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Many ornamental crops are polyploid or even exist at different ploidy levels. Polyploid QTL analysis tools have been developed in recent years, yet they are limited in the population types they accept. Biparental populations are nowadays being regarded as a limited tool for QTL discovery, as only a limited number of QTLs occurs in an experimental cross and their effects might not be stable across genetic backgrounds. Genome-Wide Association Studies include more genetic diversity but suffer from (hidden) genetic structure and low frequency of QTL alleles. Both factors influence QTL detection and effect estimation, decreasing the sensitivity of QTL analysis. Alternatively, multiparental populations (MPP) can be used, potentially combining multiple QTLs and QTL alleles with known population structure and balanced allele frequencies. Breeding populations of interconnected crosses also constitute a form of MPP and QTLs identified in them might be more applicable to commercial cultivars. To perform QTL analysis in polyploids, mixed models or Bayesian approaches that consider pedigree information are recommended. During the analysis, QTL effects are ideally estimated using Identity by Descent (IBD) alleles (genomic regions that originate from the same ancestor) which can be obtained through haplotype estimation. Although MPPs could thus be a powerful set-up to estimate polyploid haplotypes, a software gap was identified as no current polyploid haplotyping tools are able to utilize MPP pedigree information to obtain haplotypes across an MPP. In order to utilize MPPs to their full extent and expand polyploid QTL analyses to encompass typical breeding populations, new haplotyping tools must be developed.

European fruit tree canker, caused by Neonectria ditissima, is an important disease of pome fruit worldwide. Apple cultivars differ in their levels of susceptibility to N. ditissima. In order to design an effective plant resistance test, we examined the effectiveness of two resistance parameters: infection frequency and lesion growth. Both parameters were evaluated in parallel tests using 10 apple cultivars in three experimental years, applying seminatural infection of leaf scars (infection frequency) or inoculation of artificial wounds (lesion growth). We compared six parameters for lesion growth, of which a new parameter, lesion growth rate (LGR), appeared to be the best with respect to reproducibility and statistical significance. LGR is defined as the slope of the regression of lesion size versus time. The slope was estimated for each lesion, employing a common start date and a lesion-specific end date determined by the girdling of the lesion. The two parameters (infection frequency and LGR) were examined in separate experiments and in three successive years, and provided complementary information and resulted in reproducible conclusions on the relative resistance levels to N. ditissima of the tested cultivars. The presented methods can be used to develop strategies for the control of European fruit tree canker (e.g., in the breeding of new apple cultivars with high levels of resistance to N. ditissima).

Thanks to recent advances in high-throughput genotyping tools and software for genetic analyses, it is now possible to perform QTL mapping and genome-wide association analysis in tetraploid roses and to establish the effect of favorable SNP marker haplotype(s) (“plus-alleles”). The challenge is how to use these tools and technologies for rose breeding in a cost-effective way. At least four points need to be addressed: (1) which steps of the breeding process may benefit from marker information; (2) what is the value of the identified plus-alleles for the trait; (3) where in the breeding germplasm do these plus-alleles occur, and (4) how can plants carrying these plus-alleles be selected efficiently. Here we discuss for which purposes markers may be applied.

Black spot disease (Diplocarpon rosae) is the most important leaf disease of garden roses in warm humid areas. Although partial resistance to black spot has been shown to be moderately heritable, the responsible quantitative trait loci (QTL) remain unidentified. Because of the interspecific nature and high heterozygosity in commercial roses, as well as the relatively small research input compared to row crops, the genomic resources available for rose are limited. To effectively identify markers associated with QTL controlling black spot resistance, abundant markers across the genome and careful phenotyping are required. Fifteen inter-related diploid rose populations with black spot resistant cultivar R. wichuraiana ‘Basye’s Thornless’ in the genetic background were assessed based on the percent of total foliage covered with lesions in June, October and November of 2016 in College Station. Broad sense heritability was estimated at 0.51 which indicates black spot partial resistance is a moderately heritable trait. Genotyping-by-sequencing technology was used to generate SNP markers for linkage map construction. Previous anchor SSR markers were used to designate the linkage group number. The final consensus map used for black spot QTL detection contained 791 SNP covering 430 cM with the biggest gap being 6.6 cM on LG4. One major black spot QTL was discovered on LG3 explaining ~13% of the total phenotypic variance (equaling approximately 26% of the genetic variation) using pedigree-based analysis among all fifteen populations.

Acidity is a critical component of the apple fruit consumption experience. In previous biparental family studies, two large-effect acidity QTLs were reported using freshly harvested fruit. Objectives of this study were to determine the number and location of QTLs for acidity variation in a large apple breeding program and ascertain the quantitative effects and breeding relevance of QTL allelic combinations at harvest and after commercially relevant periods of cold storage. Pedigree-connected germplasm of 16 full-sib families representing nine important breeding parents, genotyped for the 8K SNP array, was assessed for titratable acidity at harvest and after 10- and 20-week storage treatments, for three successive seasons. Using pedigree-based QTL mapping software, FlexQTL™, evidence was found for only two QTLs, on linkage groups 16 (the reported Ma locus) and LG 8 (here called Ma3) that jointly explained 66 ± 5% of the phenotypic variation. An additive allele dosage model for the two QTLs effectively explained most acidity variation, with an average of + 1.8 mg/L at harvest per high-acidity allele. The more high-acidity alleles, the faster the depletion with storage, with all combinations appearing to eventually converge to a common baseline. All parent cultivars and selections had one or two of the four possible high-acidity alleles. Each QTL had a rare second high-acidity allele with stronger or reduced effect. Diagnostic SNP markers were identified for QTL alleles derived from distinct sources. Combined QTL effects highlighted utility of the DNA-based information in new cultivar development for targeting desired fruit acidity levels before or after storage.

BackgroundGenetic modification of allergenic foods such as apple has the potential to reduce their clinical allergenicity, but this has never been studied by oral challenges in allergic individuals.MethodsWe performed oral food challenges in 21 apple-allergic individuals with Elstar apples which had undergone gene silencing of the major allergen of apple, Mal d 1, by RNA interference. Downregulation of Mal d 1 gene expression in the apples was verified by qRT-PCR. Clinical responses to the genetically modified apples were compared to those seen with the wild-type Elstar using a visual analogue scale (VAS).ResultsGene silencing produced two genetically modified apple lines expressing Mal d 1.02 and other Mal d 1 gene mRNA levels which were extensively downregulated, that is only 0.1-16.4% (e-DR1) and 0.2-9.9% (e-DR2) of those of the wild-type Elstar, respectively. Challenges with these downregulated apple lines produced significantly less intense maximal symptoms to the first dose (Vmax1) than with Elstar (Vmax1 Elstar 3.0mm vs 0.0mm for e-DR1, P=0.017 and 0.0mm for e-DR2, P=0.043), as well as significantly less intense mean symptoms per dose (meanV/d) than with Elstar (meanV/d Elstar 2.2mm vs 0.2mm for e-DR1, P=0.017 and 0.0mm for e-DR2, P=0.043). Only one subject (5%) remained symptom-free when challenged with the Elstar apple, whereas 43% did so with e-DR1 and 63% with e-DR2.ConclusionThese data show that mRNA silencing of Mal d 1 results in a marked reduction of Mal d 1 gene expression in the fruit and reduction of symptoms when these apples are ingested by allergic subjects. Approximately half of the subjects developed no symptoms whatsoever, and virtually all subjects wished to consume the apple again in the future.

International audience; Although many peach QTLs responsible for the variability of traits have been identified and published so far, the number of molecular markers currently used in breeding is still limited. One of the reasons is the large QTL intervals produced, in part, by the limited progeny size. Here we report a QTL mapping approach that enlarges the progeny size by analyzing jointly multiple progenies. Our analysis included 1467 individuals from eighteen Prunus progenies, 13 from intra-specific crosses and five inter-specific between peach and closely related species. The progenies were grown in five locations, with no duplication between orchards. Data from phenology, tree, flower and fruit traits, fruit quality and yield measured in different locations and years were subjected to different standardization methods and integrated in a single data file. The populations were genotyped with the 9K SNP Illumina array, which increased considerably the marker density compared to previous studies. The QTL analysis was conducted with FlexQTLTM software. Here we describe and discuss the preliminary QTLs obtained for some of the traits analyzed (maturity date, percentage of red skin color and soluble solid content). The identification of donors of favorable alleles will represent an important tool for marker-assisted breeding. This study has been conducted in the frame of the Fruit Breedomics European project.

Horticultural crop improvement would benefit from a standardized, systematic, and statistically robust procedure for validating quantitative trait loci (QTLs) in germplasm relevant to breeding programs. Here, we describe and demonstrate a strategy for developing reference germplasm sets of perennial, clonally propagated crops, especially those with long juvenile periods. Germplasm is chosen to efficiently represent important members of larger pedigree-connected genepools. To facilitate validation of multiple QTLs, genome-wide representation of alleles is optimized for designated important breeding parents (IBPs) by estimating average allelic representation in relatives. The strategy and arising principles were demonstrated in a simulated germplasm set. Strong statistical power can be achieved with a carefully chosen germplasm set composed of IBPs, their numerous unselected progenies and close relatives, and all available founders and intermediate ancestors. Crop Reference Sets were developed in the marker-assisted breeding (MAB)-enabling “RosBREED” project as a base resource for QTL validation in US breeding germplasm of apple (Malus × domestica), peach (Prunus persica), and sweet cherry (Prunus avium) consisting of 467, 452, and 268 individuals, respectively. These sets adequately represent the most designated IBPs, have distinct advantages for QTL validation over other germplasm arrangements of equal size, and are recommended as a base resource for QTL validation by breeders of these US crops. The strategy described here can be used to develop efficient reference germplasm sets suiting other breeding genepools or to calculate the statistical power for QTL validation of germplasm sets already established.

Patients with Oral Allergy Syndrome (OAS) to fresh apple may tolerate low allergenic apple cultivars. We aimed to investigate if the low allergenic properties of Elise and Santana, as previously identified in a Dutch population, could be generalised within North West Europe within the birch pollen region with regard to both the prevalence and degree of sensitization. Prick-to-prick tests (PTP) were performed in eighty-five adult patients with OAS to fresh apple in Great Britain, Switzerland and Northern Italy, before the birch pollen season, using the putatively low allergenic apple cultivars Elise, Santana, Granny Smith, Modi and Mcintosh, as well as the putatively high allergenic apple cultivars Golden Delicious and Kanzi. No significant differences in percentages of negative responses of PTPs were found between the three countries. Negative responses did not differ from negative responses to the different apple cultivars we previously found in 2006/2007 in the Netherlands. The size of the PTPs of all apple cultivars tested were correlated to the size of the skin prick tests with birch pollen. These results add to the indications for the low allergenic properties of the low allergenic apple cultivars Santana and Elise, as the number of negative responses were reproducible in three countries within the birch pollen region and were similar to previous results in the Netherlands. These results justify oral challenge studies with Elise and Santana within the birch pollen region, to establish the low allergenic properties for the benefit for apple allergic consumers for definite conclusions.

P>Background: As oral allergy syndrome (OAS) symptoms to apple are frequent, we aimed to identify low allergenic apple cultivars and to validate the prick-to-prick skin prick test (SPT) as a suitable screening method. Methods: Sixty-eight apple cultivars were tested by SPTs in 33 Dutch adults with OAS, before and during the birch pollen season in 2006 and 2007, respectively. Three cultivars yielding the largest number of negative SPTs (Elise, Santana and Pink Lady (R)) and one reference cultivar (Golden Delicious) were subsequently tested by single-blind oral food challenges (SBFC) just after picking in fall 2007 (fresh) and in spring 2008 (stored), outside the birch pollen season and preceded by SPTs. In spring, Santana was replaced by Modi (R). Results: In fresh apples, OAS symptoms of Elise, as measured by cumulative scores on a Visual Analogue Scale VASt, were significantly lower than those of Santana, Pink Lady and Golden Delicious (P = 0.021; 0.040 and 0.005, respectively). VASt scores of Santana were significantly lower than those of Golden Delicious (P = 0.049). In stored apples, VASt scores of Elise were significantly lower than that of Golden Delicious (P = 0.038). VASt scores of fresh apples did not differ significantly from stored apples, except in Golden Delicious (spring

SummaryMany people who are allergic to birch pollen are also allergic to apple fruit, due to cross- allergenicity. Since apples are the most extensively consumed fruit in Europe, it is highly relevant to develop a hypo-allergenic apple.Apples with significantly reduced levels of the allergen, Mal d 1, may allow many apple allergics to eat them without an allergic reaction. We are currently collaborating to develop a hypo-allergenic apple within the European Integrated Research Project, ISAFRUIT (www.isafruit.org). Hypo-allergenic apple plants (Malus × domestica Borkh., ‘Elstar’) with decreased levels of Mal d 1 mRNA were produced by RNA interference (RNAi) technology. Ten genetically modified (GM) apple lines were selected. In vitro plantlets were first transferred to a greenhouse, then grafted onto wild-type M.9 rootstock to promote the development of fruit-producing trees. Levels of Mal d 1 gene silencing were measured repeatedly by quantitative real-time PCR. Compared to leaf samples from wild-type ‘El...

Fruit ripening can be considered as a complex set of biochemical and physiological changes occurring at the end of the developmental stage. Ripe fruit texture notably affects overall quality and consumer appreciation. Excessive softening limits shelf-life and storability, thereby increasing disease susceptibility and economic loss. Fruit softening is a process due to the depolymerisation of different polysaccharide classes, an event controlled by a synergic and coordinated action of several enzymes among which expansins play a fundamental role. To date, six expansin genes are known to be expressed during apple fruit ontogeny, from full bloom up to fruit ripening. We identified a novel expansin apple homolog (Md-Exp7) sharing high sequence similarity with specific-ripening expansin genes of other crops. A functional marker (Md-Exp7SSR) based on an SSR motif located within the untranslated region of the gene was developed and mapped on Linkage Group 1 of the apple and pear genomes in a region where one major apple QTL for fruit firmness had been previously identified. The allelic composition of 31 apple varieties for the SSR marker was associated with differences in fruit softening.

A Bayesian approach to analyze complex traits is presented that can help plant eneticists and breeders in exploiting the marker and phenotypic data on pedigreed populations as available from ongoing breeding programs. The statistical model for the quantitative trait may include non-genetic and genetic components. The latter component can be divided into QTL on known marker linkage groups, major genes and a polygenic component. The full probability model, prior assumptions on model variables are presented and criterion for model selection and posterior inferences are given. Simulated data on a known pedigreed population structure of the EU project HiDRAS was used to illustrate the use of the Bayesian approach to analyze complex traits. It was shown that estimates for QTL parameters were more accurate when non-genetic factors were included in the model and when a polygenic component was included when not all linkage groups were analyzed simultaneously. The Bayesian approach has been implemented into the software package FlexQTL and allows plant breeders explore their pedigreed populations for segregating QTL alleles that are relevant in their breeding program.

Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699; International audience; An integrated consensus genetic map for apple was constructed on the basis of segregation data from four genetically connected crosses (C1 = Discovery x TN10-8, C2 = Fiesta x Discovery, C3 = Discovery x Prima, C4 = Durello di Forli x Fiesta) with a total of 676 individuals using CarthaGene(R) software. First, integrated female-male maps were built for each population using common female-male simple sequence repeat markers (SSRs). Then, common SSRs over populations were used for the consensus map integration. The integrated consensus map consists of 1,046 markers, of which 159 are SSR markers, distributed over 17 linkage groups reflecting the basic chromosome number of apple. The total length of the integrated consensus map was 1,032 cM with a mean distance between adjacent loci of 1.1 cM. Markers were proportionally distributed over the 17 linkage groups (chi(2) = 16.53, df = 16, p = 0.41). A non-uniform marker distribution was observed within all of the linkage groups (LGs). Clustering of markers at the same position (within a 1-cM window) was observed throughout LGs and consisted predominantly of only two to three linked markers. The four integrated female-male maps showed a very good colinearity in marker order for their common markers, except for only two (CH01h01, CH05g03) and three (CH05a02z, NZ02b01, Lap-1) markers on LG17 and LG15, respectively. This integrated consensus map provides a framework for performing quantitative trait locus (QTL) detection in a multi-population design and evaluating the genetic background effect on QTL expression

In apple breeding fruit quality is a crucial aspect to guarantee commercial success of new varieties. Among the several quality attributes, individual sugars and acid components, as well as texture, are considered important features due to their significant contribution to sensory quality and consumer's acceptance. In traditional breeding, however, selection for these particular traits is a time consuming process, due to the long unproductive juvenile phase of apple seedlings. This step can be assisted to date by the use of molecular markers, an important diagnostic tool useful to anticipate and assist the identification of novel apple varieties characterized by superior fruit quality behaviour. However, the routinely implementation of molecular markers in breeding programs is still limited. In this study a new approach named Pedigree Based Analysis will be used on six full-sib progenies and their pedigree (composed by 15 varieties, represented by founders and ancestors), to target the main set of quantitative trait loci (QTLs). This strategy will allow the identification of the most valuable alleles present in the breeding activities of both Italian institutes. The ultimate goal of the Laimburg - FEM joint project is the identification and validation of molecular markers as a suitable tool for Marker Assisted Breeding in the two on-going apple breeding programs.

Grapevine (Vitis vinifera L.) is one of the most valuable crops in the world. The most studied and interesting traits are strictly related to quality and disease resistance. Viticulture has often been plagued by encounters with new parasites that still represent a major constraint. This is a particularly important issue because, even though some inter-specific varieties (hybrids) between V. vinifera and Vitis spp. are widely present, the majority of cultivated grapevines are pure V. vinifera varieties, which are highly susceptible to pathogen attack. Fungal diseases, such as downy (DM) and powdery (PM) mildew, represent some of the most severe plagues and growers are obliged to use pesticides to prevent serious yield loss. Fungicides represent in fact the majority of plant protection products employed and viticulture one of the most intensively cultivated crops in terms of chemical usage. As a consequence, the research applied to breeding for resistance and the deployment of new resistant grapevine varieties are strongly encouraged as a step towards sustainable agriculture. Nowadays, grapevine genetics and genomics information, together with the associated technologies, are rapidly developing, leading to numerous discoveries with potential application such as the genome sequencing. Despite these advances, traditional breeding approaches are still dominant, while Marker-Assisted Breeding (MAB) implementation has been minimal both at the national and international level. In this study we focus on the genetic characterization of numerous Vitis hybrids, donors of resistance to DM and/or PM, in order to identify selection signatures. In particular, 86 hybrids of European origin and of 100 American hybrids, along with 30 related V. vinifera varieties, have been genotyped at 70 SSR loci. These markers have been chosen based on their physical distance in order to have 10 SSRs well-scattered along each of the 7 chromosomes that carry Resistance Gene Analog (RGA) clusters according to the literature. Based on the SSR profiles, the historical pedigree information has been checked and, following the true-to-typeness validation for most of the studied hybrids, the Identity By Descent (IBD) analysis has been performed, tracing the allelic flow through the successive generations. Here we report preliminary 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. Subsequently, the genotyping analysis will be extended to the other 12 chromosomes (120 SSRs) and possibly to new crucial genotypes. The final result of this study will be the release of molecular markers valuable for grapevine MAB, upon their validation in ad hoc segregating populations.

Rose, as many other important ornamental, vegetable and field crops, is polyploid. This poses constraints in genetic analyses due to the occurrence of multiple alleles at marker and trait loci and the existence of multiple allele dosages. Developments in marker discovery (next generation sequencing), detection (SNP arrays) and analysis (software for dosage scoring) now make it feasible to develop high-density molecular marker maps for the homologous chromosomes in tetraploids separately, and thus perform QTL analysis in tetraploids. We developed a SNP array for rose to develop genetic maps in tetraploid garden roses and cut roses, which are to be used for inheritance studies and genetic mapping. Here we have indicated the general strategy followed for developing a SNP array and for scoring and using the SNP data generated, and elaborated on the activities undertaken to use the WagRhSNP Axiom array in rose. The array design is not proprietary but can be used by all researchers working in rose

To date, molecular markers have been made available for many economically important traits. Unfortunately, lack of knowledge of their allelic variation 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 may be exploited for marker-assisted breeding (MAB), while a breeding program may include several alleles. Selection for only these alleles means that many favourable genotypes are ignored, which decreases efficiency and leads to genetic erosion. A new approach, called pedigree genotyping, allows the identification and exploitation of the majority of alleles present in an ongoing breeding program. This is achieved by including breeding material itself in QTL detection, so covering multiple generations and linking many crosses through their common ancestors in the pedigree. The principle of Identity by Descent (IBD) is utilised to express the identity of an allele of a modern selection in terms of alleles of founding cultivars. These founder alleles are used as factors in statistical analysis. Co-dominant markers, like SSR (= microsatellite) markers, are essential in this approach since they are able to connect cultivars, breeding selections and progenies at the molecular marker level by monitoring specific chromosomal segments along family trees. Additional advantages of the use of breeding genetic material are (1) a major reduction in experimental costs since plant material is already available and phenotyped by default (2) continuity over generations within breeding programs with regard to marker research (3) the testing of QTL-alleles against a wide range of genetic backgrounds, making results generally applicable (4) possibility to explore intra- as well as inter-QTL interactions. Fruit firmness in apple is used as an example to illustrate the principles of this powerful approach to detect QTLs and estimate their allelic variation. Prospects for strawberry are also indicated

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

Genetic linkage maps of the Japanese pear (Pyrus pyrifolia Nakai) cultivar `Housui¿ and the European pear (Pyrus communis L.) cultivar `Bartlett¿ were constructed based on Amplified Fragment Length Polymorphism markers (AFLPs), Simple Sequence Repeat markers (SSRs) (from pear, apple and Prunus), isozymes, and phenotypic traits by using their F1 progenies. The map of the female parent `Bartlett¿ consisted of 256 loci including 178 AFLPs, 76 SSRs (32 pear, 39 apple, 5 Prunus SSRs), 1 isozyme and a self-incompatibility locus on 19 linkage groups over a total length of 1020 cM. The map of `Housui¿ contained 180 loci including 110 AFLPs, 64 SSRs (29 pear, 29 apple, 6 Prunus SSRs), 2 phenotypic traits and 4 other markers on 20 linkage groups encompassing a genetic distance of 995 cM. These 2 pear maps were aligned using 37 co-dominant markers that showed segregating alleles in both parents. Out of 80 tested SSR markers developed from apple, more than four-fifth could produce discrete amplified fragments in pear. Thirty-eight apple SSR markers showed 39 segregating loci in the linkage map of `Bartlett¿, while 27 markers produced 29 loci in `Housui¿. All pear linkage groups could be successfully aligned to the apple consensus map by at least 1 apple SSRs, suggesting that positions and linkages of SSR loci were well conserved between pear and apple. The self-incompatibility locus (S locus) was mapped to linkage group 17 in Japanese and European pears as well as apple. Our results are the first major effort in comparative mapping of pear and apple

To date, molecular markers are available for many economically important traits. 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. A new approach, called Pedigree Genotyping, 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 utilised to express the identity of an allele of a modern selection in terms of alleles of founding cultivars. These founder alleles are used as factors in statistical analyses. Co-dominant markers like SSR (microsatellite) markers are essential in this approach since they are able to connect cultivars, breeding selections and progenies at the molecular marker level by monitoring specific chromosomal segments along family trees. Additional advantages of the use of breeding genetic material are (1) a major reduction in experimental costs since plant material is already available and phenotyped by default (2) continuity over generations within breeding programs with regard to marker research (3) the testing of QTL-alleles against a wide range of genetic backgrounds, making results generally applicable, (4) intra- as well as inter-QTL interactions can be explored. Fruit firmness in apple will be used as an example to illustrate the principles of this powerful approach to detect QTLs and estimate their allelic variation

Durable resistance to scab (Venturia inaequalis) of newly introduced cultivars is needed to achieve a considerable reduction of pesticide use. However, the assessment in the field on the level and durability of scab resistance is time and space consuming. A proper and fast indoor test should be a convenient tool to discard cultivars with a limited level of resistance at an early stage. As a result, field tests can include only the better cultivars. This approach has been tried out by comparing field data with data from a glasshouse test, comprising twelve new and seven well-known susceptible and resistant (with and without Vf) cultivars which have been tested with six isolates of scab from different origins, virulence and aggressiveness, including race 6 and 7. Young trees on M.9 rootstock were infected and after a 17 day period at high humidity, sporulation and chlorosis have been observed. If the set of isolates is broad and well-chosen it seems possible to assess susceptibility and possibly also durability. To optimize the choice of isolates, it is desirable to know the pedigree of the cultivars that are tested. In addition, this procedure allows the use of highly virulent and aggressive races, that should be avoided in field tests for the risk of spreading

The availability of suitable genetic markers is essential to efficiently select and breed apple varieties of high quality and with multiple disease resistances. Microsatellites (simple sequence repeats, SSR) are very useful in this respect since they are codominant, highly polymorphic, abundant and reliably reproducible. Over 140 new SSR markers have been developed in apple and tested on a panel of 7 cultivars and 1 breeding selection. Their high level of polymorphism is expressed with an average of 6.1 alleles per locus and an average heterozygosity (H) of 0.74. Of all SSR markers, 115 have been positioned on a genetic linkage map of the cross ‘Fiesta’ × ‘Discovery’. As a result, all 17 linkage groups, corresponding to the 17 chromosomes of apple, were identified. Each chromosome carries at least two SSR markers, allowing the alignment of any apple molecular marker map both with regard to identification as well as to orientation of the linkage groups. To test the degree of conservation of the SSR flanking regions and the transferability of the SSR markers to other Rosaceae species, 15 primer pairs were tested on a series of Maloideae and Amygdaloideae species. The usefulness of the newly developed microsatellites in genetic mapping is demonstrated by means of the genetic linkage map. The possibility of constructing a global apple linkage map and the impact of such a number of microsatellite markers on gene and QTL mapping is discussed.

International audience; The Venturia inaequalis-Malus pathosystem was one of the first for which gene-for-gene relationships were demonstrated following the discovery of such relationships between Melampsora lini and flax by Flor in the 1950s. An understanding of these relationships forms the basis for monitoring pathotypes of V. inaequalis at the population level and is employed to assess the usefulness of resistance genes for breeding durable resistance to scab. These pathotypes are difficult to accommodate in the current system of nomenclature for V. inaequalis races where each new combination of avirulence alleles is assigned a simple numerical descriptor as its name. We propose a system that is better suited to the increasing complexities of combinations of genes involved in both race-specific and race-nonspecific recognition by the host, while at the same time updating the name of scab resistance loci (Rvik) and QTL loci (Qvik) to international standards. For the race-specific interactions, the basic premise is that each Rvik-AvrRvik and Qvik-AvrQvik relationship should be represented by a differential host (k), abbreviated to h(k), carrying only the specific Rvik or (major) Qvik resistance allele and an isolate of the pathogen having lost only the complementary allele at the AvrRvik or AvrQvik locus, race (k), with k representing the number of the specific interaction. Races lacking more than one avirulence gene at different loci will be identified as race (k,l,m,...) and apple hosts carrying multiple scab resistance genes as host (k,l,m,...). The proposed system has some continuity with the current system, but should simplify the presentation and interpretation of studies on avirulence alleles in V. inaequalis at the population level. Gene-for-gene relationships reported to date for this pathosystem are reviewed, some inconsistencies clarified, and several new interactions added. The gene-for-gene relationships of European isolates collected in the last decade have been studied in order to establish a new set of reference isolates that represent various V.inaequalis races.

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 a single cross. Consequently, only one or two favourable alleles of the related quantitative trait loci (QTL) are identified and exploitable for marker-assisted breeding (MAB), whereas a breeding program may include several alleles. Our novel employed approach, namely pedigree-based analysis (PBA), allows for 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. 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, 120 hybrids of American origin and 100 European hybrids, along with 44 related V. vinifera cultivars, have been genotyped at 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 identity-by-descent (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 genotypes donors of resistance to downy mildew in north-eastern Italy.

International audience; Key message: 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. Abstract: 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 (TM) 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.

Phytophthora fragariae var. fragariae is the causal agent of red stele (red core) root rot in strawberry (Fragaria spp.). The inheritance of resistance to one isolate of this fungus was studied in 12 segregating populations of F.×ananassa derived from crosses between four resistant cultivars (‘Climax’, ‘Redgauntlet’, ‘Siletz’, and ‘Sparkle’) and three susceptible cultivars (‘Blakemore’, ‘Glasa’, and ‘Senga’ Sengana’). The analysis clearly supports the hypothesis of a single segregating dominant resistance gene. It is proposed that this gene be designated Rpf2.

The resistance of the USA and Canadian differential series of strawberry (Fragaria sp.) genotypes was assessed against nine USA isolates (A1-A4, A6-A10) and three Canadian isolates (NS2-NS4) of Phytophthora fragariae var. fragariae. The resistance of part of the UK series was also examined. Of the 157 host genotype-isolate combinations tested, 13 were classified differently from earlier reports. These differences can be explained by the existence of different clones under the same cultivar name (Aberdeen and Perle de Prague), the substitution of Aberdeen by Sparkle, which differ in their resistance, and by the application of different criteria for resistance. Here, incomplete resistance was considered as resistance. The discernment of the US differential series can be improved by including the UK differential Perle de Prague and the Canadian differential Sparkle. The Canadian series can be improved by including Perle de Prague and the US differential Aberdeen. This leads to one unified differential set for North America.The results also allow the proposition of a formal gene-for-gene model which, in turn, provides for a universal differential series for this pathosystem.

The commercial strawberry (Fragaria x ananassa) resistance gene Rpfl conferring resistance to various isolates of Phytophthora fragariae, was mapped using 7 RAPD markers. A DNA fragment representing a RAPD marker linked to susceptibility was cloned, sequenced and converted into a sequence characterized amplified region (SCAR) marker. Next, SCAR primers to the resistant allele (SCAR-R) were developed based upon a deletion region between susceptible and resistant plants. The SCAR-R primers were tested on a F1 progeny of 60 plants in which Rpf1 segregated in a 1:1 ratio. SCAR-R primers amplified DNA from resistant plants only. The SCAR-R primers and three RAPD primers linked to and surrounding the Rpfl gene were used to screen numerous European and North American strawberry genotypes. The molecular data supported the currently known plant resistance testing and indicates that the resistance gene region has been conserved in most crosses. The linkage to Rpfl with these markers was lost in some genotypes due to crossing-over, for example the subsequent generations of ‘Stelemaster’. The accuracy of these molecular markers for the detection of the gene demonstrates that they can be used in a marker-assisted strawberry breeding programme.

European canker, caused by the fungus Neonectria ditissima, is a severe problem in apple production both in Sweden and in many other northern European countries. Even when applying fungicides and good horticultural practices, canker damage occurs almost yearly in nurseries and orchards. Some years, devastating outbreaks destroy numerous trees. To date, complete resistance to N. ditissima is not known in apple. For further research and plant breeding, heritable variation in quantitative resistance should be investigated by phenotyping large sets of cultivars. In the present project, 55 apple cultivars were screened for resistance to N. ditissima. One-year-old shoots from mature trees were inoculated in the greenhouse with a standardized volume and concentration of conidia suspension using different inoculation methods. Two-year-old trees of five cultivars were inoculated in the field. Length of the occurring cankers was measured at regular intervals throughout a period of up to three months. The investigated cultivars showed considerable differences in colonization rate. In cultivars known to be highly resistant, i.e., ‘Santana’, lesions progressed much slower compared to susceptible cultivars like ‘Cox’s Orange Pippin’ and ‘James Grieve’. Since the inoculation-based phenotyping is demanding in labour and time (duration), especially when the test is performed on grafted trees, qPCR-based assessment of fungal biomass at early stages of infection was explored as an alternative or complementary approach for phenotyping.

Mal d 1 is not equally distributed over the apple. We aimed to examine the influence of the location of pricking in the apple on prick-to-prick skin prick test (PTP) results. PTPs were performed in autumn 2007 and spring 2008, before the birch pollen season, in 32 Dutch adults with symptoms of oral allergy to fresh apple, using apples harvested in autumn 2007. PTPs with fresh intact and unpeeled Pink Lady, Golden Delicious, Elise, Santana and Modi apples were performed using material obtained from approximately 2cm near the stalk (top), and the middle region. All PTP responses were greater when performed with apple material near the stalk than from the middle region. In 2007, these differences were statistically significant for Pink Lady, Golden Delicious and Elise, and in 2008, for Pink Lady and Modi. When performing PTPs, the apple should be pricked near the stalk rather than in the middle.

Race specific resistance to red core (red stele) root rot, caused by Phytophthora fragariae var. fragariae, is known to occur in the cultivated strawberry (Fragaria × ananassa Duch.), but frequently this resistance does not completely prevent infection. We therefore developed a classification method which distinguishes partial and complete resistance. It accounts for differences in the aggressiveness of isolates and in the appropriateness of experimental conditions for infection. This method is based on the microscopically assessed disease severity of a tested strawberry genotype relative to that of an universally susceptible reference cultivar. If the tested genotype is significantly (P≤0.01) less diseased, it is considered to possess resistance. Data from 18 genotype-isolate combinations, including five genotypes (‘Blakemore’, ‘Md683’, ‘Redgauntlet’, ‘Del Norte’, ‘Yaquina A’) and four North American isolates (A2, A4, A6 and A10) demonstrated the validity of our classification scheme.

Strawberry is one of the five fruit crops included in the USDA-funded multi-institutional and trans-disciplinary project, “RosBREED: Enabling Marker-Assisted Breeding in Rosaceae”. A Crop Reference Set (CRS) was developed of 900 genotypes and seedlings from 40 crosses representing the breadth of relevant diversity and encompassing founders used in breeding the domesticated strawberry. Individual native species and cultivar genotypes were included along with 10 progeny from 36 of the crosses of genotypes representing eastern and western North American and European short day and remontant cultivars. This CRS has been phenotyped in five U.S. states. Over 14 fruit quality traits have been studied, as well as remontancy, truss size, peduncle length, crop estimate, plant architecture, and disease resistance. The phenotyping conducted in the first growing season showed considerable variability amongst the genotypes and the locations for all of the characteristics. General and specific combining ability variance components were determined from the populations in order to provide breeders with guidance on the most effective breeding strategies for incorporating the superior traits from this germplasm into their programs.

Apple (Malus x domestica Borkh.) is one of the most important fruit trees grown in Europe and around the world for human consumption, and therefore plant breeders aim at producing new apple varieties with high fruit quality. The availability of molecular markers suitable for marker-assisted selection could greatly increase the efficiency and power of breeding. The recent release of the cv. Golden Delicious genome sequence contributed to an exponential increase in the number of Malus sequences publicly available, while the successful achievement of two apple expressed sequence tag (EST) projects permitted the development of molecular markers from coding sequences. Here we present the setting up and mapping of new EST-based markers specific for fruit development and fruit quality traits. Since a large proportion of the ESTs used in our work were transcriptionally characterized and some of them co-localize within quantitative trait locus regions controlling fruit quality traits, the data reported will be effective in the identification of candidate genes. Due to the high level of polymorphism present in the Malus genome, 70% of the entire set of ESTs analyzed were polymorphic and 80% of them were successfully located using the conventional map-based approach. Fifty new EST-based markers were placed on the apple reference genetic map Fiesta x Discovery, thus enhancing the saturation of some regions, and 17 on Prima x Fiesta. Finally, another 17 markers were located on the Golden Delicious genome sequence using an in-silico approach.

In this paper we present an overview of current developments in sequencing that offer the possibility to generate large numbers of markers in ornamental crops. The prospects of this new sequence technology for the application of markers in breeding of outcrossing and/or polyploid crops are discussed using examples in rose and lily.

Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699; International audience; Apple cultivars and breeding lines that represent much of the diversity currently present in major European breeding programmes and are genetically related by their pedigree were examined for the trueness of their identity and parentage by consistency in marker scores using a genome-covering set of 80 microsatellite (SSR) markers and an ‘identity-by-descent’ approach. One hundred and twenty-five individuals were validated for the trueness-to-type of both their parents and 49 were validated for one of their parents, their second being unknown (23 individuals) or not available in this study (26 individuals). In addition, 15 individuals for which we lacked one of or both the direct parents were validated by consistency with tested parents of earlier generations. Furthermore, the identity of 28 founder cultivars was validated, their marker scores being consistent with descending cultivars and breeding lines. Four of the eight triploids identified were clearly shown to have arisen from unreduced egg cells. The assumed pedigree of 15 further individuals was found to be incorrect; fully consistent pedigrees were suggested for three of the cultivars. The pedigrees of a further eight individuals were confirmed through inference from the molecular data.

International audience; A series of 21 multiplex (MP) polymerase chain reactions containing simple sequence repeat (SSR) markers spanning most of the apple genome has been developed. Eighty-eight SSR markers, well distributed over all 17 linkage groups (LGs), have been selected. Eighty-four of them were included in 21 different MPs while four could not be included in any MPs. The 21 MPs were then used to genotype approximately 2,000 DNA samples from the European High-quality Disease-Resistant Apples for a Sustainable agriculture project. Two SSRs (CH01d03 and NZAL08) were discarded at an early stage as they did not produce stable amplifications in the MPs, while the scoring of the multilocus (ML) SSR Hi07d11 and CN44794 was too complex for large-scale genotyping. The testing of the remaining 80 SSRs over a large number of different genotypes allowed: (1) a better estimation of their level of polymorphism; as well as of (2) the size range of the alleles amplified; (3) the identification of additional unmapped loci of some ML SSRs; (4) the development of methods to assign alleles to the different loci of ML SSRs and (5) conditions at which an SSR previously described as ML would amplify alleles of a single locus to be determined. These data resulted in the selection of 75 SSRs out of the 80 that are well suited and recommended for large genotyping projects

Apple scab, caused by the fungal pathogen Venturia inaequalis, is one of the most devastating diseases for the apple growing in temperate zones with humid springs and summers. Breeding programs around the world have been able to identify several sources of resistance, the Vf from Malus floribunda 821 being the most frequently used. The appearance of two new races of V. inaequalis (races 6 and 7) in several European countries that are able to overcome the resistance of the Vf gene put in evidence the necessity of the combination of different resistance genes in the same genotype (pyramiding). Here, we report the identification and mapping of a new apple scab resistance gene (Vd3) from the resistant selection “1980-015-25” of the apple breeding program at Plant Research International, The Netherlands. This selection contains also the Vf gene and the novel V25 gene for apple scab resistance. We mapped Vd3 on linkage group 1, 1 cM to the south of Vf in repulsion phase to it. Based on pedigree analysis and resistance tests, it could be deduced that 1980-015-25 had inherited Vd3 from the founder “D3.” This gene provides resistance to the highly virulent EU-NL-24 strain of race 7 of V. inaequalis capable of overcoming the resistance from Vf and Vg.

Candidate genes involved in ethylene production during ripening

Tree Genetics & Genomes, 2 (4), ISSN:1614-2950, ISSN:1614-2942

V f is the most widely used resistance gene in the breeding for scab resistant apple cultivars. Distorted segregation ratios for V f -resistance have frequently been reported. Here we revealed that sub-lethal genes caused the distorted segregation. The inheritance of V f was examined in six progenies by testing linked molecular markers. Three progenies showed distorted segregations that could be explained by three sub-lethal genes (sl1, sl2 and sl3), of which sl1, sl2 were closely linked to V f . The s11 gene was located at about 14 cM from V f and expressed itself only in the presence of another independently segregating sub-lethal gene sl3. Only the double homozygous recessive genotypes (sl1sl1 sl3sl3) were lethal, which occurred at first as dwarf and poor vigour plants during the first three months after germination. The sl2 gene was also linked to V f and its lethality was expressed prior to seed germination and also required the homozygous recessive presence of sl3. The map position of sl3 has not yet been identified. The linkage of V f to sub-lethal genes usually results in a shortage of V f -resistant progenies. But in some exceptional crosses, it will lead to abundance of resistant seedling.

A set of test crosses of diploid potatoes was used to identify QTLs for foliage resistance against Phytophthora infestans and QTLs for foliage maturity type, and to assess their genetic relationship. The most important locus for both traits was found on chromosome 5 near marker GP21: the allele of marker GP21 that is associated with resistance to late blight is also associated with late foliage maturity. An additional QTL with a small effect on foliage maturity type was identified on chromosome 3, and additional QTLs for late blight resistance were found on chromosomes 3 and 10. Another QTL was detected on chromosome 7 when resistance was adjusted for the effect of foliage maturity type. The additional QTLs for resistance against P. infestans on chromosomes 3 and 10 seem to be independent of foliage maturity type and are not affected by epistatic effects of the locus on chromosome 5. The effects of the additional QTLs for resistance are small, but early maturing genotypes that necessarily have the allele for susceptibility for late blight on chromosome 5 may benefit from the resistance that is provided by these QTLs on chromosomes 3 and 10.

Four classes of apple allergens (Mal d 1, -2, -3 and -4) have been reported. By using PCR cloning and sequencing approaches, we obtained genomic sequences of Mal d 2 (thaumatin-like protein) and Mal d 4 (profilin) from the cvs Prima and Fiesta, the two parents of a European reference mapping population. Two copies of the Mal d 2 gene (Mal d 2.01 A and Mal d 2.01 B) were identified, which primarily differed in the length of a single intron (378 or 380 nt) and in one amino acid in the signal peptide. Both Mal d 2.01 A and Mal d 2.01 B were mapped at identical position on linkage group 9. Genomic characterization of four Mal d 4 genes (Mal d 4.01 A and B, Mal d 4.02 A and Mal d 4.03 A) revealed their complete gDNA sequences which varied among genes in length from 862 to 2,017 nt. They all contained three exons of conserved length: 123, 138, and 135 nt. Mal d 4.01 appeared to be duplicated in two copies and located on linkage group 9. Mal d 4.02 A and Mal d 4.03 A were single copy genes located on linkage group 2 and 8, respectively.

Although fire blight, caused by the bacterium Erwinia amylovora, is one of the most destructive dis- eases of apple (Malus · domestica) worldwide, no ma- jor, qualitative gene for resistance to this disease has been identified to date in apple. We conducted a quan- titative trait locus (QTL) analysis in two F1 progenies derived from crosses between the cultivars Fiesta and either Discovery or Prima. Both progenies were inocu- lated in the greenhouse with the same strain of E. am- ylovora, and the length of necrosis was scored 7 days and 14 days after inoculation. Additive QTLs were identified using the MAPQTL software, and digenic epi- static interactions, which are an indication of putative epistatic QTLs, were detected by two-way analyses of variance. A major QTL explaining 34.3-46.6% of the phenotypic variation was identified on linkage group (LG) 7 of Fiesta in both progenies at the same genetic position. Four minor QTLs were also identified on LGs 3, 12 and 13. In addition, several significant digenic interactions were identified in both progenies. These results confirm the complex polygenic nature of resis- tance to fire blight in the progenies studied and also reveal the existence of a major QTL on LG7 that is stable in two distinct genetic backgrounds. This QTL could be a valuable target in marker-assisted selection to obtain new, fire blight-resistant apple cultivars and forms a starting point for discovering the function of the genes underlying such QTLs involved in fire blight control.

Non-specific lipid transfer proteins (nsLTPs) of Rosaceae fruits, such as peach, apricot, cherry, plum and apple, represent major allergens for Mediterranean atopic populations. As a first step in elucidating the genetics of nsLTPs, we directed the research reported here towards identifying the number and location of nsLTP (Mal d 3) genes in the apple genome and determining their allelic diversity. PCR cloning was initially performed on two cultivars, Prima and Fiesta, parents of a core apple mapping progeny in Europe, based on two Mal d 3 sequences (AF221502 and AJ277164) in the GenBank. This resulted in the identification of two distinct sequences (representing two genes) encoding the mature nsLTP proteins. One is identical to accession AF221502 and has been named Mal d 3.01, and the other is new and has been named Mal d 3.02. Subsequent genome walking in the upstream direction and DNA polymorphism analysis revealed that these two genes are intronless and that they could be mapped on two homoeologous segments of linkage groups 12 and 4, respectively. Further cloning and sequencing of the coding and upstream region of both Mal d 3 genes in eight cultivars was performed to identify allelic variation. Assessment of the deduced nsLTP amino acid sequences gave a total of two variants at the protein level for Mal d 3.01 and three for Mal d 3.02. The consequences of our results for allergen nomenclature and the breeding of low allergenic apple cultivars are discussed.

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

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

A gene-for-gene model is presented which explains interactions between cultivars of strawberry and races of Phytophthora fragariae var. fragariae, the causal agent of red core (red stele) root rot. The model allows the constitution of a universal differential set of strawberry genotypes and the characterizing of fungal isolates into races, the genotyping of strawberry cultivars and selections in a breeding programme, and facilitates the search for linked molecular markers for more efficient selection for resistance.

Bulked segregant analysis (BSA) was used to identify seven random amplified polymorphic DNA (RAPD) markers linked to the Rpf 1 gene. Rpf 1 confers resistance to Phytophthora fragariae var. fragariae, the causal agent of red stele root rot in Fragaria spp. The bulked DNAs represented subsets of a F1 population obtained from the cross Md683×Senga Sengana which consisted of 60 plants and segregated in a 1:1 ratio for resistance or susceptibility to race 2.3.4 isolate NS2 of P. fragariae. Seven markers were shown to be linked to Rpf 1 and were generated from four primers; five of these markers were in coupling phase and two in repulsion phase with respect to the gene. A linkage map of this resistance gene region was generated using JoinMap 2.0TM. The manner in which Rpf 1 and the linked markers co-segregated indicated that they are inherited in a disomic fashion. These markers could enable gene pyramiding and marker-assisted selection of resistance genes in strawberry breeding programmes.

A gene-for-gene model is postulated to explain the observed interactions between cultivars of strawberry and races of Phytophthora fragariae. Five interacting resistance (R1 · R5) and avirulence (Avr1 Avr5) factors explain all the available data involving 15 host genotypes, including the USA and Canadian differential series, and 12 pathogen isolates from North America. Interactions between pathogen isolates and UK and German differentials are also explained by the proposed model. The model makes it possible to develop a universally applicable differential series, to present a systematic, unequivocal nomenclature of races, and to increase the efficiency of breeding programs.