Comparison of RAPD and AFLP marker analysis as a means to study the genetic structure of Botrytis cinerea populations

To assess the genetic relationships of Botrytis cinerea populations in Almeria (Spain), 44 isolates of B. cinerea, collected from six commercial greenhouses (subpopulations), were analysed by Random Amplified Polymorphic DNA ( RAPD) and amplified-fragment length polymorphism (AFLP). Polymorphisms were more frequently detected per primer with AFLP than with RAPD ( 16 compared to 4). However, RAPD detected polymorphisms more frequently per loci than AFLP (56% compared to 32%). The analysis of population structure revealed that the genetic diversity within subpopulations (H-S) accounted for 96% of the total genetic diversity (H-T), while genetic diversity among subpopulations represented only 4% of the total diversity, independently of whether they were analysed with RAPD or AFLP markers. The relative magnitude of gene differentiation between subpopulations (G(ST)) and the estimate of the number of migrants per generation (N-m) averaged similar values when estimated with RAPD or AFLP markers (0.039 and 0.036, or 12.32 and 13.39, respectively). The results obtained in dendrograms were in accordance with the gene diversity analysis. However, the diversity of B. cinerea was higher when analysed by RAPD than with AFLP. In these cases, the isolates could not be grouped by greenhouse or fungicide resistance (except those sensitive to carbendazim and resistant to procymidone). Both the RAPD and AFLP technologies are suitable for studies of genetic structure of B. cinerea populations, although RAPD generated more polymorphisms per loci than AFLP, and provided a better explanation of the genetic relationships between isolates.