua Liu ◽

Xiaoyi Fu ◽

Tiantian Gu ◽

...

Keyword(s):

Powdery Mildew ◽

Leaf Rust ◽

Puccinia Triticina ◽

Wheat Breeding ◽

Seedling Stage ◽

Adult Plant ◽

Breeding Lines ◽

Adult Plant Stage ◽

Lr Genes ◽

Plant Stage

Powdery mildew and leaf rust, caused by Blumeria graminis f. sp. tritici (Bgt) and Puccinia triticina (Pt), respectively, are widespread diseases of wheat worldwide. Utilizing resistant cultivars is considered as the most economical, environmental-friendly, and effective method to control these diseases. In the present study, a collection of 2,978 wheat accessions consisting of 1,394 advanced breeding lines, 1,078 Chinese cultivars, 291 introduced cultivars, 132 lines containing alien chromosomes, and 83 landraces was tested for reactions to powdery mildew and leaf rust. The results indicated that 659 (22.1%) wheat accessions were highly resistant to a widely prevalent Bgt isolate, E09, at the seedling stage, and 390 were consistently resistant to the mixture of Bgt isolates at the adult-plant stage. Meanwhile, 63 (2.1%) accessions were highly resistant to leaf rust at the adult-plant stage, of which 54 were resistant to a predominant and highly virulent Pt race, THTT, at the seedling stage. Notably, 17 accessions were resistant to both powdery mildew and leaf rust. To detect known genes for resistance to powdery mildew and leaf rust, these accessions were tested with gene-specific or tightly linked markers for seven Pm genes (Pm2, Pm4, Pm5, Pm6, Pm8, Pm21, and Pm24) and ten Lr genes (Lr1, Lr9, Lr10, Lr19, Lr20, Lr24, Lr26, Lr34, Lr37, and Lr46). Of the 659 powdery mildew-resistant accessions, 328 might carry single Pm genes and 191 carry combined Pm genes. Pm2 was detected at the highest frequency of 59.6%, followed by Pm8, Pm6, Pm21, Pm4, and Pm5, while Pm24 was not detected. Besides, 139 accessions might contain unknown Pm genes different from those tested in this study. In the 63 accessions resistant leaf rust, four Lr genes (Lr1, Lr10, Lr26, and Lr34) were detected in 41 accessions either singly or in combination, while six genes (Lr9, Lr19, Lr20, Lr24, Lr37, and Lr46) were not detected. Twenty-two accessions might contain unknown Lr genes different from those tested in this study. This study not only provided important information for rationally distributing resistance genes in wheat breeding programs, but also identified resistant germplasm that might have novel genes to enrich the diversity of resistance sources.

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Relative Ratio of Mature Pustules: A Simple Method to Assess Partial Resistance of Barley to Puccinia hordei

Plant Disease ◽

10.1094/pdis-91-3-0301 ◽

2007 ◽

Vol 91 (3) ◽

pp. 301-307 ◽

Cited By ~ 1

Author(s):

Guo-Liang Jiang ◽

Thierry C. Marcel ◽

Fernando Martínez ◽

Rients E. Niks

Keyword(s):

Partial Resistance ◽

Recombinant Inbred Lines ◽

Seedling Stage ◽

Puccinia Hordei ◽

Optimal Time ◽

Adult Plant ◽

Simple Method ◽

Adult Plant Stage ◽

Relative Ratio ◽

Plant Stage

In plant breeding and germplasm evaluation, large-scale assessment of quantitative resistance is desirable, but feasible only if a simple and accurate measure is available. In several plant-pathogen systems, latent period (LP) is a parameter that is well correlated with the level of partial resistance observed in field trials. However, measuring LP or relative LP (RLP), i.e., relative to the reference accessions, is laborious. We investigated the value of relative ratio of mature pustules (RRMP, relative to the susceptible control) as a simple and rapid alternative to replace LP estimation in barley to barley leaf rust (Puccinia hordei). A set of 103 F9 recombinant inbred lines (RILs) derived from a cross L94 × Vada was sown in a greenhouse compartment, and was inoculated at the seedling stage with isolate Uppsala or 24, and at the adult plant stage with isolate 24. In demarcated sections of leaves, the number of mature pustules was counted several times after inoculation. The ratio of mature pustules (RMP) and LP50 were calculated to assess RRMP and RLP, respectively, and to identify the quantitative trait loci (QTLs) contributing to the genetic variation. The contrasts in RRMP among accessions were highest when the susceptible reference line had developed 70 to 90% mature orange pustules, the immature infection sites being visible as pale flecks. At this optimal time of observation, the correlation between RRMP and RLP in both the seedling stage and the adult plant stage was highly significant (r = -0.82 ~-0.98). Compared with RLP, RRMP was much easier and simpler to measure and still showed good correspondence with RLP in the identification of QTLs for partial resistance. In another experiment at the seedling stage with 25 barley cultivars and lines inoculated with isolate 1.2.1, the coefficient of correlation between RRMP and RLP was -0.98. Therefore, we conclude that RRMP should have great application potential in breeding programs and germplasm screening and could be used in fundamental studies as well.

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Assessment and modeling using machine learning of resistance to scald (Rhynchosporium commune) in two specific barley genetic resources subsets

Scientific Reports ◽

10.1038/s41598-021-94587-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Houda Hiddar ◽

Sajid Rehman ◽

Berhane Lakew ◽

Ramesh Pal Singh Verma ◽

Muamar Al-Jaboobi ◽

...

Keyword(s):

Machine Learning ◽

Seedling Stage ◽

Fine Tuning ◽

Adult Plant ◽

Growth Stages ◽

Sources Of Resistance ◽

Leaf Scald ◽

Adult Plant Stage ◽

Plant Stage ◽

Filtering Approach

AbstractBarley production worldwide is limited by several abiotic and biotic stresses and breeding of highly productive and adapted varieties is key to overcome these challenges. Leaf scald, caused by Rhynchosporium commune is a major disease of barley that requires the identification of novel sources of resistance. In this study two subsets of genebank accessions were used: one extracted from the Reference set developed within the Generation Challenge Program (GCP) with 191 accessions, and the other with 101 accessions selected using the filtering approach of the Focused Identification of Germplasm Strategy (FIGS). These subsets were evaluated for resistance to scald at the seedling stage under controlled conditions using two Moroccan isolates, and at the adult plant stage in Ethiopia and Morocco. The results showed that both GCP and FIGS subsets were able to identify sources of resistance to leaf scald at both plant growth stages. In addition, the test of independence and goodness of fit showed that FIGS filtering approach was able to capture higher percentages of resistant accessions compared to GCP subset at the seedling stage against two Moroccan scald isolates, and at the adult plant stage against four field populations of Morocco and Ethiopia, with the exception of Holetta nursery 2017. Furthermore, four machine learning models were tuned on training sets to predict scald reactions on the test sets based on diverse metrics (accuracy, specificity, and Kappa). All models efficiently identified resistant accessions with specificities higher than 0.88 but showed different performances between isolates at the seedling and to field populations at the adult plant stage. The findings of our study will help in fine-tuning FIGS approach using machine learning for the selection of best-bet subsets for resistance to scald disease from the large number of genebank accessions.

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Screening Wild Oat Accessions from Morocco for Resistance to Puccinia coronata

Plant Disease ◽

10.1094/pdis-12-12-1150-re ◽

2013 ◽

Vol 97 (12) ◽

pp. 1544-1548 ◽

Cited By ~ 9

Author(s):

M. Y. A. Tan ◽

M. L. Carson

Keyword(s):

The United States ◽

Seedling Stage ◽

Puccinia Coronata ◽

Adult Plant ◽

United States Department ◽

Wild Oat ◽

Rust Disease ◽

Adult Plant Stage ◽

Plant Stage ◽

Moderately Resistant

Here, we report the screening of 332 new accessions of 11 different wild oat (Avena) species from the United States Department of Agriculture National Small Grains Collection in Aberdeen, ID, for resistance to crown rust disease, caused by Puccinia coronata f. sp. avenae. This collection originated from Morocco and includes Avena agadiriana, A. atlantica, A. barbata, A. damascena, A. eriantha, A. hirtula, A. longiglumis, A. magna, A. murphyi, A. sterilis, and A. wiestii. After screening this collection with a highly diverse population of P. coronata f. sp. avenae, 164 accessions (49%) were rated moderately resistant to resistant in the preliminary screen at the seedling stage and 181 accessions (55%) rated moderately resistant to highly resistant in the adult plant stage. Although none of the accessions showed a highly resistant response consistently in the seedling stage, 20 accessions did display a highly resistant response in the adult plant stage. Both seedling as well as adult plant resistance was found in 150 (45%) of the accessions. Virulence in P. coronata has been reported to all resistance genes currently being used in North American oat cultivars. The new resistance sources presented here are potentially new sources for future breeding. The resistance found in 52 accessions of A. magna and A. murphyi with the AACC genome is especially valuable because these should be relatively easy to transfer into hexaploid A. sativa.

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