The genome sequence and effector complement of the flax rust pathogen Melampsora lini

Rust fungi cause serious yield reductions on crops, including wheat, barley, soybean, coffee, and represent real threats to global food security. Of these fungi, the flax rust pathogen Melampsora lini has been developed most extensively over the past 80 years as a model to understand the molecular mechanisms that underpin pathogenesis. During infection, M. lini secretes virulence effectors to promote disease. The number of these effectors, their function and their degree of conservation across rust fungal species is unknown. To assess this, we sequenced and assembled de novo the genome of M. lini isolate CH5 into 21,130 scaffolds spanning 189 Mbp (scaffold N50 of 31 kbp). Global analysis of the DNA sequence revealed that repetitive elements, primarily retrotransposons, make up at least 45% of the genome. Using ab initio predictions, transcriptome data and homology searches, we identified 16,271 putative protein-coding genes. An analysis pipeline was then implemented to predict the effector complement of M. lini and compare it to that of the poplar rust, wheat stem rust and wheat stripe rust pathogens to identify conserved and species-specific effector candidates. Previous knowledge of four cloned M. lini avirulence effector proteins and two basidiomycete effectors was used to optimize parameters of the effector prediction pipeline. Markov clustering based on sequence similarity was performed to group effector candidates from all four rust pathogens. Clusters containing at least one member from M. lini were further analyzed and prioritized based on features including expression in isolated haustoria and infected leaf tissue and conservation across rust species. Herein, we describe 200 of 940 clusters that ranked highest on our priority list, representing 725 flax rust candidate effectors. Our findings on this important model rust species provide insight into how effectors of rust fungi are conserved across species and how they may act to promote infection on their hosts.This work was funded by a grant from the CSIRO Transformational Biology Capability Platform to Adnane Nemri. Claire Anderson was supported by an ARC Discovery Grant (DP120104044) awarded to David A. Jones and Peter N. Dodds

Rule-based expert system for detection of coffee rust warnings in Colombian crops

The coffee rust is a devastating disease that causes large economic losses across the world. The severity of this disease changes over time so the farmers are not fully aware of the economic importance of the rust disease in the coffee crops. From a computational science perspective, several investigations have been proposed to decrease the effects caused by the coffee rust appearance. One of the most important proposals is the use of expert systems. This paper proposes a novel rule-based expert system in which the knowledge base contains the variables and the set of rules that define the problem. The Buchanan methodology is used to design the proposed system. Experiment results present an average accuracy of 66,67% to detect a correct warning of coffee rust levels

Effects of sowing time on pink snow mould, leaf rust and winter damage in winter rye varieties in Finland

Disease infection in relation to sowing time of winter rye (Secale cereale) was studied in southern Finland in order to compare overwintering capacity of modern rye varieties and to give recommendations for rye cultivation. This was done by using three sowing times and four rye varieties in field trials conducted at three locations in 1999–2001. The early sown rye (beginning of August) was severely affected by diseases caused by Puccinia recondita and Microdochium nivale, whereas postponing sowing for two weeks after the recommended sowing time resulted in considerably less infection. The infection levels of diseases differed among rye varieties. Finnish rye varieties Anna and Bor 7068 were more resistant to snow mould and more winter hardy than the Polish variety Amilo, or the German hybrid varieties Picasso and Esprit. However, Amilo was the most resistant to leaf rust. In the first year snow mould appeared to be the primary cause of winter damage, but in the second year the winter damage was positively correlated with leaf rust. No significant correlation between frit fly infestation and winter damage or disease incidence of snow mould or leaf rust was established. The late sowing of rye (in the beginning of September) is recommended in Finland, particularly with hybrid varieties, to minimize the need for chemical plant protection in autumn

Stem rust of wheat

Stem rust is an occasional, but devastating disease of wheat. Epidemics occur when there is a carry over of stem rust from the previous season, susceptible varieties of wheat are grown, and warm humid conditions in the spring encourage disease development

Influence of weather parameters on progress of rust disease severity in pea (Pisum sativum L.)

Decision to apply one or more fungicide spray will depend on the risk of rust epidemic in a particular year. Rust epidemic is determined by interaction of three important factors namely, susceptible host, virulent pathogen and the most important i.e. favourable environment for a particular period of time. Therefore, it is necessary to study the correlation between different meteorological parameters and rust severity. Present study revealed that rust dis-ease generally appeared 60 days after sowing and was subsequently increased with a period of time till harvest (4.17 to 64.17 per cent). Disease was observed at a maximum temperature of 16.85 to 24.79áµ’C, 8.09 to 12.27áµ’C minimum temperature, 90.30 to 95.70 percent morning Relative Humidity (RH), 54.80 to 78.40 percent afternoons RH, 0.10 to 5.45mm rainfall and wind velocity of 3.93 to 4.23 km/hr. The correlation between different meteorological parameters and rust severity revealed that per cent disease severity showed highly positive correlation with maxi-mum temperature (r = 0.977), minimum temperature (r = 0.704), rainfall (r = 0.039) and wind velocity(r = 0.093) whereas disease severity show negative correlation with morning(r=-0.925) and afternoon RH (r = -0.926). It was observed that the rust severity is highly influenced by the different weather parameters such as temperature, relative humidity, rainfall and wind velocity. This information will help the researchers in formulating the forecasting model for the rust disease in pea and will also supports farmers in decision making regarding time of occurrence of rust epi-demic and thereby, allow timely scheduling and need based utilization of fungicides accordingly for the management of pea rust

A microsatellite marker for yellow rust resistance in wheat

Bulk segregant analysis (BSA) was used to identify molecular markers associated with yellow rust disease resistance in wheat (Triticum aestivum L.). DNAs isolated from the selected yellow rust tolerant and susceptible F-2 individuals derived from a cross between yellow rust resistant and susceptible wheat genotypes were used to established a "tolerant" and a "susceptible" DNA pool. The BSA was then performed on these DNA pools using 230 markers that were previously mapped onto the individual wheat chromosomes. One of the SSR markers (Xgwm382) located on chromosome group 2 (A, B, D genomes) was present in the resistant parent and the resistant bulk but not in the susceptible parent and the susceptible bulk, suggesting that this marker is linked to a yellow rust resistance gene. The presence of Xgwm382 was also tested in 108 additional wheat genotypes differing in yellow rust resistance. This analysis showed that 81% of the wheat genotypes known to be yellow rust resistant had the Xgwm382 marker, further suggesting that the presence of this marker correlates with yellow rust resistance in diverse wheat germplasm. Therefore, Xgwm382 could be useful for marker assisted selection of yellow rust resistances genotypes in wheat breeding programs

Effects of Varieties, Cutting Health and Fungicide Application on Chrysanthemum White Rust

White rust caused by fungal pathogen Puccinia horiana P. Henn. is one devastated disease that could make significant economic loss in chrysanthemum production. The study of effects of varieties, cutting health and fungicide application on chrysanthemum white rust was established. The treatments were arranged in split-split plot completely randomized design with three replications. Three chrysanthemum varieties i.e. cv. Puma White, Reagent Purple and Town Talk served as main plot. Seedlings with 20 % intensity of white rust infection and symptomless functioned as sub plot, while fungicide application on the transplanted cutting (no fungicide) and dithiocarbamate (AntracolR 75 WP, 2 g L-1) application served as sub-sub plot. Result showed genetic background of the cultivars significantly determined the degree of infection of white rust. Reagent Purple exhibited least disease intensities. Fungicide application was less effective in controlling white rust development, yet gave significant impact on the plant height and number of leaves of chrysanthemum plants. Cuttings selection based on the visual observation on the presence or absence of white rust pustules symptom did not gave significant differences on the further development of the disease. The symptomless cuttings were also infected with this fungal disease after the cuttings were planted under plastic house

Insidensi Dan Intensitas Serangan Penyakit Karat Putih Pada Beberapa Klon Krisan

. Rahardjo I.B. and Suhardi. 2008. Incidence and Intensity of White Rust Disease on Several Chrysanthemum Clones. White rust disease is one of constrain in increasing the production of chrysanthemum flower. White rust disease on chrysanthemum caused by Puccinia horiana. One of the control alternative was the use of resistant variety. The aim of the experiment was to know incidence and disease intensity of white rust on chrysanthemum clones. The experiment was done in Plastichouse at Indonesian Ornamental Crop Research Institute, Segunung (1.100 m asl), from September 2002 to February 2003. Evaluations were done on 13 chrysanthemum promising clones from selection in 2000. The treatments consisted of 13 chrysanthemum promising clones namely : 116.44, 116.53, 116.57, 125.14, 130.8, 131.1, 133.59, 133.7, 133.95, 135.6, 136.1, 136.11, 150.4, var. Saraswati, and var. White Reagent. RCBD with 3 replications were used in this experiment. The results of the experiment showed that clone 136.10 indicated good characteristic, with latest of disease infection (133 days after planting), lowest disease incidence at 15 weeks after planting (12.67%), and the second lowest for disease intensity (5.08%) after clone 133.95 (4.6%). While clone 136.10 showed lowest disease intensity on harvesting time (4.44%)

Cedar apple rust (1996)

In Missouri, cedar apple rust can be a destructive apple disease if you don't use adequate controls. It also attacks red cedars, as the name implies, causing unsightly galls, but damage is usually minimal. Understanding of the disease cycle of this rust fungus is necessary for proper identification and control.Revised 2/96/5M