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The entomopathogenic hyphomycete Beauveria brongniartii is a promising candidate for biocontrol of economically important agricultural and forest pests. Assessment of genetic relatedness of this species appears to be essential to gain insight into the monitoring of such biocontrol products. Distinction of Beauveria spp. strains with different virulence to target organisms revealed to be a serious constraint in the development of successful biocontrol using these important species. Thus, there is a need to find ways to monitor these strains when applied to natural agents. We have used amplified fragment length polymorphism (AFLPs) markers to estimate genetic variations among fourteen isolates (ten B. brongniartii, two B. bassiana (BALSAMO) VUILLEMIN and two Nomuraea rileyi (FARLOW) SAMSON) obtained from different geographical origins and hosts with differing virulence to scarabs. Seven different AFLP primer combinations yielded a total of 229 AFLP fragments comprised between 30 (EcoRI-ACA/Tru1l-C) to 57 (EcoRI-AAG/Tru1l-CTT) AFLP markers with an average of 54 amplified fragments per primer combination. Fragment size varied between 50-541 base pairs (bp) among the ten B. brongniartii isolates analysed in this study achieving a good resolution between the isolates. The cluster analysis based on genetic distance values clustered all isolates at above 0.40 similarity and demonstrated that some B. brongniartii isolates from distinct geographical origins and various hosts showed a greater genetic variability.