A wealth of previously unknown pedigree information has been generated for apple (Malus x domestica) through recent studies and an ongoing pedigree identification project using SNP array data. This information has been postulated to be useful in a number of ways for germplasm collections and breeding programs. For example, pedigree information is an important part of genetic characterization of material in germplasm collections. Germplasm collections often seek to preserve cultivars that currently lack commercial relevance but have regional or historical significance or are phenotypically interesting. Pedigree information is often limited on such material. With pedigree information, an accurate genetic structure of these collections can be conveyed to breeders who wish to incorporate novel germplasm into new cultivars. To illustrate ways in which this newly generated pedigree information can be used, we provide examples involving accessions from the germplasm collection Okowerk and the breeding association "apfel:gut e.V.", which focus in the development of apples for regional organic production. Both organizations are located in northern Germany. Despite focusing on regional apple cultivars and genetic diversity, many of their accessions and breeding lines are common, cosmopolitan, and foundational cultivars. However, the SNP-based analyses also reveal regionally specific founders, not true-to-type accessions, and genetically unique historical cultivars. This new information has benefitted these organizations by providing genetic characterization that was previously lacking, enabling them to better utilize these genetic resources. Additionally, this information will also be useful in the context of an ongoing larger scale apple pedigree reconstruction project.

With the advent of genetic maps for apple that carry common transferable markers, it is possible to investigate genomic relationships between genes present in different accessions. Co-dominant markers, such as microsatellites, are particularly useful for this purpose. In recent years, genetic markers have been developed for a number of resistance genes for apple scab (Venturia inaequalis). In this paper, we present the discovery of a new scab resistance gene (Vh8) that maps to linkage group 2 (LG2). We then bring together the findings from different research groups on other scab resistance genes that also map to LG2 in an attempt to delineate their arrangement. These other genes comprise major genes (Vh2, Vr, Vbj and Vr2), as well as several race specific quantitative trait loci (QTLs) from 'Discovery' and 'TN10-8'. Results indicate that Vh2 and Vr are probably identical, and that Vh2/Vr, Vh8, Vbj and at least one of the QTLs are closely linked to each other on the lower half of LG2. A putative map of this gene cluster is presented. The fourth major gene, Vr2, maps at a significant distance from this gene cluster at the top end of LG2. We discuss the consequences of resistance gene cluster arrangements on breeding strategies for durable resistance to apple scab and the use of marker-assisted selection.

Pyrus communis and Malus x domestica inoculated respectively with Venturia pirina and Venturia inaequalis give susceptible or resistance symptoms with large similarities. We addressed the question whether the two species of Venturia could exhibit reciprocal relationships with Pyrus communis and Malus x domestica. Trees of the apple cultivars: 'Gala' (susceptible to V inaequalis) and 'Discovery' (polygenic resistant) and the pear cultivars: 'Pierre Corneille' (susceptible to V pirina) and 'Navarra' (polygenic resistant) were inoculated in the glasshouse with very aggressive monoconidial strains of V inaequalis (EU-B04) and V pirina (Pca). Three days after inoculation, conidia germination, germ tube formation and appressoria differentiation were observed in all combinations. There were no clear differences in the percentage of germinated conidia and the appressoria index between host and non-host interaction. Six days after inoculation, a dense subcuticular network of stromatic strands was observed in the susceptible interaction. The resistant hosts were characterized by a reduced primary stroma and the epidermal cells were modified. In the case of the non-host relationships, much reduced primary stroma with few conidia were observed on the susceptible (to the compatible Venturia species) host only. The leaf reaction was limited to a very small number of cells. Fourteen days after inoculation, macroscopic symptoms of sporulation appeared on the susceptible cultivars. In non-host relationships, no additional modification of the microscopic aspects was observed. In conclusion, in this experiment, non-host interactions with V inaequalis and V. pirina were observed but were reduced to very limited microscopic aspects.

Fire blight, caused by the bacterial pathogen Erwinia amylovora, is one of the most destructive diseases of apple (Malus x domestica). In order to analyse the genetic determinism of resistance to fire blight in apple, a quantitative trait analysis (QTL) approach was used. A F1 progeny of 164 individuals derived from a cross between the apple cultivars `Prima? and `Fiesta? was inoculated in greenhouse conditions. Seven copies per genotype were used. The length of the necrosis observed on shoots was scored 7 and 14 days after inoculation. The MapQTL software was used for QTL analyses, using two previously built maps of the parents, and the symptoms scored on shoots. Digenic interactions between all pairwise combinations of genetic markers were tested using a two-way ANOVA model with the SAS software. QTL were detected at the same locations both 7 and 14 days after inoculation. Two weak effect QTL deriving from `Prima? were detected on linkage groups (LG) 3 and LG16. One strong effect QTL deriving from `Fiesta? was detected on LG7 that explained 46.6% of the phenotypic variation observed in the progeny. Two additional significant (P

The identification of Venturia inaequalis races able to overcome the well-known and widely used Vf-scab resistance gene has instigated the search and characterisation of new sources of resistance in germplasm collections. Various new sources of scab resistance in Italian germplasm were tested to determine their inheritance as part of the EU-D.A.R.E. project. The cultivar 'Durello di Forli' showed a very low scab susceptibility to different Venturia inaequalis inocula under various test conditions. This paper is a report on the preliminary characterisation of this new source of scab resistance identified by a race 6 strain of Venturia inaequalis.

A breeding program for fire blight resistance in pear was initiated 23 years ago at INRA Angers-Beaucouze by Thibault (1990). Numerous crosses have been made using resistant parental cultivars such as 'Harrow Sweet', US309, or 'Michigan 437' and high fruit quality parental cultivars such as 'William's' or 'Pierre Corneille'. The parents were crossed according to a very wide crossing design similar to an incomplete diallel design. Some of the parents were also related to each other resulting in an even more complex relationship network. To evaluate fire blight resistance, seedlings 20-30 cm tall were inoculated with a reference strain of Erwinia amylovora. Three weeks after inoculation, seedlings were scored for progression of the disease in the stem. Using the software REML VCE developed by Groeneveld (1996) for animal breeding, we estimated the narrow-sense heritability of fire blight resistance in this breeding population, using more than 17000 seedling data and 123 parental/ancestor pedigree information. The mathematical method used in this software is based on the 'individual genetic model' (maximum-likelihood procedure). The estimated heritability value was 0.40 (+/- 0.04). Best linear unbiased predictors of the additive genetic values of the parents and higher ancestors were also estimated. The applicability of the methodology and the results are discussed.

ABSTRACT The major scab resistance gene Vf, extensively used in apple breeding programs, was recently overcome by the new races 6 and 7 of the fungal pathogen Venturia inaequalis. New, more durable, scab resistance genes are needed in apple breeding programs. F(1) progeny derived from the cross between partially resistant apple cv. Discovery and apple hybrid 'TN10-8' were inoculated in the greenhouse with eight isolates of V. inaequalis, including isolates able to overcome Vf. One major resistance gene, Vg, and seven quantitative trait loci (QTL) were identified for resistance to these isolates. Three QTL on linkage group (LG)12, LG13, and LG15 were clearly isolate-specific. Another QTL on LG5 was detected with two isolates. Three QTL on LG1, LG2, and LG17 were identified with most isolates tested, but not with every isolate. The QTL on LG2 displayed alleles conferring different specificities. This QTL co-localized with the major scab resistance genes Vr and Vh8, whereas the QTL on LG1 colocalized with Vf. These results contribute to a better understanding of the genetic basis of the V. inaequalis-Malus x domestica interaction.

Conservation of apple genetic resources in France is carried out by many amateur groups and various governmental and non-govern mental organizations. A recent survey listed about 20 000 apple accessions planted in 180 different sites. Passport data, morphological and agronomical descriptors have been collected for a part of this material. INRA in collaboration with partners involved in germplasm conservation started to collect the data and enter them in a national Database. However the data are not informative enough to assess the numerous cases of misidentification and synonyms. Molecular markers were investigated as a tool to solve these issues. 142 French local cultivars were screened with nine SSR markers. 139 alleles were detected which allowed the discrimination between 122 different cultivars by providing each of them with a single allelic profile. Seven pairs of cultivars were proved to be genetically identical: each of them can be considered as synonyms. Factorial and cluster analysis did not reveal any significant structure of the genetic variability within the sample of cultivars.

In the frame of the D.A.R.E. project, five mapping populations have been studied for partial scab resistance against several races of Venturia inaequalis. A main objective was to identify QTLs (quantitative traits loci) with broad spectrum of resistance towards a wide range of strains of the fungus. Genetic markers (mainly SSR and AFLP) were tested on each population and genetic maps were constructed for both parents of each population. Meanwhile, pathological tests with several isolates of different races of V inaequalis were performed. Four major genomic regions appear to be involved in scab resistance: they are located on linkage groups (LG) LG-1, LG-2, LG-11, and LG-17. Some other linkage groups carry either QTLs or major resistance genes that are isolate specific: a QTL on LG-5, Vd on LG-10, and Vg on LG-12. The QTL region located on LG-17 clearly exhibited the widest spectrum of resistance.

Scab, caused by the fungus Venturia inaequalis, is one of the most important diseases of apple (Malus x domestica). The major resistance gene, Vf, has been widely used in apple breeding programs, but two new races of the fungus (races 6 and 7) are able to overcome this gene. A mapped F1 progeny derived from a cross between the cultivars Prima and Fiesta has bee n inoculated with two monoconidial strains of race 6. These strains originated from sporulating leaves of 'Prima' and a descendant of 'Prima' that were grown in an orchard in northern Germany. 'Prima' carries the Vf resistance gene, whereas 'Fiesta' lacks Vf. A large variation in resistance and (or) susceptibility was observed among the individuals of the progeny. Several quantitative trait loci (QTLs) for resistance were identified that mapped on four genomic regions. One of them was located in the very close vicinity of the Vf resistance gene on linkage group LG-1 of the 'Prima' genetic map. This QTL is isolate specific because it was only detected with one of the two isolates. Two out of the three other genomic regions were identified with both isolates (LG-11 and LG-17). On LG-11, a QTL effect was detected in both parents. The genetic dissection of this QTL indicated a favourable intra-locus interaction between some parental alleles.

Resistance to pests and diseases is a highly desirable objective in fruit breeding but is a long-term endeavor. it requires appropriate tests for early screening and an analysis of host-parasite interactions for durability of resistance. Host resistance is considered durable when it remains effective for a long period despite an intensive exposure to the parasite. Durability has to be the key-point of any fruit breeding programme for resistance. Non-durable resistance is usually associated with a hypersensitive reaction (HR) and major gene resistance which often occur in multiple allelic series and/or complex loci. HR resistance or race-specific resistance is often rendered ineffective because the pathogen population shifts genetically to avoid the resistance gene. Resistance of a more durable nature against fungi and bacteria is often polygenic and based upon the additive or interaction effects of a few to several genes not promoting a hypersensitive reaction. The more complex the genetics of the resistance, the more difficult it is for the pathogen to evolve to a form that can overcome the resistance. Polygenic resistance is usually associated with a quantitative expression that is characterized by a continuous variation between susceptibility and resistance. To approach the number of genes involved in polygenic resistance (QTL) and the relative effect of each of these genes, they have to be mapped on the genome. Marker-assisted selection (MAS) gives the possibility to recombine QTL for resistance; major genes could be associated with QTL. The combining of resistance genes is desired to: acquire a higher level of resistance against a particular pathotype, obtain resistance against a broader range of pathotypes, and combine different mechanisms of resistance. The current situation of fruit crops-monocultivar orchards established for several years-enhances the selection pressure on the pathogen population and results in population shifts which could be dramatic. Guidelines have to be proposed to predict the evolutionary potential of pathogen populations based on analysis of their genetic structure; the most important parameters to consider are reproductive/mating systems and gene/genotype flow. Pathogens that have the greatest risk of breaking down resistance genes are those that possess a mixed reproduction system, with one sexual cycle per growing season and asexual reproduction during the epidemic phase, and a high potential for gene flow. Several examples of different strategies used by fruit breeders will be reported mainly on Coffea, Musa, Prunus and Malus. Fruit breeders can use the lessons learned from deploying resistance genes in annual crops and selecting resistance in forest trees and apply these to their strategies for fruit tree improvement.

Most of today's apple cultivars are susceptible to scab (Venturia inaequalis) and powdery-mildew (Podosphaera leucotricha). The use of large amounts of fungicides in orchard raises ecological problems, consumer's health concerns in addition to the economic cost. The D.A.R.E. project aims at developing knowledge, methodologies, plant and pathogen material to achieve durable genetic resistance towards these pathogens in the future. The resistance/susceptibility of European cultivars towards several V. inaequalis and P. leucotricha inocula was assessed. A large part of this plant material showed partial or complete resistance to numerous V. inaequalis inocula. The European collection of V. inaequalis strains was settled. A core-orchard including partial and complete scab resistant cultivars was planted in each participating country. This orchard network will enable partners to observe the possible appearance of new V. inaequalis races and to assess the plant resistance stability ill different environmental conditions. Monoconidial strains of P. leucotricha were isolated and are now tested on a range of apple cultivars to define whether physiological races exist or not. The genetic mapping of major genes and QTLs involved in fungi resistance is in progress. A gene pyramiding strategy was initiated by crossing genotypes carrying complete and partial resistance to mildew and scab. Consumer's preferences were tested with scab resistant cultivars.

The scab-resistance gene Vf derived from Malus floribunda 821, has been widely used in apple breeding programmes. This major gene is located on linkage group of the cultivar 'Prima' in the genetic map constructed by Maliepaard et al. (1998). Two new races of the fungus Venturia inaequalis(is able to overcome the resistance conferred by Vs have been identified (Parisi et al., 1993; Roberts and Crute, 1994). In the present study, the progeny from the cross 'Prima' x 'Fiesta' was inoculated with a monoconidial strain of race 6. This strain had already been shown to be able to break down the resistance of Vf but not the resistance of the progenitor M. floribunda 821 itself (Parisi and Lespinasse. 1996). Fourteen and 21 days after inoculation, plants were scored for resistance/susceptibility level. A QTL analysis was performed using the software MCQTL. A strong QTL (LOD 6 to 7) was found in the region of VS on linkage group the resistance allele was associated with the presence of the Vf allele. This QTL was able to explain between 17% and 20% of the variation in disease symptoms. The confidence interval of the QTL did not allow us to determine whether this partial resistance was located on the Vf gene itself or close to Vf but excluding it.

yGenetic parameters (narrow-sense heritabilities and genetic correlations) were estimated for major agronomical traits in apple from large unbalanced data sets, with the help of wide-pedigree information. The software REML VCE (Groeneveld 1996) took into account the complex pedigree of the French apple-breeding population, thanks to the restricted maximum likelihood procedure combined with the construction of the entire relationship matrix between hybrids planted in the field and their ancestors. Narrow-sense heritability estimates ranged from 0.34 to 0.68 for traits exhibiting a normal distribution. Heritability values around 0.35-0.40 were obtained for fruit characteristics (size, texture, flavour, juice content, attractiveness, russeting). Higher values of heritability were obtained for vigour, assessed by the circumference of the trunk (0.51), and powdery mildew resistance (0.68). Additive genetic correlations between traits were also estimated. showing a very high relationship between fruit-quality traits. Vigour and powdery mildew resistance were slightly correlated with the other traits. Utilization of the 'individual genetic model' for the estimation of genetic parameters and breeding values in apple is discussed.

Disease resistance is a major objective in apple breeding programmes, mainly for scab (caused by Venturia inaequalis) and powdery mildew (Podosphaera leucotricha). Recently, many new scab-resistant cultivars have shown susceptibility when inoculated by a new race of V. inaequalis, showing the vulnerability of monogenic resistance when confronted with pathogen dynamics. In this framework, the main European research teams involved in apple breeding, genetics and pathology have begun to coordinate their efforts in order to develop a large research programme on durable resistance. This project aims to characterise and analyse the genetic bases of the interaction between apple and its two main pathogens. The objectives include: genetic dissection of scab resistance; analysis of pathogen diversity in Europe; deployment of a European network of core orchards; evaluation of the efficiency of marker assisted selection; and propositions of new breeding strategies.

Les arguments émis contre l'application de la sélection assistée par marqueurs (SAM) chez les arbres forestiers, notamment les problèmes potentiels liés au manque de déséquilibre de liaison entre locus dans les populations panmictiques, sont reconsidérés en raison de la baisse des coûts et surtout de l'automatisation des techniques de marquage moléculaire issues de la technique RAPD (random amplified polymorphic DNA).La construction de cartes génétiques sa- turées pour les individus d'une population d'amélioration élite devrait permettre de contourner ce problème.Cette proposition est présentée et discutée.Les stratégies de cartographie génétique et de détection des facteurs génétiques contrôlant les caractères quantitatifs (QTL) s'appuyant sur des pedigrees couramment rencontrés dans les programmes d'amélioration forestiers (familles de demi-frères et de plein-frères) sont envisagées.Afin d'illustrer la faisabilité de la sélection assistée par marqueurs, des propositions sont faites pour les programmes de sélection du pin maritime et de l'eucalyptus.Les gains génétiques et le coût de la SAM sont évalués dans des cas concrets et comparés à d'autres stratégies permettant une efficacité de la sélection identique.arbre forestier / sélection intrafamille assistée par marqueurs / multiplication végétative / marqueurs moléculaires / QTL / Pinus pinaster / Eucalyptus Summary -Marker-assisted selection in forest tree breeding programs as illustrated by two examples: maritime pine and eucalyptus.The arguments raised against the feasibility of mar- ker-assisted selection (MAS) in forest trees, especially the expected absence of linkage disequilibrium between markers and quantitative trait loci (QTL) in large random mating populations, are reconsidered.A decrease in costs and automation of the random amplified polymorphic DNAs (RAPD) technique make it possible to construct single-tree maps for every individual of an elite breeding population: an extreme alternative to dealing with linkage equilibrium.Mapping strategies and QTL detection using existing pedigrees in forestry breeding programs (half-sib and full-sib progenies) are presented and discussed.The feasibility of MAS is illustrated for the maritime pine and eucalyptus breeding program.Genetic gains and costs associated with the use of molecular markers are evaluated and compared to other strategies that aim to obtain a similar selectionefficiency.forest trees / within-family marker-assisted selection / vegetative propagation / molecular markers / QTL / Pinus pinaster / Eucalyptus

In a full-sib progeny of a mating between heterozygous parents, the analysis of marker-trait associations using dominant RAPD (random amplified polymorphic DNA) markers allows the detection of specific quantitative trait loci (QTL) for each parent of the cross.Here we develop a method aimed at estimating the breeding value of such QTL alleles in the population, for the incorporation of marker-assisted selection in operational forest tree-breeding programs.The proposed methodology expands on the pseudo-testcross QTL mapping strategy which is based on the selection of single dose markers present in one parent and absent in the other.It specifically exploits the fact that one of the parents of the full-sib family is double null for the RAPD markers bracketing the QTL so that, by looking at its half-sib family, 'band present' allele frequencies of the two markers can be obtained at the population level.The half-sib family of the other parent, which is doubly heterozygous, is then used to estimate the average effect (ie, the additive effect) of the two QTL alleles.QTL / breeding value / full-sib / half-sib / pseudo-testcross Résumé -Détermination des effets moyens des allèles à un QTL spécifique détecté par la stratégie du pseudo-testcross.Dans une famille de pleins-frères issue du croise- ment entre deux individus hétérozygotes, l'analyse des associations entre des marqueurs moléculaires dominants (RAPD, polymorphisme de l'ADN amplifié au hasard) et des caractères quantitatifs permet de détecter des locus impliqués dans l'expression des varia- tions phénotypiques de caractères quantitatifs (QTL).Ces QTL sont spécifiques de chacun des parents du croisement.Nous développons ici un modèle permettant de déterminer la valeur générale des allèles au QTL au sein de la population, en vue d'une utilisation dans les programmes de sélection chez les arbres forestiers.La méthode proposée prolonge la localisation de QTL spécifiques par la stratégie du pseudo-testcross, basée sur la sélection de marqueurs à simple dose présents chez un parent et absents chez l'autre.Elle exploite le fait qu'un des deux parents de la famille de plein-frères est homozygote nul pour les deux marqueurs RAPD bordant le QTL.Ainsi, en observant l'une de ses descendances de demi-frères, il est possible d'estimer les fréquences dans la population des allèles codant pour la présence de bande RAPD.Une descendance de demi-frères issue de l'autre parent double hétérozygote aux marqueurs bordant le QTL est alors utilisée pour déterminer les effets moyens (additifs) des allèles au QTL.QTL / valeur additive / plein-frère / demi-frère / pseudo-testcross

Random Amplified Polymorphic DNA (RAPDs) were used for genetic mapping and QTL detection in an F2 selfed progeny of maritime pine. The seedlings were raised for two years in a greenhouse under accelerated growth conditions. Total height was measured at different maturation stages and corresponding QTLs were located in different genomic regions, providing an explanation for the absence of juvenile-mature correlation for height. Within each shoot cycle, QTL for traits related to the initiation of foliar primordia in the bud and the elongation of the stem were mapped in different chromosomes, suggesting that the activity of the apical and subapical meristems was controlled by separate genetic mechanisms.Rapid mapping rely on the use of arbitrary primers and PCR-based technique to amplify polymorphic DNA fragments. These markers are anonymous and may be physiologically irrelevant if one want to understand the biological meaning of the detected QTLs. As part of our mapping programme, we are currently developping a map based on protein markers reveal by 2-D PAGE. Such translated regions of the genome might be very useful for the characterization of QTLs.

Height and diameter of 257 twenty-year-old maritime pine (Pinus pinaster Ait.) trees, originating from a factorial mating design, were subdivided in annual height increments (AHI) and annual diameter increments (ADI). Cumulative and annual data of both traits were compared using two different genetic models. The two traits exhibited very different genetic expressions. For cumulative data, the heritability increased steadily with age for height and was very stable for diameter. For annual data, this evolution did not reveal any particular trend for AHI but appeared much more stable for ADI. Different effects seemed to be involved in the variation of annual increments: year and residual effects were 5 and 2.5 times more important for AHI than for ADI, respectively; in contrast, family and individual effects were 10 and 15 times more important for ADI than for AHI, respectively. Serial correlations calculated at the full-sib family mean level also showed different patterns: low values and rapid decrease of correlations for successive AHI, and high values and a linear decrease for successive ADI. As trees aged, the genetic expression of height growth appeared to be more unstable than for diameter growth. Interpretations about these expressions and their consequences for early selection are discussed.

A provenance trial of maritime pine comprising 25 provenances (table I) and located in the south-east of France was studied at 8, 9 and 13 years of age. The results show a high variability for growth and sensibility to the coccid Matsucoccus feytaudi at the regional level, but no differentiation for form traits (see table III, analysis 1). At the species range level, however, significant provenance differences appear for all characters (see table III, analyses 2 and 3). Atlantic provenances are the most vigorous and among the most resistant to the coccid (see figs 1 and 2). Corsican provenances show an intraracial variation for form and a great sensibility to the insect (see figs 1 and 2). The Moroccan origin appears to be completely resistant to the insect, while the south-eastern populations are intermediate for vigor and form but quite sensitive to the pest (see figs 1 and 2). These results raise the problem of the use of the local populations as reproductive material in the south-east In this respect, interracial hybridization may be an alternative method for genetic improvement of maritime pine.