Proof of concept of Bayesian integrated QTL analyses across pedigree-related families from breeding programs of an outbreeding species. Results include QTL confidence intervals, individuals' genotype probabilities and genomic breeding values. Bayesian QTL linkage mapping approaches offer the flexibility to study multiple full sib families with known pedigrees simultaneously. Such a joint analysis increases the probability of detecting these quantitative trait loci (QTL) and provide insight of the magnitude of QTL across different genetic backgrounds. Here, we present an improved Bayesian multi-QTL pedigree-based approach on an outcrossing species using progenies with different (complex) genetic relationships. Different modeling assumptions were studied in the QTL analyses, i.e., the a priori expected number of QTL varied and polygenic effects were considered. The inferences include number of QTL, additive QTL effect sizes and supporting credible intervals, posterior probabilities of QTL genotypes for all individuals in the dataset, and QTL-based as well as genome-wide breeding values. All these features have been implemented in the FlexQTL(™) software. We analyzed fruit firmness in a large apple dataset that comprised 1,347 individuals forming 27 full sib families and their known ancestral pedigrees, with genotypes for 87 SSR markers on 17 chromosomes. We report strong or positive evidence for 14 QTL for fruit firmness on eight chromosomes, validating our approach as several of these QTL were reported previously, though dispersed over a series of studies based on single mapping populations. Interpretation of linked QTL was possible via individuals' QTL genotypes. The correlation between the genomic breeding values and phenotypes was on average 90 %, but varied with the number of detected QTL in a family. The detailed posterior knowledge on QTL of potential parents is critical for the efficiency of marker-assisted breeding.

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To quantify the magnitude and the spatial spread of grapevine downy mildew secondary sporangia, 4685 Plasmopara viticola single lesion samples were collected from 18 plots spread across central Europe. Disease symptoms were collected on two to 22 sampling dates per plot between 2000 and 2002. Four multiallelic microsatellite markers were used for genotypic identification of pathogen samples. Genetic analysis showed more than 2300 site-specific P. viticola genotypes, indicating that populations are genetically rich demographic units. Approximately 70% of the genotypes were sampled once and 14% were sampled twice throughout the various epidemics. In the 18 populations only seven genotypes (0.3%) were identified more than 50 times. Three genotypes particularly successful in causing disease through secondary cycles showed mainly a clustered distribution. The distance of sporangial migration per secondary cycle was less than 20 m and their plot colonization rate was calculated at around 1-2 m 2 day -1 . Downy mildew epidemics of grapevine are therefore the result of the interaction of a multitude of genotypes, each causing limited (or a few) lesions, and of a dominant genotype able to spread stepwise at plot-scale. These findings contrast with current theories about grapevine downy mildew epidemiology, which postulate that there is massive vineyard colonization by one genotype and long-distance migration of sporangia.

SUMMARY To examine the within- and among-population genetic structure of Plamopara viticola oosporic populations in Europe, 8991 lesions from 32 vineyard plots were collected and analysed. Four multi-allelic microsatellite markers were used to genotype the pathogen. All populations had high levels of gene and genotypic diversity. Most populations were in Hardy-Weinberg equilibrium and thus randomly mating. Among P. viticola populations, significant low to moderate genetic differentiation was observed, even between geographically close populations. This genetic differentiation was also evident in the neighbour-joining phylogenetic genetic distance tree, showing clear substructure and distinguishing mainly five clusters based on geographical origin. Significant isolation by distance was found in central European P. viticola populations, suggesting a step-wise migration model. No significant isolation by distance was found within Greek populations, most probably owing to natural geographical barriers such as the sea and mountains, as well as the frequent population bottlenecks occurring in these populations, preventing natural migration among populations. The high variability of P. viticola provides explanation for its successful infestation of the heterogeneous European vineyards in the last 125 years after its introduction.