The diversity and genetic differentiation of populations of Fusarium species associated with sorghum fields, both endophytes obtained from sorghum performing and non performing plants and isolates obtained from two sampling periods were investigated. Fusarium specific Internal Transcribed Spacer 2 (FITS2) primers set were used to assess genetic variability of 32 isolates from susceptible Fusarium spp. endophytes from Sorghum tissues. Fusarium thapsinum (Gibberella thapsina) with 68.75% of the isolates constituted the majority of Fusarium spp. isolated in performing plants. Gibberella thapsina species identified are described as non-pathogenic and associated to performing plant of sorghum. Previously, some species of Fusarium thapsinum have been recognized as pathogenic and responsible for yield losses in several cereal crops including Sorghum bicolor produced in Burkina Faso. The other Fusarium spp. identified in this study including Fusarium subglutinans, Fusarium chlamydosporum, Gibberella intermedia, Fusarium dlaminii, Fusarium oxysporum, Fusarium proliferatum, and Fusarium spp. An additional unknown fungi species were also identified. A diverse population of 10 sequence types was found, although 8 sequence types represented nearly two-thirds of the isolates studied. The sequence types were placed in different phylogenetic clades within Fusarium spp., and endophytic isolates were not monophyletic. Phylogenetic analysis from Neighbor-Joining/UnWeighted Neighbor-Joining showed a high genetic relationship among these 32 isolates of Fusarium spp. and high variation in FITS sequence of them. The use of specific phylomarker of the genus Fusarium allowed to identify the endophytic species of this genus and to establish the phylogenetic relationships between the endophytic species of Fusarium. The phylogenetic analysis revealed three groups of the fungi. However, no relationship between these groups and the geographical origins of these fungi has been established.
Key words: Fusarium thapsinum, endophyte, FITS2 marker, sorghum.
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