Sugarcane Brown Rust Research Articles

Prospecting brown rust of sugarcane in São Paulo-Brazil under climate change scenarios

Climate change can cause significant shifts in the occurrence and severity of agricultural diseases, altering the distribution of phytosanitary problems with severe economic, social, and environmental consequences. Despite their importance, these new geographic and temporal distributions of plant diseases still demand scrutiny. In the present study, we prospect the geographic distribution of sugarcane brown rust (Puccinia melanocephala) considering average temperature and relative humidity in the main producing region of the state of São Paulo. The geographic database was structured using GIS with projections of future climate change provided by IPCC. Mathematical logic equations were defined and applied to data of average temperature and relative humidity, resulting in monthly maps of climate favorability for the occurrence of the disease. Prospective maps for three future periods (2011-2040, 2041-2070, and 2071-2100) and two greenhouse gas emission scenarios were compared to the reference period (1961-1990). The analysis considered months from December to May. Our study shows a tendency of decrease in the favorability for the disease in a longer term (2071-2100), more noticeable in the scenario A2 than in B1. These results suggest; however, that this disease demands attention in the management of the producing region for future climate scenarios.

The Impact of Sugarcane Brown Rust and Host Resistance on the Phyllosphere Bacterial Community

The Impact of Sugarcane Brown Rust and Host Resistance on the Phyllosphere Bacterial Community

Assessing concordance between two methods for sugarcane brown rust evaluation

Assessing concordance between two methods for sugarcane brown rust evaluation

Predictive Modeling of Brown Rust of Sugarcane Based on Temperature and Relative Humidity in Florida.

Logistic regression models were developed from 5 years (2014 to 2018) of disease severity and weather data in an attempt to predict brown rust of sugarcane at the Everglades Research and Education Center in Belle Glade, Florida. Disease severity (percentage area of the top visible dewlap leaf covered by rust) was visually assessed in the field every 2 weeks for two varieties susceptible to brown rust. A total of 250 variables were derived from weather data for 10- to 40-day periods before each brown rust assessment day. A subset of these variables were then evaluated as potential predictors of severity of brown rust based on their individual correlation or their biological meaningfulness. Analyses of correlation and stepwise logistic regression allowed us to identify afternoon humid thermal ratio (AHTR), temperature-based duration variables, and their interaction terms as the most significant variables associated with brown rust epidemics of sugarcane in Florida. The nine best predictive models were identified based on model accuracy, sensitivity, specificity, and estimates of the prediction error. The prediction accuracy of these models ranged from 73 to 85%. Single-variable model BR2 (based on AHTR) classified 89% of the epidemic and 81% of the nonepidemic status of the disease. More than 83% of the epidemics and 81% of the nonepidemic status of sugarcane brown rust was correctly classified via multiple-variable models. These models can be used as components of a rust disease warning system to assist in the management of brown rust epidemics of sugarcane in south Florida.

Detection of Key Brown Rust Resistance Gene, Bru1, in 200 Sugarcane (Saccharum L.) Ancestral Species and Landraces Using a Four-Primer Molecular Marker

Sugarcane brown rust is a fungal disease with global distribution that is caused by Puccinia melanocephala, and is responsible for severe yield and sucrose losses in sugarcane production. The most effective strategy of controlling the disease is breeding and cultivating resistant varieties. Bru1 is a major gene that has been demonstrated to confer resistance to P. melanocephala strains from different parts of the globe. R12H16 and 9O20-F4 are two molecular markers that have been previously reported to be closely associated with Bru1, and are often used in brown rust resistance identification during sugarcane germplasm evaluation activities. In the present study, a novel type of molecular marker based on four primers is used to detect Bru1 among 200 sugarcane ancestral species and landraces from the China National Germplasm Repository of Sugarcane (NGRS). According to the results, among the 200 tested materials, 125 materials, such as 51NG63, Katha, and Uba, Bru1 could be detected based on bands corresponding to those in POJ2878, indicated that the 125 (62.5%) materials contained Bru1, and the detection rates of Bru1 in 69 sugarcane ancestral species and 131 landraces were 73.9% and 56.5%, respectively. These results indicated that the sugarcane ancestral species and landraces conserved in the China NGRS contain abundant brown rust-resistant materials, which could provide resources that could facilitate the breeding of brown rust-resistant sugarcane varieties.

Machine learning approaches reveal genomic regions associated with sugarcane brown rust resistance

Sugarcane is an economically important crop, but its genomic complexity has hindered advances in molecular approaches for genetic breeding. New cultivars are released based on the identification of interesting traits, and for sugarcane, brown rust resistance is a desirable characteristic due to the large economic impact of the disease. Although marker-assisted selection for rust resistance has been successful, the genes involved are still unknown, and the associated regions vary among cultivars, thus restricting methodological generalization. We used genotyping by sequencing of full-sib progeny to relate genomic regions with brown rust phenotypes. We established a pipeline to identify reliable SNPs in complex polyploid data, which were used for phenotypic prediction via machine learning. We identified 14,540 SNPs, which led to a mean prediction accuracy of 50% when using different models. We also tested feature selection algorithms to increase predictive accuracy, resulting in a reduced dataset with more explanatory power for rust phenotypes. As a result of this approach, we achieved an accuracy of up to 95% with a dataset of 131 SNPs related to brown rust QTL regions and auxiliary genes. Therefore, our novel strategy has the potential to assist studies of the genomic organization of brown rust resistance in sugarcane.

Detection of polymorphic simple-sequence repeat markers that show linkage to a novel sugarcane brown rust disease resistance gene in resistant and susceptible genetic pools

AbstractSugarcane brown rust, caused by Puccinia melanocephala, is one of the main diseases of sugarcane in China. The identification and discovery of new resistance genes have important theoretical and practical significance for preventing outbreaks of brown rust and ensuring the sustainable production of sugarcane. To screen for polymorphic simple-sequence repeat (SSR) molecular markers for localization of brown rust resistance genes, we used two populations that are suitable for genetic linkage map construction and mapping of new resistance genes to construct resistant and susceptible genetic pools. We then screened 449 pairs of primers to identify polymorphic SSR markers in the parental lines and the resistant/susceptible genetic pools. The results showed that 25 pairs of primers directed amplification of polymorphic DNA fragments between the parents of the cross combination ‘Yuetang 03-393’ × ‘ROC 24’, and 16 pairs of primers amplified polymorphic fragments between the parents of the cross combination ‘Liucheng 03-1137’ × ‘Dezhe 93-88’. Four pairs of primers (SMC236CG, SCESSR0928, SCESSR0636 and SCESSR2551) amplified polymorphic DNA fragments between the parental lines and the resistant/susceptible genetic pools in ‘Yuetang 03-393’ × ‘ROC 24’. The results of this study will establish a solid foundation for the mapping of new brown rust resistance genes, genetic linkage map construction and the development of closely-associated molecular markers in sugarcane.

Evaluation of some fungicides for Management of Sugar cane rust (Puccinia melanocephela) disease in Finchaa Sugar Estate, Horo -Guduru Wollega, Oromia Regional State, Ethiopia

Sugarcane (Saccharum officinarum L.) is an important industrial, monocotyledonous perennial cash crop. Sugarcane brown rust (Puccinia melanocephela Syd. & P. Syd) is one of the most devastating diseases. Sugar cane brown rust is new for Ethiopia and currently only fincha sugar Estate is affected.

Assessment of Sugarcane Brown Rust (<i>Puccinia melanocephela</i>) Disease Intensity in Finchaa Sugar Estate, Horo - Guduru Wollega, Oromia, Ethiopia

Sugarcane (Saccharum officinarum L.) is an important industrial cash crop. Sugarcane brown rust (Puccinia melanocephela Syd. & P. Syd) is one of the most devastating diseases. The current study was carried out to assessing the sugarcane brown rust disease intensity in Finchaa Sugar Estate, Ethiopia, during the main cropping season of 2016. The field survey was conducted on sugarcane-cultivated fields of Finchaa Sugar Estate. These fields were under age of five three to eight months. A total of 126 fields were assessed. For the fields three components of disease intensity were assessed i.e. disease prevalence, disease incidence and disease severity. From the three disease, intensity severity is directly related to yield losses of the crop. Among those fields; the disease was prevalent on 123 (97.62%) fields. The result of this survey indicates that the distribution of brown rust severity varies from variety to variety and it was varied with the age of sugar cane crop. The assessed data also showed there were about seven sugar cane varieties and they differ in reaction of sugar cane rust disease. The method of data analysis was descriptive statistics. The mean maximum of disease severity (22.5%) was recorded on SP70/1284 variety while the least disease severity (11.0%) was recorded on the variety C132. An incidence of 95.0% on SP70/1284 cultivar and 81.5% were recorded on variety C132. Generally the report indicated that the appropriate management method should be implemented.

Developing genetically segregating populations for localization of novel sugarcane brown rust resistance genes

Brown rust caused by Puccinia melanocephala H. Sydow & P. Sydo is an important sugarcane disease that severely threatens sugarcane production in China. Breeding and planting resistant cultivars is the most cost-effective and efficient strategy for the control the disease. In addition, exploration, research, and utilization of resistant genes are the basis for resistance breeding. In the present study, four sugarcane varieties without the Bru1 gene and highly resistant to brown rust were used as male parents, and four varieties highly susceptible to brown rust were used as the female parents to configure hybrids. Six F1 hybrid populations were subjected to authenticity determination using SSR markers, brown rust resistance phenotype identification using artificial inoculation, and molecular detection of Bru1 gene. The results showed that the genetic segregation ratios in F1 hybrid populations of Yuetang 03-393 (HS) × ROC24 (HR) and Liucheng 03-1137 (HS) × Dezhe 93-88 (HR) were 3R:1S and 1R:3S, respectively, and Bru1 gene was not detected in their F1 hybrids. The results indicated that two dominant novel genes controlled brown rust resistance in Yuetang 03-393 (HS) × ROC24 (HR) and two recessive novel genes controlled brown rust resistance in Liucheng 03-1137 (HS) × Dezhe 93-88 (HR). Two genetically segregating populations that could be used for the localization of novel brown rust resistance genes were developed in the present study, and could lay a suitable foundation and provide theoretical reference for the analysis of the genetic mechanism of brown rust resistance, genetic map construction, mapping of novel resistance genes and the development of closely associated molecular markers in the future.

Screening of Polymorphic SSR Molecular Markers Between Resistant and Susceptible Parents for Localization of Brown Rust Resistance Gene

Sugarcane brown rust induced by Puccinia melanocephala is an important global disease. Exploring novel resistance genes and breeding varieties with durable resistance is the most economical and effective way of controlling brown rust. The establishment of complete and high-density molecular genetics maps is a key prerequisite for the discovery and location of sugarcane brown rust resistance genes. To obtain more polymorphic simple sequence repeat (SSR) markers for the construction of genetic linkage maps, six highly resistant varieties and six highly susceptible varieties were used as parents to screen the primers with clear bands, obvious polymorphism, and good repeatability. The highest numbers of polymorphic primers were obtained from the parental group of Liucheng 03-1137 × Dezhe 93-88 (52.38%). Ten pairs of primers including mSSCIR34 exhibited high polymorphism in the parental group of Liucheng 03-1137 × Dezhe 93-88. Here, we recommend ten SSR pairs of polymorphic primers including mSSCIR34 to use in the mapping populations of Liucheng 03-1137 × Dezhe 93-88. The polymorphic primers could facilitate the construction of genetic maps and lay an appropriate foundation for the localization of brown rust resistance genes and development of molecular genetics linkage markers.

Timing and frequency of fungicide applications for the management of sugarcane brown rust

The frequency and application timing of fluxapyroxad + pyraclostrobin fungicides for management of sugarcane brown rust, caused by Puccinia melanocephala, was evaluated during two growing seasons (2016 and 2017) in Belle Glade, FL. Although the rust epidemic duration was longer in 2017 than in 2016, three applications of fluxapyroxad + pyraclostrobin during early, mid, and late epidemic season at three week-intervals resulted in 40–42% decrease of disease severity on the top visible dewlap leaf (expressed as the area under disease progress curve). These fungicide applications were also associated with a 27–35% increase in mean stalk weight as compared to untreated control plants. Two fungicide applications during early and mid-epidemic season resulted in similar stalk weight gain (25–32%) and 30–39% reduction of disease severity as compared to untreated control. Single applications either during early or mid-epidemic season were the least effective in reducing rust severity and increasing mean stalk weight. Therefore, at least two applications of fluxapyroxad + pyraclostrobin initiated during early epidemic season are necessary for best management of sugarcane brown rust in Florida. Based on increase of estimated commercial yields, the most beneficial chemical control was achieved with two rather than three fungicide sprays at three to four weeks intervals.

Molecular insights into brown rust resistance and potential epidemic based on the Bru1 gene in sugarcane varieties and new elite clones

In most sugarcane cultivation areas, sugarcane brown rust (SBR), caused by Puccinia melanocephala, is an economically important fungal disease that leads to severe yield loss in susceptible cultivars. Bru1, which is the major dominant SBR resistance gene, has been widely used in the prediction of brown rust resistance in sugarcane. In this study, three panels of sugarcane germplasms, the major varieties approved over the past 10 years and new elite clones in the current national regional trial, together with one panel of Saccharum spontaneum, were employed in estimating the possibility of SBR epidemic and to assess the efficiency of 9O20-F4-HaeIII in eliminating false positives. Among the current top five varieties used as sucrose feedstock, accounting for more than 68.9% of the total cultivated area, all were highly resistant to SBR, although only three harboring Bru1. Two major varieties Yuetang60 and Guitang46 without harboring Bru1 were highly susceptible to SBR, together with highly susceptible Funong41, which need prudent promotion. Approximately 60.5% of the 38 new elite clones were Bru1 positive. Considering the susceptibility of Liucheng03-1137, which exhibits a strong promotion momentum, together with Funong41, Guitang46, Yuetang60, and Yunzhe06-47, four were favored by the enterprise due to their superior sucrose content and good stalk yield, despite their high susceptibility to SBR, and additional Yuetang93-159, one current top five varieties with declining resistance, which results in a potential risk for brown rust epidemic. Furthermore, low frequency of the wild germplasm of S. spontaneum from five different countries was Bru1 positive. In addition, a perfect molecular diagnostic result was observed in all modern sugarcane clones using two dominant markers, and HaeIII can prevent the occurrence of false positive results when the 9O20-F4 PCR products of S. spontaneum are digested by RsaI. The prevalent chewing cane Badila without Bru1 is highly resistant to SBR. Our results provide valuable information for the extension of sugarcane varieties and a batch of novel SBR resistance sources with superior comprehensive characters for crossbreeding, and for SBR-resistant gene pyramiding by crossing or through mining and using of new SBR-resistant genes.

An overview of sugarcane brown rust in Cuba

Multiple pathogens affect sugarcane, among them Puccinia melanocephala, the causal agent of brown rust. This disease was first reported in Cuba in 1979 when it was responsible for a severe attack on the main sugarcane variety B4362. The aims of the present study were to give an overview of sugarcane brown rust in Cuba and show the current disease situation in the country. A retrospective analysis regard to sugarcane cultivar composition resistant to brown rust in Cuba was carried out. In addition 154 genotypes, including the most used progenitors in the breeding program and commercial varieties were evaluated under natural infection conditions. The identity of P. melanocephala was verified by Polymerase Chain Reaction (PCR) and by sequencing the ITS1 region. After the introduction of P. melanocephala into Cuba, the susceptible variety, B4362, was replaced by Ja60-5 which remained resistant until 1998. Since 2002, a varietal policy supported by a governmental resolution establishing that any single cultivar cannot occupy more than 20 % of the production area for each production company, local area and province, has been applied. Out of the genotypes evaluated, 49 showed resistance to the disease and 35 intermediate behavior, while 39 were susceptible and 31, highly susceptible. P. melanocephala was detected by PCR in all symptomatic samples and its identify confirmed by sequencing the ITS1 region. The adopted measurement together with permanent phytosanitary monitoring and commercial release of resistant or intermediate cultivars succeeded in avoiding any new epidemic. Inoculum pressure was reduced, even on susceptible and highly susceptible varieties since, by resolution, they cannot occupy more than 10 % of the planted area.

Putative resistance-associated genes induced in sugarcane in response to the brown rust fungus, Puccinia melanocephala and their use in genetic diversity analysis of Louisiana sugarcane clones

Development of resistant cultivars is the main control measure against sugarcane brown rust caused by Puccinia melanocephala. Durability is uncertain, since the pathogen possesses adaptive ability to overcome host plant resistance. A differential gene expression study utilizing suppressive subtraction hybridization was conducted to identify brown rust responsive genes in sugarcane. The expression patterns of 11 out of 217 unigenes of the subtractive library representing biosynthetic pathways, defense-related genes, and signaling genes were analyzed in L 99-233, a cultivar exhibiting quantitative resistance, L 01-299, a resistant cultivar with the major resistance gene Bru1, and two susceptible cultivars, Ho 95-988 and L 09-125, at 24 h, 48 h, 72 h, and 1 week after inoculation with P. melanocephala using (semi)quantitative RT-PCR. All genes showed message accumulation upon infection in susceptible and resistant cultivars, but the maintenance of high amounts of mRNAs of the genes for a prolonged time period appeared to be the most important factor contributing to brown rust resistance. Differences in the time-course of gene expression were detected between L 01-299 and L 99-233 suggesting variable mechanisms for resistance between the cultivars. The markers derived from the brown rust responsive genes provided usefulness in genetic diversity assay of Louisiana sugarcane gene pool.

Molecular insights into the origin of the brown rust resistance gene Bru1 among Saccharum species.

Analysis of 387 sugarcane clones using Bru 1 diagnostic markers revealed two possible sources of Bru 1 in Chinese cultivars: one from Saccharum spontaneum and another from Saccharum robustum of New Guinea. Sugarcane brown rust (SBR) is an important fungal disease in many sugarcane production areas around the world, and can cause considerable yield losses in susceptible sugarcane cultivars. One major SBR resistance gene, named Bru1, initially identified from cultivar R570, was shown to be a major SBR resistance source in most of the sugarcane producing areas of the world. In this study, by using the two Bru1-associated markers, R12H16 and 9O20-F4, we surveyed the presence of Bru1 in a Chinese sugarcane germplasm collection of 387 clones, consisting of 228 hybrid cultivars bred by different Chinese sugarcane breeding establishments, 54 exotic hybrid cultivars introduced from other countries and 105 clones of sugarcane ancestral species. The Bru1-bearing haplotype was detected in 43.4% of Chinese sugarcane cultivars, 20.4% of exotic hybrid cultivars, and only 3.8% of ancestral species. Among the 33 Chinese cultivars for which phenotypes of resistance to SBR were available, Bru1 was present in 69.2% (18/26) of the resistant clones. Analyses of the allelic sequence variations of R12H16 and 9O20-F4 suggested two possible sources of Bru1 in Chinese cultivars: one from S. spontaneum and another from S. robustum of New Guinea. In addition, we developed an improved Bru1 diagnostic marker, 9O20-F4-HaeIII, which can eliminate all the false results of 9O20-F4-RsaI observed among S. spontaneum, as well as a new dominant Bru1 diagnostic marker, R12E03-2, from the BAC ShCIR12E03. Our results provide valuable information for further efforts of breeding SBR-resistant varieties, searching new SBR resistance sources and cloning of Bru1 in sugarcane.

Molecular Detection of Bru1 Gene and Identification of Brown Rust Resistance in Chinese Sugarcane Germplasm

Sugarcane brown rust induced by Puccinia melanocephala is an important global disease. Bru1 is a major brown rust resistance gene and has been shown to provide broad-spectrum resistance against various brown rust pathogen strains originating from different countries. Thus, brown rust resistance genes have important implications for sugarcane brown rust resistance breeding programs. The objectives of this study were to (1) assess the level of resistance of common sugarcane crossbreeding parents to P. melanocephala, (2) determine the distribution of the Bru1 gene in common sugarcane crossbreeding parents in China, (3) screen, evaluate, and select rust-resistant parental lines to improve the efficiency of breeding for brown rust resistance. Brown rust resistance in 101 common sugarcane breeding parents was collected from the Chinese National Nursery of Sugarcane Germplasm Resources and was scored and identified at the seedling stage and was assayed for the presence of the brown rust resistance gene Bru1. The results showed that Bru1 was detected in 48 (47.5 %) resistant clones out of the 101 tested parental lines, indicating that brown rust resistance in common sugarcane breeding parents in China is primarily controlled by Bru1. The apparent absence of Bru1 from the other 29 resistant and 24 susceptible parental lines suggested that they may carry brown rust resistance-associated genes other than Bru1. These results may facilitate future efforts to breed varieties with improved resistance to brown rust and may provide additional resistant parental lines for selecting and planting elite-resistant varieties to effectively control brown rust disease in sugarcane.

Molecular Diagnostic of Both Brown and Orange Sugarcane Rust and Evaluation of Sugarcane Brown Rust Resistance in Tucuman, Argentina, Using Molecular Markers Associated with Bru1 a Broad-Range Resistance Allele

Fil: Racedo, Josefina. Consejo Nacional de Investigaciones Cientificas y Tecnicas; Argentina. Gobierno de Tucuman. Ministerio de Desarrollo Productivo. Estacion Experimental Agroindustrial Obispo Colombres; Argentina

Screening for Resistance to Sugarcane Brown Rust With Controlled-conditions Inoculation.

Breeding for resistance is the primary control measure for brown rust of sugarcane. Resistance screening utilizing natural infection symptom severity ratings provides erratic results. Therefore, a method accomplishing infection and disease expression under controlled conditions was evaluated to determine whether it could provide accurate resistance ratings for seedlings and clones with known and unknown reactions. Seedlings from crosses between parents with different levels of resistance were inoculated with increasing concentrations of urediniospores. Inoculum concentration affected disease severity and the frequency of resistant progeny in crosses. Brown rust resistance is a heritable trait; however, parental reaction was not a consistent determinant of progeny distribution across resistance rating categories. These results suggest that seedling inoculation may be misleading for the evaluation of brown rust resistance. Clone resistance reactions could not be reliably determined for susceptible clones in single inoculations. Ratings for controlled-conditions inoculation and field natural infection severity were not correlated. Multiple inoculations under controlled conditions accurately identified resistant and susceptible clones, with severe infection resulting from any single inoculation indicating susceptibility. Therefore, controlled-conditions inoculation has the potential to be useful in limited studies to characterize parents in a recurrent selection program and for basic studies of resistance to brown rust.

Screening for Sugarcane Brown Rust in the First Clonal Stage of the Canal Point Sugarcane Breeding Program

Sugarcane (Saccharum spp.) brown rust (caused by Puccinia melanocephala Syd. & P. Syd.) was first reported in the United States in 1978 and is still one of the great challenges for sugarcane production. A better understanding of sugarcane genotypic variation in response to brown rust will help optimize breeding and selection strategies for disease resistance. Brown rust ratings were scaled from non-infection (0) to severe infection (4) with intervals of 0.5 and routinely recorded for genotypes in the first clonal selection stage of the Canal Point sugarcane breeding program in Florida. Data were collected from 14,272 and 12,661 genotypes and replicated check cultivars in 2012 and 2013, respectively. Mean rust rating, % infection, and severity in each family and progeny of female parent were determined, and their coefficients of variation (CV) within and among families (females) were estimated. Considerable variation exists in rust ratings among families or females. The families and female parents with high susceptibility or resistance to brown rust were identified and ranked. The findings of this study can help scientists to evaluate sugarcane crosses and parents for brown rust disease, to use desirable parents for crossing, and to improve genetic resistance to brown rust in breeding programs.