Fusion of Region Extraction and Cross-Entropy SVM Models for Wheat Rust Diseases Classification

Wheat rust diseases are one of the major types of fungal diseases that cause substantial yield quality losses of 15%–20%every year.The wheat rust diseases are identified either through experienced evaluators or computerassisted techniques.The experienced evaluators take time to identify the disease which is highly laborious and too costly.If wheat rust diseases are predicted at the development stages,then fungicides are sprayed earlier which helps to increase wheat yield quality.To solve the experienced evaluator issues,a combined region extraction and cross-entropy support vector machine(CE-SVM)model is proposed for wheat rust disease identification.In the proposed system,a total of 2300 secondary source images were augmented through flipping,cropping,and rotation techniques.The augmented images are preprocessed by histogram equalization.As a result,preprocessed images have been applied to region extraction convolutional neural networks(RCNN);Fast-RCNN,Faster-RCNN,and Mask-RCNN models for wheat plant patch extraction.Different layers of region extraction models construct a feature vector that is later passed to the CE-SVM model.As a result,the Gaussian kernel function in CE-SVM achieves high F1-score(88.43%)and accuracy(93.60%)for wheat stripe rust disease classification.

Control of Wheat Stripe Rust and Ensuring High Yield of Crops under Planting of Wheat Variety Mixtures

Wheat stripe rust has become the most dangerous disease which threaten safe yield of wheat in Sichuan Province. It is meaningful to provide technique support for integrated disease control by exploring the effective control measures of wheat stripe rust. Wheat stripe rust dynamic developments of all-planting and mixed-planting have been systematically investigated in this study by taking different mixed-planting combinations among 6 wheat varieties with different resistance levels. The results of this experiment show that the mixed-plantings of 4 and 6 wheat varieties can delay the occurance of wheat stripe rust,slow the speed of disease and decline the damage of disease as well as stabilize yield of wheats.

Forecast Model for Occurrence Degree of Wheat Stripe Rust Using Meteorological Data

[Objective] The aim of this study is to establish the model for forecasting wheat stripe rust occurrence condition using meteorological factors. [Method] Based on the data of wheat stripe rust occurrence degrees in its past prevalent years and the meteorological data at corresponding periods, the methods of grey correlation analysis and fuzzy mathematics were employed to establish the forecast model for four pathogenesis indices according to the time sequence before winter, Early March, Early April and Middle May. Thus, the criterion for forecasting the occurrence degree of wheat stripe rust was obtained based on the distribution method of arithmetic progression. [Result] The model corresponding to meteorological conditions for forecasting wheat stripe rust was successfully established. According to the verification, the forecasting results before winter and in Early Mar. were more severer than the real occurrence condition, while the forecasting results in Early Apr. and Middle May were basically consistent with real values. [Conclusion] The results of the present study may avail the control of wheat stripe rust in Henan Province.

Screening of Wheat Cultivars for High Temperature Resistance to Stripe Rust from Wheat Resources in Huanghuai Growth Area

[Objective] The study aimed to screen wheat cultivars with high temperature resistance to stripe rust from the wheat resources in Huanghuai growth area. [Method] Seedlings of 165 wheat cultivars from Huanghuai growth area were identified by wheat stripe rust under high temperature; then the wheat cultivars showing stripe rust at seedling stage were further used to identify the same resistance in field. [Results] 13 cultivars were proved to be stripe rust resistant under high temperature, and the expression stages of stripe rust in the 13 cultivars were revealed. The field identification results confirmed the identification results at seedling stage via inoculation of mixed stripe rust of physiological races. The stripe resistances of wheat cultivars were also proved to be non-race-specific. [Conclusion] Wheat resources in Huanghuai growth area are abundant in wheat cultivars with high temperature resistance to stripe rust.

Postulation of seedling leaf rust resistance genes in 84 Chinese winter wheat cultivars

Wheat leaf rust（caused by Puccinia triticina） is one of the most important fungal diseases in China. There are tens of winter wheat cultivars which are approved to be released by the government at a national level and more than 100 wheat cultivars at the provincial level. But there is no information about leaf rust（Lr） genes in these cultivars, which makes it difficult for farmers and breeders to select which cultivars they should plant in their fields and use in their breeding programs. The objective of this paper was to identify the leaf rust resistant genes at seedling stage present in the 84 commercial wheat cultivars from China that have been released in the past few years. A set of 20 near isogenic lines with Thatcher background and 6 lines with known Lr genes were used to test the virulence of 12 races of P. triticina（Pt）. By comparing the infection types（ITs） produced on the 84 cultivars by the 12 Pt races with the ITs on the differential sets, the Lr genes were postulated. In addition, 8 molecular markers of Lr genes such as Lr9, Lr10, Lr19, Lr20, Lr21, Lr24, Lr26 and Lr29, which are closely linked to or co-segregated with the Lr gene, were used for further validation of the genes in the 84 Chinese winter wheat cultivars. Twelve Lr genes, including Lr1, Lr3,（Lr3bg）,（Lr3ka）, Lr11, Lr13, Lr14 a, Lr16, Lr26, Lr27, Lr30 and Lr31 were postulated to be present either singly or in combinations in these Chinese wheat cultivars. Lr3 and Lr26 were detected most often in the tested cultivars, with frequencies of 51.2 and 38.1%, respectively. No wheat Lr genes were detected in 16 cultivars, and 4 cultivars may carry unknown Lr genes other than those used in this study. Lr9, Lr20, Lr21, Lr24, Lr25 and Lr29 were not present in any of the 84 tested accessions.

Quantifying the effects of stripe rust disease on wheat canopy spectrum based on eliminating non-physiological stresses

The wheat canopy reflectance spectrum is affected by many internal and external factors such as diseases and growth stage. Separating the effects of disease stress on the crop from the observed mixed signals is crucial for increasing the precision of remote sensing monitoring of wheat stripe rust. The canopy spectrum of winter wheat infected by stripe rust was processed with the difference-in-differences(DID) algorithm used in econometrics. The monitoring accuracies of wheat stripe rust before and after processing with the DID algorithm were compared in the presence of various external factors, disease severity, and several simulated satellite sensors. The correlation between the normalized difference vegetation index processed by the DID algorithm(NDVI-DID) and the disease severity level(SL) increased in comparison with the NDVI before processing. The increase in precision in the natural disease area in the field in the presence of large differences in growth stage, growth, planting, and management of the crop was greater than that in the controlled experiment. For low disease levels(SL < 20%), the R2 of the regression of NDVI-DIDon SL was 38.8% higher than that of the NDVI and the root mean square error(RMSE) was reduced by 11.1%. The increase in precision was greater than that for the severe level(SL > 40%).According to the measured hyperspectral data, the spectral reflectance of three satellite sensor levels was simulated. The wide-band NDVI was calculated. Compared with the wide-band NDVI and vegetation indexes(VI) before DID processing, there were increases in the correlation between SL and the various types of VIS-DID, as well as in the correlation between SL and NDVI-DID. It is feasible to apply the DID algorithm to multispectral satellite data and diverse types of VISfor monitoring wheat stripe rust. Our results improve the quantification of independent effects of stripe rust infection on canopy reflectance spectrum,increase the precision of remote sensing monitoring of wheat stripe rust, and provide a reference for remote sensing monitoring of other crop diseases.

Identification and Molecular Tagging of Leaf Rust Resistance Gene (Lr24) in Wheat

This research was aimed to develop AFLP markers co-segregated with gene Lr24 and validate the using for marker assisted selection （MAS）. An F2 population developed from the cross between the resistant line TcLr24 and the susceptible line Thatcher was tested for resistance to the Puccinia triticina races BGQQ and SHRT using for genetic analysis and molecular marker. A total of 224 AFLP primer combinations were used to test the resistant and susceptible parents, as well as the resistant bulk and the susceptible bulk. Four AFLP markers, P-AGA/M-CTT289 bp, P-AGC/M-CAC1ss bp, P-AGC/M- CAC162 bp, and P-ACG/M-CGC239 bp, were co-segregated with Lr24. The AFLP fragment from the primer combination P- ACG/M-CGC was cloned, sequenced and converted into a STS marker named as ASTS212. Thatcher backgrounded NILs and 115 varieties were examined by using this STS marker and the marker SCS13026oz developed by Gupta. 5R615, 5R616, IR13, and 1R17 were identified and validated to contain gene Lr24. The marker is dominant and may be useful in identification the resistance gene Lr24 in wheat and wheat breeding programs.

Seedling and adult plant resistance to leaf rust in 46 Chinese bread wheat landraces and 39 wheat lines with known Lr genes

Wheat leaf rust,caused by Puccinia triticina(Pt),is an important foliar disease that has an important influence on wheat yield.The most economic,safe and effective way to control the disease is growing resistant cultivars.In the present study,a total of 46 wheat landraces and 34 wheat lines with known Lr(leaf rust resistance)genes were inoculated with 16Pt pathotypes for postulating seedling resistance gene(s)in the greenhouse.These cultivars and five wheat differential lines with adult plant resistance(APR)genes(Lr12,Lr22b,Lr34,Lr35 and Lr37)were also evaluated for identification of slow rusting resistance in the field trials in Baoding,Hebei Province of China in the 2014–2015 and 2015–2016 cropping seasons.Furthermore,10 functional molecular markers closely linked to 10 known Lr genes were used to detect all the wheat genotypes.Results showed that most of the landraces were susceptible to most of the Pt pathotypes at seedling stage.Nonetheless,Lr1 was detected only in Hongtangliangmai.The field experimental test of the two environments showed that 38 landraces showed slow rusting resistance.Seven cultivars possessed Lr34 but none of the landraces contained Lr37 and Lr46.Lr genes namely,Lr9,Lr19,Lr24,Lr28,Lr29,Lr47,Lr51 and Lr53 were effective at the whole plant stage.Lr18,Lr36 and Lr45 had lost resistance to part of pathotypes at the seedling stage but showed high resistance at the adult plant stage.Lr34 as a slowing rusting gene showed good resistance in the field.Four race-specific APR genes Lr12,Lr13,Lr35 and Lr37 conferred good resistance in the field experiments.Seven race-specific genes,Lr2b,Lr2c,Lr11,Lr16,Lr26,Lr33 and LrB had lost resistance.The 38 landraces showed slow rusting resistance to wheat leaf rust can be used as resistance resources for wheat resistance breeding in China.

Effects of UV-B radiation intensity and timing on epidemiological components of wheat stripe rust

Stripe rust caused by Puccinia striiformis f. sp. tritici is an important wheat disease worldwide that is greatly influenced by environmental conditions. Ultraviolet B(UV-B) radiation is one important environmental factor affecting the occurrence and epidemiology of wheat stripe rust. Investigating UV-B radiation effects on the epidemiology of stripe rust may be conducive to monitoring and predicting this disease. In this study, wheat seedlings were exposed to UV-B radiation during different periods under laboratory conditions and radiation effects on epidemiological components of wheat stripe rust were investigated. Results showed that incubation period was shortened, and the infection efficiency, sporulation quantity and disease index increased when UV-B radiation was performed only pre-inoculation. When the UV-B radiation was performed only postinoculation or both pre-and post-inoculation, the incubation period was prolonged, and the infection efficiency, sporulation quantity and disease index were reduced. When healthy wheat seedlings were inoculated using urediospores collected from wheat leaves irradiated by UV-B only post-inoculation or both pre-and post-inoculation, infection efficiency, sporulation quantity and disease index were also reduced. However, in the latter, the disease incubation period did not differ under varying UV-B radiation intensities compared to that when wheat leaves were not treated with UV-B radiation. Overall, the effects of direct exposure of wheat plants to UV-B radiation with different intensities in different periods on epidemiological components of wheat stripe rust were systematically explored, and the results suggest that the effects of UV-B radiation increased gradually with the increase of UV-B radiation intensity. This information provides a basis for monitoring and predicting this disease as well as for conducting further studies on pathogen virulence variation.

A SSR Marker for Leaf Rust Resistance Gene Lr19 in Wheat

Microsatellite was carded out in Thatcher, six near-isogenic lines and F2 progeny of TcLr19xThatcher to develop molecular markers for leaf rust resistance gene Lr19. Thirteen primer pairs were screened, of which one primer pair Xgwm44 displayed polymorphsim in the population of TcLr 19, Thatcher, and their F2 generations. One marker closed linked to Lr19 resistance trait was obtained, and was named Xgwm44139bp with the genetic distance 0.9 cM. The research shows that Lr19 has more potential in marker-assisted breeding programs in wheat and provides a step stone for mapping genetic map, physical map and the eventual cloning.

Grain yield losses in yellow-rusted durum wheat estimated using digital and conventional parameters under field conditions

The biotrophic fungus Puccinia striiformis f. sp. tritici is the causal agent of the yellow rust in wheat. Between the years 2010–2013 a new strain of this pathogen(Warrior/Ambition),against which the present cultivated wheat varieties have no resistance, appeared and spread rapidly. It threatens cereal production in most of Europe. The search for sources of resistance to this strain is proposed as the most efficient and safe solution to ensure high grain production. This will be helped by the development of high performance and low cost techniques for field phenotyping. In this study we analyzed vegetation indices in the Red,Green, Blue(RGB) images of crop canopies under field conditions. We evaluated their accuracy in predicting grain yield and assessing disease severity in comparison to other field measurements including the Normalized Difference Vegetation Index(NDVI), leaf chlorophyll content, stomatal conductance, and canopy temperature. We also discuss yield components and agronomic parameters in relation to grain yield and disease severity.RGB-based indices proved to be accurate predictors of grain yield and grain yield losses associated with yellow rust(R2= 0.581 and R2= 0.536, respectively), far surpassing the predictive ability of NDVI(R2= 0.118 and R2= 0.128, respectively). In comparison to potential yield, we found the presence of disease to be correlated with reductions in the number of grains per spike, grains per square meter, kernel weight and harvest index. Grain yield losses in the presence of yellow rust were also greater in later heading varieties. The combination of RGB-based indices and days to heading together explained 70.9% of the variability in grain yield and 62.7% of the yield losses.

Association Analysis of SP-SNPs and Avirulence Genes in Puccinia striiformis f. sp. tritici, the Wheat Stripe Rust Pathogen

Puccinia striiformis f. sp. tritici (Pst) is one of the pathogenic fungi on wheat, caused stripe rust that is a great threat for wheat production all over the world. Intensive efforts have been made to study genetics of wheat resistance to this disease, but few on avirulence of the pathogen due mainly to the nature of obligate biotrophism and the lack of systems for studying its genetics and molecular manipulations. To overcome these limitations, a natural Pst population comprising 352 isolates representative of a diverse virulence spectrum was genotyped using 97 secreted protein-single nucleotide polymorphism (SP-SNP) markers to identify candidate avirulence genes using association analysis. Among avirulence genes corresponding to 19 resistance genes, significantly associated SP-SNP markers were detected for avirulence genes AvYr1, AvYr2, AvYr6, AvYr7, AvYr8, AvYr44, AvYrExp2, AvYrSP, and AvYrTye. These results indicate that association analysis can be used to identify markers for avirulence genes. This study has laid the foundation for developing more SP-SNPs for mapping avirulence genes using segregating populations that can be generated through sexual reproduction on alternate hosts of the pathogen.

Postulation of Seedlings Resistance Genes to Yellow Rust in Commercial Wheat Cultivars from Yunnan Province in China

The objective of this study was to characterize yellow （stripe） rust resistance gene（s） in 52 commercial wheat cultivars from Yunnan Province in China, and to provide information for their rational deployment in field. Seedlings of wheat cultivars were inoculated with 25 differential isolates ofPuccinia striiformis from foreign and home to postulate resistance genes to yellow rust, and then validated by pedigree. There were 10 probable resistance genes characterized in these cultivars, in which, Yr9 was most commonly postulated to be present in thirteen cultivars. Yr21, the second, was present in four cultivars. Yr8, the third, were present in three cultivars. Yr6, Yrl 7 and Yr26, the fourth, was present in two cultivars respectively. The other gene（s） such as, Yr2＋YrA, Yr7 and Yr27, were only present in single cultivar（s）; unknown gene（s） or gene（s） combination（s） were present in 22 cultivars. One cultivar （Yunmai 42） had no resistance gene tested in this study. Cultivars such as Yunmai 52, Mian 1971-98, Kunmai 4, and Yunmai 56 carried effective genes and can be popularized mainly; Yr9 should be planted with other Yr genes. In the meantime other effective genes should be introduced to realize gene diversity for controlling wheat yellow rust. Yunmai 42 should be reduced to avoid rust breakout. Unknown gene cultivars should be utilized and be researched deeply.

Status and strategies in breeding for rust resistance in wheat

Wheat along with rice and maize is fulfilling half of the calories demands of the world. Global Wheat production has increased tremendously since green revolution in 1960’s and helped in minimizing hunger and malnutrition. Developing countries, which consume 60% of the global wheat production, have shown a higher yield increase than the developed countries in the past [1]. It was driven by the hunger prevalence in these countries and was attributable to the introduction of high yielding and rusted resistant semi dwarf varieties developed under the collaborative efforts of International and National research systems during the last 50 years. Whereas, climate change and the emergence of new pests and diseases are threatening the food sustainability. The evolution of new races of disease pathogens like stem rust (Ug 99) is of serious concern. In order to feed the ever increasing population we have to increase wheat production at the rate 1.6% which can be achieved by developing high yielding varieties having a good tolerance level for biotic and abiotic stresses.

Occurrence and Epidemic Regularity of Wheat Stripe Rust in Nanchong City of Sichuan Province

In order to realize monitoring and early warning and comprehensive management of wheat stripe rust and to reduce its occurrence in Nanchong City, the occurrence and epidemic regularity of wheat stripe rust in Nanchong was studied by system monitoring and general survey, resistance identification, physiological race monitoring and meteorological data analysis. The initial occurrence location and spreading pathway of Puccinia striiformis f. sp. tritici （Pst） were first verified; there were two infection peaks of wheat stripe rust in Nanchong and one to three epidemic peaks in fields, in which the occurrence area of the first epidemic peak played a pivotal role in disease prevalence in that year; the cumulative occurrence area in late January was positively correlated with annual occurrence area, with the correlation coefficient of 0.769 ; the prediction model for infected field rate, diseased plant rate and annual occurrence area was established. The internal reason for heavy occurrence and prevalence of wheat stripe rust in Nanchong was the decline or loss of wheat resistance against stripe rust, as well as the appearance of physiological races of Pst, which later became dominant races. Large fluctuation of temperature in warm winter and spring and more fog and dew days were external reasons responsible for prevalence of stripe rust. From 2002 to 2014 ,the accuracy rate of short-term prediction of wheat stripe rust reached 100%, while that of me- dium-term and long-term prediction reached over 98% and 95%, respectively, 5% -15% higher than that of the years before 1998.

Molecular Screening and Resistance Evaluation of American Wheat Cultivars to Chinese Stripe Rust Races

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is one of the major diseases of wheat in China. In order to asses the resistance levels and existing Yr genes among 59 wheat cultivars （lines） from the Pacific Northwest （PNW） of the United States, to provide resistance resources for genetic improvement of wheat stripe rust resistance in China, 59 wheat cultivars （lines） from PNW of the United States were infected by 3 mixed races of predominant Chinese stripe rust races CRY31, CRY32, and CRY33 to evaluate their resistance at seedling and adult plant stages, and screened with molecular markers tightly linked to currently effective all-stage resistance genes YrlO, Yrl5 and adult plant resistance genes Yrl8, Yr39. Of 59 American cultivars （lines）, five cultivars （lines）, Expresso, 02W50076, ACS52610, WA008012, and WA00801833, had all-stage resistance, showing resistance to mixed races of CRY31, CRY32, and CRY33 at both seedling and adult plant stages. 33 cultivars （lines） had adult plant resistance, only showing resistance to stripe rust at adult stage. Based on the molecular screening, none of the 59 PNW cultivars （lines） had the polymorphic bands of linked markers to YrlO. There were 12, 33 and 29 cultivars （lines） which bad polymorphic bands of linked markers to Yr15, Yr18 and Yr39, accounting for 20, 55 and 49% of the 59 PNW cultivars （lines）, respectively. All these results suggested that Yr15, Yr18 and Yr39 were widespread among PNW cultivars （cultivars） and could be utilized in Chinese wheat stripe rust resistance breeding.

Identification of AFLP Markers Linked to Leaf Rust Resistance Genes Using Near Isogenic Lines of Wheat

The present investigation was undertaken to find molecular markers linked to leaf rust resistance genes, Lr9 and Kharchia local mutant KLM4-3B. Preliminary AFLP analysis was carried out with different stocks, a survey of primer combinations with different selective nucleotide indicated that for each primer combination, the number of scorable loci ranged from 34 to 123. Only a limited primer combination used in the set of parental and near isogenic lines showed a high level of polymorphism for AFLP marker. Putative AFLP marker were found to be linked to Lr9, Lr19 and KLM4-3B. The alien genes were readily identified.

PCR-based molecular markers linked to the leaf rust resistance gene Lr19 in different bread wheat cultivars

61 varieties of wheat collected in the gene fund of the Research Institute of Crop Husbandry were screened using SCAR-markers associated with the gene of resistance to brown leaf rust, Lr19. As a result of PCR analysis using SCS123 marker the 737 bp locus was detected in 48 genotypes. The expected fragment of the 688 bp was detected in 53 genotypes using the SCS253 marker. The results obtained using both markers indicate that the Lr19 gene is present on 7D chromosomes of 45 genotypes. The existence of the Lr19 gene has not been proven only for 5 from the 61 analyzed wheat genotypes.

Ultrastructural Changes in the Interaction Between Puccinia striiformis and Wheat Cultivar with Slow-Rusting Resistance

Ultrastructural changes in both pathogen and host cells in the interaction between Puccinia striiformis and wheat cultivar （Libellula） with slow-rusting resistance were observed by transmission electron microscopy. Observations revealed marked changes in ultrastructure of both pathogen and host cells. In the pathogen respect, there were many vesicles appeared in the intercellular hyphae and gradually fused into bigger vacuoles, a number of fat drops and electron-dense granules accumulated, mitochondria became swollen and some of them degraded into vesicles, and the plasmalemma of intercellular hyphae became dark. In the haustoria, the cytoplasm degraded gradually and developed a vacuole in the center, fat drops increased, the extrahaustorial matrix widened with a great amount of electron-dense fibrillar and granular materials, and most of the haustoria died with in conjunction with the disappearance of fat drops and other organelles. Structural defense of the host, including formation of cell wall apposition, collar and papilla, occurred in the host respect. Host resistance expression and cytological features occurring in the slow-rusting resistance were discussed.

Molecular Markers for Leaf Rust Resistance Gene Lr45 in Wheat Based on AFLP Analysis

Amplified fragment length polymorphism （AFLP） analysis was carried out in Thatcher, near isogenic lines （NILs） canting different genes conferring resistance against wheat leaf rust, and TcLr45 × Thatcher F2 progenies were used to develop markers for Lr45 gene. Sixty AFLP primer combinations were screened and most of them provided clear amplification products, 31 primer combinations displayed polymorphism of TcLr45 in 23 NILs. Two AFLP markers closely linked to the gene Lr45 were acquired： P-AGG/M-GAG261bp, which was found closely linked to the Lr45 locus at a distance of 0.6 cM on one side, and P-ACA/M-GGT105bp, which was found at a distance of 1.3 cM on the other side. The specific hands were cloned and subsequently sequenced. The 261-bp fragment produced by P-AGG/M-GAG showed 86% similarity with the sequence of Vulgate Hort I gene; the 105-bp fragment produced by P-ACA/M-GGT showed 96% similarity with the phosphatidylserine decarboxylase gene of the Triticum monococcum. Both included an open reading frame （ORF）.