Sarocladium and
Fusarium species are commonly identified as causal agents of rice sheath rot disease worldwide. However, limited knowledge exists about their genetic, pathogenic, and toxigenic diversity in sub-Saharan African (SSA) countries, where an increasing incidence of this disease has been observed. In this study, seventy fungal isolates were obtained from rice plants displaying disease symptoms in rice research programs and farmer fields in Mali, Nigeria, and Rwanda. Thus, an extensive comparative analysis was conducted to assess their genetic, pathogenic, and toxigenic diversity. The
Fusarium spp. were characterized using the translation elongation factor (
EF-1α) region, while a concatenation of Internal Transcribed Spacer (ITS) and Actin-encoding regions were used to resolve
Sarocladium species. Phylogenetic analysis revealed four
Fusarium species complexes. The dominant complex in Nigeria was the
Fusarium incarnatum-equiseti species complex (FIESC), comprising
F. hainanense,
F. sulawesiense,
F. pernambucatum, and
F. tanahbumbuense, while
F. incarnatum was found in Rwanda. The
Fusarium fujikuroi species complex (FFSC) was predominant in Rwanda and Mali, with species such as
F. andiyazi,
F. madaense, and
F. casha in Rwanda and
F. annulatum and
F. nygamai in Mali.
F. marum was found in Nigeria. Furthermore,
Fusarium oxysporum species complex (FOSC) members,
F. callistephi and
F. triseptatum, were found in Rwanda and Mali, respectively. Two isolates of
F. acasiae-mearnsii, belonging to the
Fusarium sambucinum species complex (FSAMSC), were obtained in Rwanda. Isolates of
Sarocladium, which were previously classified into three phylogenetic groups, were resolved into three species, which are
attenuatum,
oryzae, and
sparsum.
S. attenuatum was dominant in Rwanda, while
S. oryzae and
S. sparsum were found in Nigeria. Also, the susceptibility of FARO44, a rice cultivar released by Africa Rice Centre (AfricaRice), was tested against isolates from the four
Fusarium species complexes and the three
Sarocladium species. All isolates evaluated could induce typical sheath rot symptoms, albeit with varying disease development levels. In addition, liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to determine variation in the in vitro mycotoxins of the
Fusarium species. Regional differences were observed in the in vitro mycotoxins profiling. Out of the forty-six isolates tested, nineteen were able to produce one to four mycotoxins. Notably, very high zearalenone (ZEN) production was specific to the two
F. hainanense isolates from Ibadan, Nigeria, while
Fusarium nygamai isolates from Mali produced high amounts of fumonisins. To the best of our knowledge, it seems that this study is the first to elucidate the genetic, pathogenic, and toxigenic diversity of
Fusarium species associated with the rice sheath rot disease complex in selected countries in SSA.
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