Pathogenic and genetic diversity of Botrytis fabae Sand. isolates from faba bean fields in different agro-ecological zones of Northern Ethiopia

The identity and genetic diversity of the causal agent of chocolate spot (Botrytis cinerea or Botrytis fabae) in Ethiopia is still poorly defined and this hinders efforts aimed at integrated management of the disease, especially breeding for resistance. Chocolate spot disease epidemics are more severe in the moist, humid western districts of northern Ethiopia (NW) compared to the sub-humid eastern districts (NE) but knowledge of pathogen identity and genetic diversity is needed to facilitate epidemiological studies. Of a total of 120 Botrytis isolates examined, all were found to be B. fabae and none fitted the morphological description of B.cinerea. In pathogenicity tests, representative isolates caused typical chocolate spot symptoms and were re-isolated from infected leaves, indicating that B. fabae is the causal agent of chocolate spot in Ethiopia. Marked differences were found among the isolates in colony morphology and growth rate but the morphology of isolates was unrelated to their pathogenicity. A preliminary virulence (=severity of disease) test with 76 isolates revealed differences in virulence of the B. fabae isolates, with NE isolates being generally more virulent than the NW isolates. Genetic analysis based on 129 amplified fragment length polymorphism (AFLP) markers showed that genetic differentiation among pathogen populations was low (GST = 0.02 to 0.03; θ = 0.02, p = 0.05), indicating limited geographic delimitation and significant gene flow. Total gene diversity (HT = 0.22) was mostly attributable to diversity within populations (HS = 0.21). Thus, only 4.5% of the total variability was attributable to frequency differences between agroecological zones. Genotypic diversity (GD), defined as the probability that two individuals taken at random had different genotypes, was high for populations from NW and NE, and from the moist and subhumid agro-ecological zones (GD = 0.99). However, cluster analysis showed high similarity among many isolates (>75% similarity index), suggesting that such isolates have a familial structure or are clonally related. The phenetic tree revealed groups with low bootstrap values that did not reflect the grouping of isolates based on virulence or agro-ecological zone. The implications of these findings for chocolate spot resistance breeding in Ethiopia are discussed.