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Genetic Diversity in Macrophomina Phaseolina, the Causal Agent of Charcoal Rot

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Genetic Diversity in Macrophomina Phaseolina, the Causal Agent of Charcoal Rot Phytopathologia Mediterranea (2014) 53, 2, 250−268 DOI: 10.14601/Phytopathol_Mediterr-13736 RESEARCH PAPERS Genetic diversity in Macrophomina phaseolina, the causal agent of charcoal rot 1 2 3 3,4,5 MAME P. SARR , M’BAYE NDIAYE , JOHANNES Z. GROENEWALD and PEDRO W. CROUS 1 Centre National de Recherches Agronomiques, Laboratoire de phytopathologie ISRA/CNRA.BP: 53 Bambey, Senegal 2 Centre Régional AGRHYMET, Département Formation et Recherche, Niamey, Niger 3 CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands 4 Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands 5 Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands Summary. Macrophomina phaseolina (Botryosphaeriaceae) is an important soil- and seed-borne pathogen. This patho- gen has a broad geographic distribution, and a large host range. The aim of the present study was to determine the genetic variation among a global set of 189 isolates of M. phaseolina, isolated from 23 hosts and 30 soil samples in 15 countries. To achieve this goal a multi-gene DNA analysis was conducted for the following five loci, ITS, TEF, ACT, CAL and TUB. Based on these results two well-defined clusters could be delineated, one corresponding to M. phaseolina s. str., for which a suitable epitype is designated. The second clade corresponds to M. pseudophaseo- lina, a novel species occurring on Abelmoschus esculentus, Arachis hypogaea, Hibiscus sabdarifa and Vigna unguiculata in Senegal. No consistent correlation was found among genotype, host and geographic location, and both species could even occur on the same host at the same location. Although M. pseudophaseolina is presently only known from Senegal, further research is required to determine its virulence compared to M. phaseolina, and its geographic distribution. Key words: genetic diversity, Senegal, soilborne pathogen, systematics, Tiarosporella phaseolina. Introduction Macrophomina phaseolina induces diseases on a range of crops, ranging from seedling blight, root Macrophomina phaseolina, the causal agent of and stem rot, wilt, and pre- to post-emergent damp- charcoal rot, is a soil- and seed-borne polyphagous ing off, which result in decreased stem height, girth, pathogen. It causes diseases of more than 500 crop root and head weight, or death, of affected plants and non-crop species, including economically im- (Raut, 1983). The abundant production of minute portant hosts such as soybean, common bean, corn, black sclerotia of the fungus cause the rotted tissues sorghum, cowpea, peanut and cotton (Dhingra and to become blackened, and for this reason the vari- Sinclair, 1977; Ndiaye et al., 2010) (Figure 1). The fun- ous diseases are known as charcoal rot. Wrather and gus has a worldwide distribution, but is regarded Koenning (2010) stated that average yield losses due as economically more important in subtropical and to charcoal rot in the USA were estimated at about tropical countries with semi-arid climates (Wrather 27 million bushels of soybeans per year from 1996 et al., 1997, 2001). to 2009. In the Sahelian zone of West Africa (includ- ing Burkina Faso, Niger and Senegal), charcoal rot causes an average yield loss of 10%, which is equiva- Corresponding author: M.P. Sarr Fax: +221 973 63 48 lent to 30,000 t of cowpea with an estimated value E-mail: [email protected] of $US 146 million for Niger and Senegal (Ndiaye, 250 ISSN (print): 0031-9465 www.fupress.com/pm ISSN (online): 1593-2095 © Firenze University Press Genetic diversity in Macrophomina phaseolina Figure 1. Disease symptoms of Macrophomina (charcoal rot) in infested fields. A. Advanced level of infestation on cowpea (Vigna unguiculata) in an experimental field with a drip irrigation system (Agrhymet, Niger). B. Charcoal rot symptoms in a sorrel (Hibiscus sabdarifa) field during the rainy season (Agrhymet, Niger). C. Early infection in a young cowpea (Vigna unguiculata) plant, in an experimental field during the rainy season (Bambey, Senegal). 2007). However, when conditions are favourable for have previously been described in Macrophomina the growth and development of M. phaseolina, infec- (MycoBank, accessed November 2013), recent phy- tions can result in total crop failures (Orellana, 1971; logenetic studies suggest that the genus could be Tikhonov et al., 1976; Jimenez et al., 1983). Although monotypic (Phillips et al., 2013). Morphologically, it is an important plant pathogen, several case re- Macrophomina resembles species of Tiarosporella, as ports are known of M. phaseolina also acting as an members of both genera have conidia with hyaline opportunistic human pathogen (Tan et al., 2008; Srin- apical appendages. However, Tiarosporella lacks mi- ivasan et al., 2009), especially in immunosuppressed crosclerotia, the conidia do not turn brown with age, patients, including those receiving prophylactic anti- and its conidiogenous cells do not have conspicuous fungal therapy (Arora et al., 2012). percurrent proliferations (Crous et al., 2006). Macrophomina phaseolina produces asexual struc- Several recent studies have been devoted to char- tures, microsclerotia and pycnidia, which can be acterising the genetic and pathogenic variability of detected in soil and host tissue using quantitative M. phaseolina. Advances in molecular techniques and real-time PCR assays (Babu et al., 2011). Microscle- refined PCR-based technology, such as Random Am- rotia can survive in soil for 2–15 y, or in root debris plified Polymorphic DNA (RAPD), Restriction Frag- for longer periods (Cook et al., 1973; Papavizas, 1977; ment Length Polymorphism (RFLP), and Amplified Short et al., 1980; Baird et al., 2003). Once the host tis- Fragment Length Polymorphism (AFLP), have con- sues start to decompose, microsclerotia are released tributed to a better understanding of the genetic and into the soil (Hartman et al., 1999). Microsclerotia en- pathogenic variability within populations of this able the fungus to survive adverse environmental pathogen (Fuhlbohm, 1997; Su et al., 2001; Jimenez, conditions in the field (Short et al., 1980). Pycnidia 2011). In studying Brazilian populations, Almeida et develop readily on plant tissues, and range from al. (2003) reported that although a single root could being immersed to erumpent, each opening via a be infected by more than one genotype, the over- central ostiole, through which hyaline, aseptate, el- all diversity in populations was low, and that the lipsoid to ovoid conidia are discharged (Dhingra and pathogen probably lacked a sexual cycle. Several Sinclair, 1977). studies have focused on developing sets of micro- Macrophomina phaseolina (= Tiarosporella phaseo- satellite markers to study population variation in lina) is the type species of Macrophomina, which is M. phaesolina (Baird et al., 2009, 2010; Arias et al., 2011). a distinct genus in the Botryosphaeriaceae (Crous et Although these studies distinguished phylogenetic al., 2006; Slippers et al., 2013). Although five species clades in their analyses, the clades generally did not Vol. 53, No. 2, August, 2014 251 M.P. Sarr et al. Figure 2. Senegalese cities where samples of different hosts of Macrophomina strains were collected. correlate with geography or host, nor addressed spe- roots of cowpea (Vigna unguiculata), peanut (Ara- ciation. The aim of the present study was, therefore, chis hypogaea), sorrel (Hibiscus sabdarifa), sorghum to employ multi-gene sequence analyses to examine (Shorghum bicolor) and okra (Abelmoschus esculentus) a large sample of isolates representing different hosts were collected from different cropping regions of and continents, to determine if all isolates represent- Senegal. Depending on the number of diseased foci, ed a single species, or if more than one taxon were three to five plants were sampled per field, from the involved as the causes of charcoal rot. major crop production areas of Senegal. Details re- garding the geographical and host origin of all the isolates are provided in Figures 2 and 3, and Table 1. Materials and methods Fungal isolates Soil isolations. Isolates were obtained from soil us- ing a soil assay technique based on the method of All strains of M. phaseolina available at the CBS- Alabouvette (1976). Soil samples were dried in an KNAW Fungal Biodiversity Centre (CBS) in the oven at 37°C, crushed through a 1 mm mesh sieve, Netherlands, and from the working collection of mixed thoroughly, and subsamples of 5 g were taken. Pedro Crous (CPC), maintained at CBS, were in- Each subsample was submerged in 0.52% NaOCl for cluded in this study. Furthermore, from September 10 min. The soil-NaOCl mixture was washed with to November 2011, charcoal rot-affected stems or distilled water through two sieves of, respectively, 252 Phytopathologia Mediterranea Genetic diversity in Macrophomina phaseolina 180 and 45 µm mesh sizes. The residue retained on tin (ACT) gene region using primers ACT-512F and the 45 µm mesh sieve was incorporated into 100 mL ACT-783R (Carbone and Kohn, 1999); and part of of a semi-selective medium (SS medium) for M. pha- CAL gene region using primers CAL-228F and CAL- seolina. This consisted of potato dextrose agar (PDA; 737R (Carbone and Kohn, 1999). However, some of 39 g L-1) maintained at 55°C in a water bath, with the these primer pairs failed to amplify with some of the following ingredients added: 1.5 mL 0.52% NaOCl, 1 isolates, so additional combinations were used. The mL 0.5% choramphenicol dissolved in 95% alcohol, primers EF1-728F and EF 986R were used for am- and 10 mL 2.25% quintozene (PCNB). The medium plification of part of the TEF-1α gene region, ACT- was poured into 9 cm Petri dishes to solidify, and 512F and ACT-2RD for part of the actin (ACT) gene then incubated at 25ºC. region and T1-T22 for the partial beta-tubulin gene (O’Donnell and Cigelnik 1997). Host tissue isolations.Uprooted plants were rinsed The basic PCR protocol described by Lombard et under running tap water, and blotted dry with a al.
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