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Analysis of Xanthomonas oryzae pv. oryzicola Population in Mali and Burkina Faso Reveals a High Level of Genetic and Pathogenic Diversity

First, twelfth, fourteenth, and sixteenth authors: Institut de Recherche pour le Développement, UMR Résistance des Plantes aux Bioagresseurs, IRD-CIRAD-UM2, 911 Avenue Agropolis BP 64501, 34394 Montpellier Cedex 5, France; first and fifth authors: Institut de l'Environnement et de Recherches Agricoles (INERA), 01 B.P. 910 Bobo Dioulasso, Burkina Faso; second, third, and fifteenth authors: Plant Sciences Unit–Crop Protection, Institute for Agricultural and Fisheries Research (ILVO), Burg. van Gansberghelaan 96, 9820 Merelbeke, Belgium; fourth, seventh, and eleventh authors: University Bamako, FAST Laboratoire Biologie Moléculaire Appliquée (LBMA), Bamako, Mali; sixth author: Institut d'Economie Rural, Niono, Mali; eighth author: Université de La Réunion, UMR 53 Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), 15 avenue René Cassin, BP 7151, F-97715 Saint-Denis Cedex 9, Réunion, France; and ninth, tenth, thirteenth, and sixteenth authors: Bioagricultural Sciences, Colorado State University, Plant Sciences Bldg., Fort Collins 80523-1177.

Bacterial leaf streak (BLS) caused by Xanthomonas oryzae pv. oryzicola was first reported in Africa in the 1980s. Recently, a substantial reemergence of this disease was observed in West Africa. Samples were collected at various sites in five and three different rice-growing regions of Burkina Faso and Mali, respectively. Sixty-seven X. oryzae pv. oryzicola strains were isolated from cultivated and wild rice varieties and from weeds showing BLS symptoms. X. oryzae pv. oryzicola strains were evaluated for virulence on rice and showed high variation in lesion length on a susceptible cultivar. X. oryzae pv. oryzicola strains were further characterized by multilocus sequence analysis (MLSA) using six housekeeping genes. Inferred dendrograms clearly indicated different groups among X. oryzae pv. oryzicola strains. Restriction fragment length polymorphism analysis using the transcriptional activator like effector avrXa7 as probe resulted in the identification of 18 haplotypes. Polymerase chain reaction-based analyses of two conserved type III effector (T3E) genes (xopAJ and xopW) differentiated the strains into distinct groups, with xopAJ not detected in most African X. oryzae pv. oryzicola strains. XopAJ functionality was confirmed by leaf infiltration on ‘Kitaake’ rice Rxo1 lines. Sequence analysis of xopW revealed four groups among X. oryzae pv. oryzicola strains. Distribution of 43 T3E genes shows variation in a subset of X. oryzae pv. oryzicola strains. Together, our results show that African X. oryzae pv. oryzicola strains are diverse and rapidly evolving, with a group endemic to Africa and another one that may have evolved from an Asian strain.