Genetic analysis of natural variation in Botrytis cinerea field isolates identifies a single gene with a major effect on pathogenicity and sporulation

Natural populations of Botrytis cinerea from vineyards of Castilla y León, Spain, are highly diverse both genetically and physiologically. Evaluation of aggressiveness in a representative sample of field isolates collected from different Vitis varieties made it posible to identify isolates displaying large differences in their ability to cause infection. In order to perform a genetic analysis of these differences, crosses between a highly aggressive isolate (448) and a non-pathogenic isolate (371) were performed. In the progeny, a 1:1 segregation was observed for the phenotype “ability to infect”. Remarkably, the “ability to infect” strictly cosegregated with the “capacity to sporulate”. Within the pathogenic progeny large differences in aggressiveness were found, suggesting a key role for a “major pathogenicity gene” essential for the expression of a number of pathogenicity factors which segregate in the progeny. In an attempt to identify the gene responsible, a strategy based on “bulk segregant analysis (BSA)” was designed. First, the sequence of the genomes of both parental strains was determined and a list of SNPs and of small indels was elaborated. Then, two pools of genomic DNA were prepared and sequenced: a first one (P1) from a group of isolates resembling the aggressive parental strain 448, and a second one (P2) from a group of non-aggressive isolates, like parental strain 371. Finally, the distribution in both pools of the polymorphisms found between isolates 448 and 371 was analysed searching for isolate 371 specific variants exclusively found in pool P2 but absent in pool P1 and for isolate 448 specific variants found in pool P1 but absent in pool P2. A candidate region for the major pathogenicity gene to be located in has been identified which is currently being characterized. This work was supported by grants AGL2012-39876-C02-01 and AGL2015-66131-C2-1-R (MINECO, Spain).