Phenotypic and genetic characteristics of Xanthomonas citri subsp. malvacearum, causal agent of cotton blight, and identification of races in Iran A. Saeedi Madani A , A. Marefat B,D , K. Behboudi A and A. Ghasemi C A Plant Protection Department, College of Agriculture, University of Tehran, Tehran, Iran. B Plant Protection Department, College of Agriculture, University of Zanjan, Zanjan, Iran. C Plant Disease Department, Plant Protection Research Institute of Tehran, Tehran, Iran. D Corresponding author. Email: marefat@znu.ac.ir, marefat345@gmail.com Abstract. Bacterial blight was first reported on cotton (Gossypium hirsutum) in Iran in 1972 and has been observed in cotton fields in several provinces with outbreaks occurring in 2004 and 2005. This study was initiated to determine phenotypic characteristics of isolates obtained from diseased cotton plants in two different regions of Iran, discriminate pathogen races and assess the genetic diversity of the pathogen using repetitive-PCR. Thirty-seven isolates were identified as Xanthomonas citri subsp. malvacearum from biochemical and physiological tests. Repetitive-PCR genomic fingerprinting revealed two distinct groups with some variation detected within subgroups. Four different pathogen races were discriminated in pathogenicity tests: race 1 (16%), race 2 (8%), race 6 (57%) and race 18 (19%). There was no genetic distinction between isolates from the two regions suggesting a common inoculum source such as seed. Additional keywords: ERIC-PCR, Xanthomonas axonopodis pv. malvacearum. Introduction Bacterial blight is one of the most important and destructive diseases in Upland cotton (Gossypium hirsutum L.) worldwide (Bayles and Verhalen 2007). The disease is characterised by angular, waxy and water-soaked lesions on the leaf, stem and boll tissues, which gradually turn to brown, necrotic areas. Xanthomonas citri subsp. malvacearum (ex Smith 1901) Schaad et al.(2006) also known as Xanthomonas axonopodis pv. malvacearum [(Smith) (Vauterin et al. 1995)] has been identified as the causal agent of the disease. Bacterial blight was first reported on cotton in Iran in 1972, based on symptoms of the disease only (Amani 1972). The disease has been observed in cotton fields, mainly in stands of susceptible cultivars, in several provinces with an outbreak in Golestan and Garmsar during 2004 and 2005. Characterisation of a small number of isolates of the pathogen has already proved the existence of the pathogen in Iran (Arabsalmani et al. 2002). Characterisation of the pathogen was rudimentary and knowledge about races and genetic diversity of the X. citri subsp. malvacearum population in Iran was lacking. Traditionally, non-DNA-based methods such as physiological and biochemical tests have been used for characterisation and study of phenotypic variation among Xanthomonas species isolated from various host plants including cotton (Hayward 1964; Griffin et al. 1991; Verniere et al. 1993; Abdo-Hasan et al. 2008) and are still essential for identification of plant pathogenic bacteria to genus and species (Schaad et al. 2001). Accurate identification of pathogens is essential for epidemiological and ecological monitoring purposes and current genetic techniques enable the accurate differentiation of genetic variation within a population (Gabriel and De Feyter 1992). A population genetic diversity study is important to improve the understanding of its taxonomy, epidemiology and identification (Milgroom and Fry 1997). During the last 15 years, genetic diversity studies based on the presence of repetitive elements dispersed in bacterial genomes (rep-PCR) (Rademaker and de Bruijn 1997) has been used as an important tool in measuring the variation within bacterial species and has been applied to study Xanthomonas populations associated with several diseases (Lopes et al. 2001; Scortichini et al. 2001; Massomo et al. 2003; Gent et al. 2004; Marefat et al. 2006). Several Xanthomonas species have been divided into pathovars according to host specificity and several have been further differentiated into races based on their pathogenicity across different cultivars (Vicente et al. 2001). X. citri subsp. malvacearum shows a wide range of virulence (Brinkerhoff 1970; Bayles and Verhalen 2007). Hunter et al.(1968) identified 19 races and later Verma and Singh (1974) extended the number of races to 32. The distribution of these races differs between countries (Abdo-Hasan et al. 2008) but their occurrence and abundance in Iran is not known. This study was initiated to determine phenotypic characteristics of Xanthomonas isolates obtained from cotton plants in two regions of Iran, identify races of the pathogen and to assess the genetic diversity within the pathogen population. CSIRO PUBLISHING Australasian Plant Pathology, 2010, 39, 440–445 www.publish.csiro.au/journals/app Ó Australasian Plant Pathology Society 2010 10.1071/AP10098 0815-3191/10/050440