23Caffier, V., Patocchi, A., Expert, P., Bellanger, Durel, M., 24 Broggini, G.A.L, Groenwold, R., and Bus V.G.M. 2014. Virulence characterization of 25 Venturia inaequalis reference isolates on the differential set of Malus hosts. Plant Dis. 26XX:XX-XX.27 28 A set of differential hosts has recently been identified for 17 apple scab resistance genes in an 29 updated system for defining gene-for-gene (GfG) relationships in the Venturia inaequalis- 30 Malus pathosystem. However, a set of reference isolates characterized for their 31 complementary avirulence alleles is not yet available. In this paper, we report on improving 32 the set of differential hosts for h(7) and propose the apple genotype LPG3-29 as carrying the 33 single major resistance gene Rvi7. We characterized a reference set of 23 V. inaequalis 34 isolates on 14 differential apple hosts carrying major resistance genes under controlled 35 conditions. We identified isolates that were virulent on at least one of the following defined 36 Sixteen different virulence patterns were observed. In general, the isolates carried one to 38 three virulences, but some of them were more complex, with up to six virulences. This set of 39 well-characterized isolates will be helpful for the identification of additional apple scab 40 resistance genes in apple germplasm and the characterization of new GfG relationships to 41 help improve our understanding of the host-pathogen interactions in the V. inaequalis-Malus 42 pathosystem.43 44 45 3 Plant DiseaseDurable pest and disease resistance is a major breeding objective for most crops, but 46 achieving it has proven to be a challenge for breeders in the absence of truly non-race-47 specific resistances. Many genes involved in effector-triggered immunity (20) code for highly 48 polymorphic proteins containing nucleotide binding (NB) and leucine-rich repeat (LRR) 49 domains that instigate a resistance reaction in the host following recognition of the 50 complementary pathogen effector protein(s) in this specific gene-for-gene (GfG) relationship 51 (13). However, the high evolutionary potential of the pathogen effector arsenal negatively 52 affects the durability of resistance genes. To counteract, or at least delay the breakdown of 53 resistance genes by virulent races of the pathogen, breeders search for new resistance genes 54 (major genes and quantitative trait loci (QTLs)) that are effective against the already known 55 virulent races (23) and pyramid them (including 'spent' ones) to improve their durability as 56 well as increase the efficacy of the combined genes. This is based on the principle that for a 57 multiple virulent strain to develop, it will have to acquire these virulences simultaneously 58 (11). The effectiveness of this strategy relies on the availability of a set of differential hosts 59 and reference isolates to understand the genetics of the arsenal of both effectors in the 60 pathogen and resistances in the host, and their GfG relationships (34). 61 Apple scab, caused by Venturia inaequali...
The Venturia genus comprises fungal species that are pathogens on Rosaceae host plants, including V. inaequalis and V. asperata on apple, V. aucupariae on sorbus and V. pirina on pear. Although the genetic structure of V. inaequalis populations has been investigated in detail, genomic features underlying these subdivisions remain poorly understood. Here, we report whole genome sequencing of 87 Venturia strains that represent each species and each population within V. inaequalis. We present a PacBio genome assembly for the V. inaequalis EU-B04 reference isolate. The size of selected genomes was determined by flow cytometry, and varied from 45 to 93 Mb. Genome assemblies of V. inaequalis and V. aucupariae contain a high content of transposable elements (TEs), most of which belong to the Gypsy or Copia LTR superfamilies and have been inactivated by Repeat-Induced Point mutations. The reference assembly of V. inaequalis presents a mosaic structure of GC-equilibrated regions that mainly contain predicted genes and AT-rich regions, mainly composed of TEs. Six pairs of strains were identified as clones. Single-Nucleotide Polymorphism (SNP) analysis between these clones revealed a high number of SNPs that are mostly located in AT-rich regions due to misalignments and allowed determining a false discovery rate. The availability of these genome sequences is expected to stimulate genetics and population genomics research of Venturia pathogens. Especially, it will help understanding the evolutionary history of Venturia species that are pathogenic on different hosts, a history that has probably been substantially influenced by TEs.3
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