A first Pedigree-Based Analysis (PBA) approach for the dissection of disease resistance traits in grapevine hybrids

To date, molecular markers are available for many economically important traits in grapevine (Vitis vinifera L.) as well as in other fruit crops. Unfortunately, lack of knowledge of the allelic variation of the related genes hampers their full exploitation in commercial breeding programs. These markers have usually been identified in one single cross. Consequently, only one or two favourable alleles of the related QTL are identified and exploitable for Marker-Assisted Breeding (MAB), whereas a breeding program may include several alleles. Selection for just these alleles means that many favourable genotypes are ignored, which decreases efficiency and leads to genetic erosion. Our novel employed approach, namely Pedigree Genotyping or Pedigree-Based Analysis (PBA), allows the identification and exploitation of most alleles present in an ongoing breeding program. This is achieved by including breeding material itself in QTL detection, thus covering multiple generations and linking many crosses through their common ancestors in the pedigree. The principle of Identity By Descent (IBD) is used to express the identity of a modern selection allele in terms of the founding cultivars alleles, which can be used as factors in statistical analyses. In this study we focus on the genetic characterization of numerous Vitis hybrids, donors of resistance to downy and/or powdery mildew, in order to identify selection signatures. In particular, 122 hybrids of European origin and 120 American hybrids, along with 38 related V. vinifera varieties, have been genotyped at about 190 SSR loci. These markers have been chosen based on their physical distance in order to have 10 SSRs well-scattered along each chromosome. Based on the SSR profiles, the historical pedigree records have been verified. Following the trueness-to-type validation for most of the studied hybrids, the IBD analysis has been performed, tracing the allelic flow through the successive generations. Here we report results about the identification of non-vinifera genomic intervals retained into the vinifera background and the anchoring of the discovered breeding signatures to the grapevine genome. In addition, we report on the PBA-based QTL results for segregating populations coming from pedigree-supported parental materials donors of resistance to downy mildew in North-Eastern Italy