Variation in fungicide sensitivity among Rhizoctonia isolates recovered from potatoes in South Africa

Please read abstract in the article.Potatoes South Africahttp://apsjournals.apsnet.org/loi/pdishj2018Plant Production and Soil Scienc

Elephant hide and growth cracking on potato tubers caused by Rhizoctonia solani AG3-PT in South Africa

No Abstracthttp://apsjournals.apsnet.org/loi/pdishb201

Anastomosis groups and pathogenicity of Rhizoctonia solani and binucleate Rhizoctonia from potatoes in South Africa

A survey of anastomosis groups (AGs) of Rhizoctonia species associated with potato diseases was conducted in South Africa. A total of 112 Rhizoctonia solani and 19 binucleate Rhizoctonia (BNR) isolates were recovered from diseased potato plants, characterized for AG and pathogenicity. The AG identity of the isolates was confirmed using phylogenetic analysis of the internal transcribed spacer region of ribosomal DNA. Rhizoctonia solani isolates recovered belonged to AG 3-PT, AG 2- 2IIIB, AG 4HG-I, AG 4HG-III and AG 5, while BNR isolates belonged to AG A and AG R, with frequencies of 74, 6.1, 2.3, 2.3, 0.8, 12.2 and 2.3%, respectively. Rhizoctonia solani AG 3-PT was the most predominant AG and occurred in all the potato growing regions sampled whereas the other AGs occurred in distinct locations. Different AGs grouped into distinct clades with high maximum parsimony and maximum likelihood bootstrap support for both R. solani and BNR. An experiment under greenhouse conditions with representative isolates from different AGs showed differences in aggressiveness between and within AGs. Isolates of AG 2-2IIIB, AG 4HG-III and AG R were the most aggressive in causing stem canker while AG 3-PT, AG 5 and AG R caused black scurf. This is the first comprehensive survey of R. solani and BNR on potatoes in South Africa using a molecularbased approach. This is the first report of R. solani AG 2-2IIIB and AG 4 HG-I causing stem and stolon canker and BNR AG A and AG R causing stem canker and black scurf on potatoes in South Africa.Potatoes South Africa.National Research Foundation of South Africa (UID: 78566 (NRF RISP grant for the ABI3500)).http://apsjournals.apsnet.org/loi/pdishb201

Population genetic structure of Rhizoctonia solani AG 3-PT from potatoes in South Africa

Rhizoctonia solani AG 3-PT is an important potato pathogen causing significant yield and quality losses in potato production globally. However, little is known about the levels of genetic diversity and population structure of this pathogen in South Africa. A total of 114 R. solani AG 3-PT isolates collected from four geographic regions were analyzed for genetic diversity and structure using eight microsatellite loci. Microsatellite analysis found high intrapopulation genetic diversity, population differentiation and evidence of recombination. A total of 78 multilocus genotypes (MLGs) were identified with few MLGs shared among populations. Low levels of clonality (13-39 %) and high levels of population differentiation were observed among populations. Most of the loci were in Hardy-Weinberg equilibrium and all four field populations showed evidence of a mixed reproductive mode of both clonality and recombination. The PCoA clustering method revealed genetically distinct geographic populations of R. solani AG 3-PT in South Africa. This study showed that populations of R. solani AG 3-PT in South Africa are genetically differentiated and disease management strategies should therefore be applied accordingly. This is the first study of the population genetics of R. solani AG 3-PT in potatoes in South Africa and results may help to develop knowledge-based disease management strategies in South Africa and elsewhere.Potatoes South Africa and the Potato Pathology Programme at UP as well as the National Research Foundation.http://www.elsevier.com/locate/funbio2017-05-31hb2016Plant Scienc

First report of Rhizoctonia solani AG 4HG-III causing potato stem canker in South Africa

No abstract available.http://apsjournals.apsnet.org/loi/pdishb201

Identification of differentially expressed genes in tolerant and susceptible potato cultivars in response to Spongospora subterranea

Figure S1. Relative expression levels of selected potato defence genes in tolerant and susceptible potato cultivars. Expression levels of StTOSB, StSN2, StUDP, StSN1, StPRF, StLOX, StWRKY6, StMRNA, StDEF and StNBS were measured in Innovator (tolerant) and Vanderplank (susceptible) cultivars inoculated and uninoculated with Spongospora subterranea f. sp. subterranea. Amplification of StEFα‐1 and β‐tubulin gene expression was used to normalize the expression value in each sample. The relative expression values were determined against the average values of the uninoculated control samples. Data represent fold change of gene expression at 7 weeks after emergence and at 15 weeks after emergence. The average of three replicates is shown and different letters show significant differences (Student's t‐test: P < 0.05) between the two cultivars.Figure S2. Mean powdery scab disease severity and disease index of two potato cultivars evaluated for Spongospora subterranea f. sp. subterranea tuber infection. Values are log 10 transformed means of the three biological replicates for each cultivar. Bars represent the standard error.Table S1. List of differentially expressed genes in tolerant potato cultivar Innovator, inoculated with Spongospora subterranea f. sp. subterranea.Table S2. List of differentially expressed genes in susceptible potato cultivar Vanderplank, inoculated with Spongospora subterranea f. sp. subterranea.Table S3. List of genes up‐regulated in tolerant and susceptible potato cultivars inoculated/uninoculated with Spongospora subterranea f. sp. subterranea.Table S4. List of genes down‐regulated in tolerant and susceptible potato cultivars inoculated/uninoculated with Spongospora subterranea f. sp. subterranea.Powdery scab caused by Spongospora subterranea f. sp. subterranea (Sss) has recently become one of the most devastating potato diseases of economic importance in South Africa. The use of resistant cultivars has long been considered the most effective and sustainable strategy to manage the pathogen. However, little is known about the molecular mechanisms underlying resistance of potato tubers to Sss. Using RNA‐sequencing (RNA‐seq), 2058 differentially expressed genes (DEGs) were identified from two potato cultivars (tolerant and susceptible) in response to Sss infection. Analysis of the expression patterns of 10 selected defence‐response genes was carried out at two different stages of tuber growth using RT‐qPCR to validate the RNA‐seq data. Several defence‐related genes showed contrasting expression patterns between the tolerant and susceptible cultivars, including marker genes involved in the salicylic acid hormonal response pathway (StMRNA, StUDP and StWRKY6). Induction of six defence‐related genes (StWRKY6, StTOSB, StSN2, StLOX, StUDP and StSN1) persisted until harvest of the tubers, while three other genes (StNBS, StMRNA and StPRF) were highly up‐regulated during the initial stages of disease development. The results of this preliminary study suggest that the tolerant potato cultivar employs quantitative resistance and salicylic acid pathway hormonal responses against tuber infection by Sss. The identified genes have the potential to be used in the development of molecular markers for selection of powdery scab resistant potato lines in marker‐assisted breeding programmes.The Schlumberger foundation and the National Research Foundation (NRF).https://onlinelibrary.wiley.com/journal/136530592020-08-01hj2019Plant Production and Soil Scienc

Identification of differentially expressed genes in tolerant and susceptible potato cultivars in response to Spongospora subterranea f. sp. subterranea tuber infection

Powdery scab caused by Spongospora subterranea f. sp. subterranea (Sss) has recently become one of the most devastating potato diseases of economic importance in South Africa. The use of resistant cultivars has long been considered the most effective and sustainable strategy to manage the pathogen. However, little is known about the molecular mechanisms underlying resistance of potato tubers to Sss. Using RNA‐sequencing (RNA‐seq), 2058 differentially expressed genes (DEGs) were identified from two potato cultivars (tolerant and susceptible) in response to Sss infection. Analysis of the expression patterns of 10 selected defence‐response genes was carried out at two different stages of tuber growth using RT‐qPCR to validate the RNA‐seq data. Several defence‐related genes showed contrasting expression patterns between the tolerant and susceptible cultivars, including marker genes involved in the salicylic acid hormonal response pathway (StMRNA, StUDP and StWRKY6). Induction of six defence‐related genes (StWRKY6, StTOSB, StSN2, StLOX, StUDP and StSN1) persisted until harvest of the tubers, while three other genes (StNBS, StMRNA and StPRF) were highly up‐regulated during the initial stages of disease development. The results of this preliminary study suggest that the tolerant potato cultivar employs quantitative resistance and salicylic acid pathway hormonal responses against tuber infection by Sss. The identified genes have the potential to be used in the development of molecular markers for selection of powdery scab resistant potato lines in marker‐assisted breeding programmes.Figure S1. Relative expression levels of selected potato defence genes in tolerant and susceptible potato cultivars. Expression levels of StTOSB, StSN2, StUDP, StSN1, StPRF, StLOX, StWRKY6, StMRNA, StDEF and StNBS were measured in Innovator (tolerant) and Vanderplank (susceptible) cultivars inoculated and uninoculated with Spongospora subterranea f. sp. subterranea. Amplification of StEFα‐1 and β‐tubulin gene expression was used to normalize the expression value in each sample. The relative expression values were determined against the average values of the uninoculated control samples. Data represent fold change of gene expression at 7 weeks after emergence and at 15 weeks after emergence. The average of three replicates is shown and different letters show significant differences (Student's t‐test: P < 0.05) between the two cultivars.Figure S2. Mean powdery scab disease severity and disease index of two potato cultivars evaluated for Spongospora subterranea f. sp. subterranea tuber infection. Values are log 10 transformed means of the three biological replicates for each cultivar. Bars represent the standard error.Table S1. List of differentially expressed genes in tolerant potato cultivar Innovator, inoculated with Spongospora subterranea f. sp. subterranea.Table S2. List of differentially expressed genes in susceptible potato cultivar Vanderplank, inoculated with Spongospora subterranea f. sp. subterranea.Table S3. List of genes up‐regulated in tolerant and susceptible potato cultivars inoculated/uninoculated with Spongospora subterranea f. sp. subterranea.Table S4. List of genes down‐regulated in tolerant and susceptible potato cultivars inoculated/uninoculated with Spongospora subterranea f. sp. subterranea.The Schlumberger foundation and the National Research Foundation (NRF).https://onlinelibrary.wiley.com/journal/136530592020-08-01hj2019Plant Production and Soil Scienc

Relative contribution of seed tuber- and soilborne inoculum to potato disease development and changes in the population genetic structure of Rhizoctonia solani AG 3-PT under field conditions in South Africa

Understanding the contribution of seed tuber- and soilborne inocula of Rhizoctonia solani AG 3-PT in causing potato disease epidemics is an important step in implementing effective management strategies for the pathogen. A 2-year study was conducted to evaluate the contribution of each source of inoculum using an integrative experimental approach combining field trials and molecular techniques. Two distinct sets of genetically marked isolates were used as seed tuberborne and soilborne inocula in a mark-release-recapture experiment. Disease assessments were done during tuber initiation and at tuber harvest. Both inoculum sources were found to be equally important in causing black scurf disease, whereas soilborne inocula appeared to be more important for root and stolon infection, and seedborne inocula contributed more to stem canker. However, seed tuber-transmitted genotypes accounted for 60% of the total recovered isolates when genotyped using three polymerase chain reaction restriction fragment length polymorphism markers. The changes in population structure of the experimental R. solani population over the course of the growing season and across two growing seasons were investigated using eight microsatellite markers. The populations at different sampling times were somewhat genetically differentiated, as indicated by Nei’s gene diversity (0.24 to 0.27) and the fixation index (FST). The proportion of isolates with genotypes that differed from the inoculants ranged from 13 to 16% in 2013 and 2014, respectively, suggesting the possibility of emergence of new genotypes in the field. Because both soilborne and tuberborne inocula are critical, it is important to ensure the use of pathogen-free seed tubers to eliminate seed tuberborne inoculum and the introduction of new genotypes of R. solani for sustainable potato production in South Africa.Potatoes South Africa. N. Muzhinji received a studentship from the National Research Foundation and University of Pretoria.http://apsjournals.apsnet.org/loi/pdishj2018Plant Production and Soil Scienc

Development of a TaqMan PCR assay for specific detection and quantification of Pectobacterium brasiliense in potato tubers and soil

Pectobacterium brasiliense (Pb) is one of the causal agents of soft rot and blackleg diseases and has become a pathogen of economic importance in many potato production regions worldwide. Accurate, sensitive and timely identification of Pb is critical for improved management of the pathogen to mitigate yield losses. This study describes the development and validation of a TaqMan probe-based quantitative real-time PCR assay for rapid and specific detection of Pb in plant material and soil. A primer-pair that amplifies a 125-bp fragment was designed from the 16-23 s intergenic spacer region ribosomal RNA and the tRNA-Glu gene region. The specificity of the assay was evaluated with 24 isolates representative of nine different Pectobacterium and Dickeya species associated with soft rot and blackleg of potatoes. The designed Pb species-specific primers and FAM-labelled TaqMan probe were specific for detection of Pb in all the assays performed and it did not detect other Pectobacterium and Dickeya species. The TaqMan PCR assay could detect Pb DNA quantities as low as 10 fg/µl and DNA from a concentration of cells as low as 103 colony forming units/ml. The assay was capable of identifying and quantifying Pb in potato tubers and in field soils without the interference of inhibitors. The developed TaqMan PCR assay can be used for routine Pb diagnostics, surveillance and epidemiological studies.https://link.springer.com/journal/106582021-08-20hj2020Plant Production and Soil Scienc