Chromosomal Deletion in Isolates of Phytophthora infestans Correlates with Virulence on R3, R10, and R11 Potato Lines

Abstract

In Phytophthora infestans, a cluster of three dominant avirulence genes is located on the distal part of linkage group VIII. In a mapping population from a cross between two Dutch field isolates, probe M5.1, derived from an amplified fragment length polymorphism (AFLP) marker linked to the Avr3-Avr10-Avr11 cluster, hybridized only to DNA from the parent and F1 progeny that is avirulent on potato lines carrying the R3, R10, and R11 resistance gene. In the virulent parent and the virulent progeny, no M5.1 homologue was detected, demonstrating a deletion on that part of linkage group VIII. P. infestans is diploid, so the avirulent strains must be hemizygous for the region concerned. A similar situation was found in another mapping population from two Mexican strains. The deletion was also found to occur in many field isolates. In a large set of unique isolates collected in The Netherlands from 1980 to 1991, 37% had no M5.1 homologue and the deletion correlated strongly with gain of virulence on potato lines carrying R3, R10, and R11. Also, in some old isolates that belong to a single clonal lineage (US-1) and are thus highly homogenous, deletions at the M5.1 locus were detected, indicating that this region is unstable.

Molecular Genetics of Pathogenic Oomycetes

“…The map was based on 22 RFLP markers, 228 randomly amplified polymorphic DNA (RAPD) markers, and 7 avirulence genes, and it covered 10 major and 12 minor linkage groups for a total of 830.5 cM. Recently, May et al (59) Several avirulence genes, involved in triggering genotypespecific resistance, have been mapped in the P. infestans and P. sojae maps, and their cloning is under progress (53,59,100,104,105,116). Highly representative bacterial artificial chromosome (BAC) libraries are also available and have facilitated the physical mapping of Phytophthora genomes (80,116).…”

An ancestral oomycete locus contains late blight avirulence gene Avr3a , encoding a protein that is recognized in the host cytoplasm

“…R3a has since been cloned and encodes a presumed cytoplasmic coiledcoil nucleotide binding site leucine-rich repeat protein (8). Although several P. infestans Avr loci have been genetically mapped (1,9), no Avr genes have yet been reported, mainly due to difficulties encountered with positional cloning, such as high levels of repetitive DNA and aberrant segregation at the target locus. Our knowledge of the molecular basis of race evolution in this pathogen is thus limited.…”

Amplification generates modular diversity at an avirulence locus in the pathogen Phytophthora

“…We have strong indications that a change in phenotype on R3b, R10, and R11 potato lines is associated with a genome rearrangement or chromosomal deletion at that locus (van der Lee et al 2001b). Avr3 has recently been renamed to Avr3b to indicate that this Avr gene elicits resistance on plants carrying R3b but not R3a (Huang et al 2004).…”

“…Previously we identified a locus in P. infestans that carries three closely linked dominant Avr genes, Avr3, Avr10, and Avr11 (van der Lee et al 2001a(van der Lee et al , 2004. We have strong indications that a change in phenotype on R3b, R10, and R11 potato lines is associated with a genome rearrangement or chromosomal deletion at that locus (van der Lee et al 2001b).…”

“…Field isolates are genetically highly variable, not only in Central America, the center of origin of P. infestans, but also in North America and Western Europe (Goodwin et al 1992(Goodwin et al , 1998Zwankhuizen et al 1998). Polyploidy, aneuploidy, and trisomy are found in field isolates (Tooley and Therrien 1987;Gu et al 1993;Carter et al 1999;van der Lee et al 2004), and chromosomal deletions and translocations related to virulence and mating behavior have been described (Judelson 1996;van der Lee et al 2001b). P. infestans has many transposon(-like) elements that are known to contribute to genome plasticity.…”