ORIGINAL ARTICLE Difficulties in identifying Xanthomonas citri subsp. citri A pathotypes Yasser E. Ibrahim 1,2 & Mahmoud H. El Komy 1,2 & Mahmoud A. Amer 1,2 & Arya Widyawan 1 & Mohammed A. Al-Saleh 1 & Amgad A. Saleh 1,3 Received: 8 November 2018 /Accepted: 15 March 2019 # Società Italiana di Patologia Vegetale (S.I.Pa.V.) 2019 Abstract A total of 350 citrus canker bacterial isolates, representing different citrus growing regions in Saudi Arabia, were identified as Xanthomonas citri subsp. citri (Xcc). DNA alignment of the 16S-rDNA of the three citrus canker organisms (Xcc, pathotypes A, X. fuscans pv. aurantifolii, pathotype B, and C) showed that they can be distinguished by using two SNPs. All the 350 Saudi Xcc strains belonged to the 16-rDNA haplotype of Xcc-A pathotypes. Pathogenicity in leaf assays using differential citrus cultivars, grapefruit (Citrus paradisi) and Mexican lime (C. aurantifolia), divided the Saudi Arabian bacterial isolates into two groups. The first group produced typical symptoms of Xcc, including erumpent canker lesions with water-soaked margins on all hosts. However, the second group caused atypical symptoms on grapefruit leaves. REP-PCR analysis grouped Xcc strains into three clusters that were not correlated with host, pathogenicity or geographic origin. However, the Baha Xcc population had the highest genetic variability, suggesting that this region may be responsible for disseminating Xcc strains to Saudi southern citrus-growing regions through movement of contaminated planting materials. Although we were able to definitely identify the Saudi citrus canker bacteria as Xcc-A pathotypes, its pathotypes still needs more investigation to be recognized. To our knowledge, this also is the first report of occurrence of citrus canker of sweet orange in the Abha region of Saudi Arabia. Keywords Pathogenicity test . 16S-rDNA . Rep-PCR . Citrus canker . Pathotypes Introduction Citrus (Citrus spp.) has been cultivated as a commercial crop in Saudi Arabia since 1983. The total area of citrus plantation in Saudi Arabia reaches 14,884 ha, yielding approximately 150,000 tons per year (Ministry of Agriculture, Central Administration of Economic Studies and Statistics, 2011). Citrus bacterial canker caused by Xanthomonas spp. is one of the serious diseases affecting citrus production, not only in Saudi Arabia, but also worldwide (Ibrahim and Bayaa 1989; Gottwald et al. 2002). There are distinct forms of citrus bacterial canker within the genus Xanthomonas. The most widespread and severe one is the Asiatic form (Canker A) caused by X. citri subsp. citri (Xcc) (Schubert et al. 2001). The cancrosis B form caused by X. fuscans pv. aurantifolii, is a disease of lemon (C. limon) in Argentina, Paraguay, and Uruguay. Mexican lime (C. aurantifolia), sour orange (C. aurantium), and pummelo (C. grandis) are also suscepti- ble to cancrosis B. The cancrosis C form caused by X. f. pv. aurantifolii, was only reported in São Paulo state, Brazil, on Mexican lime and sour orange (Das 2003). Because symp- toms are generally similar, discrimination of the pathotypes causing these different disease forms is a challenge. The mixture of different Xanthomonas pathotypes in the same field can also be a challenge for effective control of citrus canker due to the development of new genetic recombinants through horizontal genetic exchange. Citrus * Yasser E. Ibrahim yasereid@ksu.edu.sa 1 Plant Protection Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, 11451 Riyadh, Kingdom of Saudi Arabia 2 Agriculture Research Center, Plant Pathology Research Institute, Giza, Egypt 3 Agriculture Research Center, Agricultural Genetic Engineering Research Institute, Giza, Egypt Journal of Plant Pathology https://doi.org/10.1007/s42161-019-00294-7