Downy mildew resistance QTL identification in multiple inter-specific populations of grapevine: a Pedigree-Based Analysis (PBA) approach

Downy mildew (Plasmopara viticola, DM) resistance is a desirable trait for any new grapevine (Vitis spp.) cultivar grown in temperate-humid climate, as it directly impacts on grape yield and wine quality. Therefore, determining the genetic control of this trait in relevant breeding germplasm is a high priority. The objectives of this study were (i) to determine the number and positions of Quantitative Trait Loci (QTL) for DM resistance utilizing data from multiple families and their pedigreed ancestors simultaneously, and (ii) to estimate DM resistance QTL genotype probabilities and genomic breeding values for the plant materials. The grapevine material used was an up-to-five-generation pedigree consisting of 16 founders, 10 relatives, 17 parents and 548 progeny individuals from 12 full-sib families, which were phenotyped in replicates for DM resistance and genotyped with a mid-throughput approach. In particular, as regarding phenotyping the genetic material was screened based on 11 optimized parameters, taking into account different aspect of the disease. As concerning genotyping, 190 microsatellite markers well-scattered across the grapevine genome were analyzed based on multiplex assays. These data were analysed by adopting a Pedigree-Based Analysis (PBA) using the FlexQTLTM software. Among the identified QTL, some were previously discovered while other QTL were novel. The predicted QTL genotypes show that the identified QTL were segregating in a subset of the families. The progeny varied for breeding value, with some progeny having higher breeding values than their parents. These results pinpoint the strength of the PBA approach as QTL may be missed when focussing on single full sib families. Furthermore, the simultaneous search for multiple QTL also yields estimated genomic breeding values that can be used for selecting progeny with favourable resistance.