Genetic diversity and incidence of cassava bacterial blight (CBB) caused by Xanthomonas phaseoli pv. manihotis in Burkina Faso

Cassava bacterial blight (CBB), caused by Xanthomonas phaseoli pv. manihotis (Xpm), poses a significant threat to cassava production in Burkina Faso. Prior to this study, the geographical distribution, incidence and origin of CBB introductions were poorly understood. In this investigation, we assessed the incidence of CBB in major cassava‐cropping regions and analysed the genetic diversity of 344 Xpm strains collected from 19 fields between 2015 and 2016, using a multilocus variable number of tandem repeat analysis (MLVA) scheme targeting 14 microsatellite markers. Our results reveal the presence of CBB in three out of four cropping regions, with incidences ranging from 0% to 100% at locality and variety scale. Burkina Faso's Xpm strains exhibited high genetic diversity at multiple levels, including country scale (He = 0.6), cropping region (0.43 to 0.57), locality (0.25 to 0.50) and field (0.25 to 0.52). Pairwise comparisons among populations from different cropping areas indicated a strong genetic differentiation. The categorical minimum spanning tree reveals that the Cascades region has the higher diversity indices and consequently could be the origin site of dispersion of Xpm in the other cropping regions of cassava. Human activities play a major role in the dissemination of Xpm through cassava cuttings. The importance of the sanitary state of cuttings must be emphasized in order to avoid CBB and ensure good cassava production.