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Background: Brown trout Salmo trutta have been described in terms of five major mtDNA lineages, four of which correspond to major ocean basins, and one, according to some authors, to a distinct taxon, marbled trout Salmo marmoratus. The Atlantic and Danubian lineages of brown trout meet in a poorly documented contact zone in Central Europe. The natural versus human mediated origin of the Atlantic lineage in the upper Danube is a question of both theoretical and practical importance with respect to conservation management. We provide a comprehensive population genetic analysis of brown trout in the region with the aim of evaluating the geographic distribution and genetic integrity of these two lineages in and around their contact zone., Results: Genetic screening of 114 populations of brown trout across the Danube/Rhine/Elbe catchments revealed a counter-intuitive phylogeographic structure with near fixation of the Atlantic lineage in the sampled portions of the Bavarian Danube. Along the Austrian Danube, phylogeographic informative markers revealed increasing percentages of Danube-specific alleles with downstream distance. Pure Danube lineage populations were restricted to peri-alpine isolates within previously glaciated regions. Both empirical data and simulated hybrid comparisons support that trout in non-glaciated regions north and northeast of the Alps have an admixed origin largely based on natural colonization. In contrast, the presence of Atlantic basin alleles south and southeast of the Alps stems from hatchery introductions and subsequent introgression. Despite extensive stocking of the Atlantic lineage, little evidence of first generation stocked fish or F1 hybrids were found implying that admixture has been established over time., Conclusions: A purely phylogeographic paradigm fails to describe the distribution of genetic lineages of Salmo in Central Europe. The distribution pattern of the Atlantic and Danube lineages is extremely difficult to explain without invoking very strong biological mechanisms.The peri-alpine distribution of relict populations of pure Danubian lineage brown trout implies that they colonized headwater river courses post-glacially ahead of the expansion of the Atlantic lineage. The recognition of natural as opposed to anthropogenic introgression of the Atlantic lineage into Danubian gene pools is of fundamental importance to management strategies.

Strawberry (Fragaria sp.) stands as an interesting model for studying flowering behaviour and its relationship with asexual plant reproduction in polycarpic perennial plants. Strawberry produces both inflorescences and stolons (also called runners), which are lateral stems growing at the soil surface and producing new clone plants. In this study, the flowering and runnering behaviour of two cultivated octoploid strawberry (Fragaria × ananassa Duch., 2n = 8× = 56) genotypes, a seasonal flowering genotype CF1116 and a perpetual flowering genotype Capitola, were studied along the growing season. The genetic bases of the perpetual flowering and runnering traits were investigated further using a pseudo full-sibling F1 population issued from a cross between these two genotypes. The results showed that a single major quantitative trait locus (QTL) named FaPFRU controlled both traits in the cultivated octoploid strawberry. This locus was not orthologous to the loci affecting perpetual flowering (SFL) and runnering (R) in Fragaria vesca, therefore suggesting different genetic control of perpetual flowering and runnering in the diploid and octoploid Fragaria spp. Furthermore, the FaPFRU QTL displayed opposite effects on flowering (positive effect) and on runnering (negative effect), indicating that both traits share common physiological control. These results suggest that this locus plays a major role in strawberry plant fitness by controlling the balance between sexual and asexual plant reproduction.

Fruit quality traits are major breeding targets in the Rosaceae. Several of the major Rosaceae species are current or ancient polyploids. To dissect the inheritance of fruit quality traits in polyploid fleshy fruit species, we used a cultivated strawberry segregating population comprising a 213 full-sibling F1 progeny from a cross between the variety 'Capitola' and the genotype 'CF1116'. We previously developed the most comprehensive strawberry linkage map, which displays seven homoeology groups (HG), including each four homoeology linkage groups (Genetics 179:2045-2060, 2008). The map was used to identify quantitative trait loci (QTL) for 19 fruit traits related to fruit development, texture, colour, anthocyanin, sugar and organic acid contents. Analyses were carried out over two or three successive years on field-grown plants. QTL were detected for all the analysed traits. Because strawberry is an octopolyploid species, QTL controlling a given trait and located at orthologous positions on different homoeologous linkage groups within one HG are considered as homoeo-QTL. We found that, for various traits, about one-fourth of QTL were putative homoeo-QTL and were localised on two linkage groups. Several homoeo-QTL could be detected the same year, suggesting that several copies of the gene underlying the QTL are functional. The detection of some other homoeo-QTL was year-dependent. Therefore, changes in allelic expression could take place in response to environmental changes. We believe that, in strawberry as in other polyploid fruit species, the mechanisms unravelled in the present study may play a crucial role in the variations of fruit quality.

Macrosynteny and colinearity between Fragaria (strawberry) species showing extreme levels of ploidy have been studied through comparative genetic mapping between the octoploid cultivated strawberry (F. xananassa) and its diploid relatives. A comprehensive map of the octoploid strawberry, in which almost all linkage groups are ranged into the seven expected homoeologous groups was obtained, thus providing the first reference map for the octoploid Fragaria. High levels of conserved macrosynteny and colinearity were observed between homo(eo)logous linkage groups and between the octoploid homoeologous groups and their corresponding diploid linkage groups. These results reveal that the polyploidization events that took place along the evolution of the Fragaria genus and the more recent juxtaposition of two octoploid strawberry genomes in the cultivated strawberry did not trigger any major chromosomal rearrangements in genomes involved in F. xananassa. They further suggest the existence of a close relationship between the diploid Fragaria genomes. In addition, despite the possible existence of residual levels of polysomic segregation suggested by the observation of large linkage groups in coupling phase only, the prevalence of linkage groups in coupling/repulsion phase clearly demonstrates that the meiotic behavior is mainly disomic in the cultivated strawberry.

Bulked segregant analysis combined with AFLPs was used to identify molecular markers linked to the Rca 2 gene conferring resistance to Colletotrichum acutatum pathogenicity group 2 which causes anthracnose in the octoploid strawberry Fragaria x ananassa. DNA bulks originating from a cross between the resistant cultivar 'Capitola' and the susceptible cultivar 'Pajaro' were screened with 110 EcoRI/M se IAFLP combinations. Four AFLP markers were found linked in coupling phase to Rca 2 with recombination percentages between 0% and 17.7%. Among the four markers linked to the resistance gene, two were converted into SCAR markers (STS-Rca 2417 and STS-Rca 2240) and screened in a large segregating population including 179 genotypes. The Rca 2 resistance gene was estimated to be 0.6 cM from STS-Rca 2417 and 2.8 cM from STS-Rca 2240. The presence/absence of the two SCAR markers was further studied in 43 cultivars of F. x ananassa, including 14 susceptible, 28 resistant, and one intermediate genotype. Results showed that 81.4% and 62.8% of the resistant/susceptible genotypes were correctly predicted by using STS-Rca 2417 and STS-Rca 2240, respectively. The 14 susceptible genotypes showed no amplification for either SCARs. These developed SCARs constitute new tools for indirect selection criteria of anthracnose resistance genotypes in strawberry breeding programs.

ABSTRACT Anthracnose, caused by Colletotrichum acutatum, is a major disease of the octoploid cultivated strawberry, Fragaria x ananassa The inheritance of high and intermediate level plant resistances to C. acutatum, pathogenicity group 2, was investigated in an 8 x 8 factorial design. A single dominant gene (Rca2) controlled the high-level resistance, although minor genes may also contribute to resistance in cultivars such as Belrubi. The intermediate level of resistance was quantitative and controlled by minor genes. Analysis of 26 genotypes and cultivars from Fragaria spp. showed that the dominant gene was not rare in the germ plasm of F. x ananassa and that anthracnose resistance was also present in other species of Fragaria. These findings have important implications for anthracnose resistance breeding.

Metabolic profiling by 1-dimensional (1-D) 1 H-nuclear magnetic resonance (NMR) was tested for absolute quantification of soluble sugars, organic acids, amino acids and some secondary metabolites in fruit, roots and leaves. The metabolite responsible for each peak of the 1 H-NMR spectra was identified from spectra of pure compounds. Peak identity was confirmed by the addition of a small amount of commercially-available pure substance. 1 H-NMR spectra acquisition was automated. 1 H-NMR absolute quantification was performed with a synthesised electronic reference signal and validated by comparison with enzymatic or HPLC analyses; the correlation coefficients between 1 H-NMR data and enzymatic or HPLC data were highly significant. Depending on the species and tissues, 14-17 metabolites could be quantified with 15-25 min acquisition time. The detection limit was approximately 1-9 µg in the NMR tube, depending on the compound. Quantitative data were used for (1) a genetic study of strawberry fruit quality, (2) a functional study of tomato transformants overexpressing hexokinase and (3) a study of Arabidopsis phosphoenolpyruvate carboxylase transformants with several lines showing decreased activity of the enzyme. Biochemical phenotyping of the fruits of a strawberry offspring allowed the detection of quantitative trait loci (QTL) controlling fruit quality. Comparison of the roots of wild types and hexokinase tomato transformants using principal component analysis of metabolic profiles revealed that environmental factors, i.e. culture conditions, can significantly modify the metabolic status of plants and thus hide or emphasise the expression of a given genetic background. The decrease in phosphoenolpyruvate carboxylase activity (up to 75%) in Arabidopsis transformants impacted on the metabolic profiles without compromising plant growth, thus supporting the idea that the enzyme has a low influence on the carbon flux through the anaplerotic pathway.

A two-way pseudo-testcross strategy, combined with Single Dose Restriction Fragment (SDRF) marker analysis, was used for genetic mapping in the octoploid cultivated strawberry Fragaria x ananassa (2n = 8 x = 56). Based on a 113 full-sib progeny from a cross between the variety Capitola and the clone CF1116, we generated two parental maps using Amplified Fragment Length Polymorphism (AFLP) markers. Ninety two percent of the markers (727 out of 789) showed ratios corresponding to simplex markers (the majority being SDRF markers), and 8% (62 out of 789) fitted a multiplex ratio. Linkage maps were first established using SDRF markers in coupling phase. The female map comprised 235 markers distributed among 43 co-segregation groups, giving a map size of 1,604 cM. On the male map, 280 markers were assigned to 43 co-segregation groups, yielding a map size of 1,496 cM. Once the co-segregation groups were established, their association was tested using repulsion-phase markers. In total, taking into account associations representing the same linkage groups, 30 linkage groups were detected on the female side and 28 on the male side. On the female map, 68.3% of the pairwise marker linkages were in coupling versus 31.7% in repulsion phase, and the corresponding figures on the male map were 72.2% and 27.8%, respectively. In addition, both groups linked only in the coupling phase and groups linked in the repulsion phase were characterized. The observations suggest that the meiotic behavior of the F. x ananassa genome is neither fully disomic nor fully polysomic, but rather mixed. The genome may not be as completely diploidized as previously assumed.

We have constructed nearly complete linkage maps of Pinus sylvestris (L.) using AFLP markers based on a two-way pseudo-testcross strategy in a full-sib family founded in an advanced breeding program. With 39 primer combinations, a total of 737 markers (320 from the mother and 417 from the father) segregated in a 1:1 ratio, corresponding to DNA polymorphism: heterozygous in one parent and null in the other. In the maternal parent, 188 framework markers were mapped in 12 linkage groups, equivalent to the Pinus haploid chromosome number, with a total coverage of 1,695.5 cM. In the paternal parent, 245 framework markers established a map with 15 linkage groups, spanning a genome length of 1,718.5 cM. The estimated total map length was L(F) = 1,681 cM for the female and L(M) = 1,645 cM for the male using a modified method-of-moment estimator. Combining these values with those estimated from the observed map lengths in both parents, we estimated the genome length in Scots pine to be between 1,600 and 2,100 cM. Our genome coverage was estimated to be more than 98% with a framework marker interval of 20 cM for both parents. Most of the female and male linkage groups were associated through the analysis of the intercross markers.