Genetic variability is a key requirement for breeding. Although new peach cultivars are released yearly to the market, the genetic pool of cultivated peaches is very limited. To evaluate the variability available in commercial but also in old local peach accessions we selected a panel of 1,580 accessions maintained and evaluated in four European and one Chinese germplasm collections. Phenotypic data collected over years following common protocols have been integrated in a database, generating a useful tool for breeders and researchers. These accessions were genotyped with the peach 9K SNP array v1. T. Genotypic data distributed the accessions in three main subpopulations (Occidental obtained in breeding programs, Occidental old local varieties and Chinese cultivars). Linkage disequilibrium (LD) was in agreement with previous studies reporting long extension. Phenotypic and genotypic data have been combined in a GWAS study allowing the design of markers for marker assisted selection (MAS). Preliminary analyses on quantitative traits are promising, while further analysis will be required to integrate all data in a single genome-wide association analysis.

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.

"FruitBreedomics" European project has been designed by an international consortium including scientists, stakeholders and breeding companies. One of its aims is to increase the efficiency of breeding programs in apple Malus xdomestica) and peach Prunus persica) by enabling Marker Assisted Breeding MAB) using novel genomic tools. In the frame of this project, five peach mapping populations from the UGAFL (Unite de Genetique et Amelioration des Fruits et Legumes) peach breeding program two intraspecific F-2, two interspecific F-1 derived from P. davidiana and one self-pollinated derived from 'Bolinha') segregating for mendelian traits and/or Quantitative Trait Loci QTLs) for pest resistance and fruit quality were genotyped using the 9K SNP Illumina Infinium II Bead-chip delivered by the International Peach SNP Consortium IPSC). Based on these data, genetic maps were then constructed; however mapping results were contrasted depending on the population considered. All maps aligned with the 8 pseudo-molecules of the Prunus persica Whole Genome sequence v1.0 IPGI), but the best polymorphisms and coverage were obtained with the F-2 populations, for which twenty to twenty-nine percent of the SNPs were polymorphic covering 500 loci on average. However, these loci were unevenly distributed, although covering most of the peach genome. In contrast, for the F-1 populations, only 5% of the SNPs were polymorphic in P. davidiana and the selfing of 'Bolinha' resulting in low coverage and very heterogeneous distributions. As primary consequence, this demonstrates the poor transferability of such a tool between species, even tightly related, and additionally highlights the relatively low efficiency of SNPs in term of useful polymorphism when parents belong to close peach germplasms. Consequently, regions containing QTLs and major genes could be insufficiently covered and need additional SNP development for MAB. The relevancy of using general medium-range SNP bead-chips for breeding purposes is discussed in this study.

Peach/nectarine is an important fruit tree crop in Europe and indeed worldwide. The registration of new cultivars, either for Plant Breeders' Rights or National Listing (PBR/NL) purposes in the European Union (EU), requires the completion of a distinctness, uniformity and stability (DUS) test in one of the EU Member States. The number of candidate cultivars and potentially required example cultivars entered for DUS testing is steadily increasing annually. Moreover, DUS testing of this type of tree crops requires the maintenance of large orchards, particularly with the aim of having a complete reference collection. In France, Hungary, Spain and Italy, peach tree breeding activity is characterized by an important number of cultivars available and a short turn-over of the cultivars. This situation will extend to new EU members states in the coming years, with the development of the European trade. However, although the diversification increases the number of segments, for each segment, new released cultivars are genetically closer and closer. The consequence is that it is now difficult in some cases to distinguish between cultivars. Clearly, developing means of "managing" reference collections is highly desirable in order to be able to compare candidate cultivars with the closest cultivars of common knowledge in the reference collections prior to planting them, and so reduce the number of cultivars that need to be grown, without eroding the strength of PBR and the relevance of DUS tests. Effective means of such a management include the definition of a standardised way to compare phenotypic data and to use molecular markers to eliminate the reference cultivars which do not need to be compared to the candidate cultivars. In peach tree, various molecular markers such as DNA microsatellites (SSR) have been developed and evaluated, but they have not yet been used for the characterization of large collections. Therefore, this project will generate a database compiling both phenotypic data, including standardised morphological descriptions and digital pictures, and a large data set of DNA profiles for 522 peach tree cultivars selected among the EU granted and listed cultivars.

The European fruit industry is facing economic challenges imposed by increasingly fierce international competition and decreasing fruit consumption, societal demand for a more sustainable production, and biological problems caused by climate changes. Releasing new cultivars that meet these challenges is a major goal of all European breeding programmes. However, addressing them has been slow due to the nature of fruit tree breeding: long term, low efficiency and high cost. For the past 15 years, efficient networks of fruit geneticists and genomicists have progressively been built thanks in particular to EU-funded projects. Europe has thus become a leader in research on fruit genetics aimed at enhancing fruit quality traits as well as resistance to biotic stresses. European teams working on fruit genetics have developed up-to-date tools and skills covering most of the omics fields as well as statistics and software development. Although fruit breeding is very active in Europe, very few breeding programmes are really using the output of the fruit genetics/genomics research. A few bottlenecks can explain this situation. To solve that, a new European initiative has been set up by the FruitBreedomic. This large collaborative project, has the strategic goal of improving the efficiency of current fruit breeding programmes by bridging the existing gap between molecular genetics research and application in breeding.

Peach (Prunus persica (L.) Batsch) is one of the most economically important fruit crops in temperate areas. Every year new varieties are released from breeding programmes trying to meet the requirements imposed by the market. Classical fruit tree breeding is generally slow and inefficient. Molecular markers could improve its efficiency but, although nowadays many Mendelian traits are mapped in peach and SSR markers have been found to be linked to some of the key major genes, its use in breeding programmes is still limited. Main reasons for that are insufficient linkage between the markers and the genes and the lack of markers suitable for medium-high degree of multiplexing. FruitBreedomics is a European project conceived with the strategic goal to improve the efficiency of fruit breeding by bridging the gap between scientific knowledge and application in breeding. In the frame of this project, and with the goal of obtaining SNP closely linked to agronomic interesting traits, the 9K peach SNP chip (Illumina Inc.) developed by the International Peach SNP Consortium (IPSC) has been used in both segregating populations and in germplasm collections. This chip, containing 8144 SNPs scattered on the 8 peach chromosomes, has been used in about 1,500 individuals belonging to seventeen Prunus crosses (12 peach x peach and 5 interspecific) and in 1,300 peach cultivars from different origins, including some of the founders of the current breeding programs

The architecture and action of quantitative trait loci (QTL) contributing to plant resistance mechanisms against aphids, the largest group of phloem-feeding insects, are not well understood. Comparative mapping of several components of resistance to the green peach aphid (Myzus persicae) was undertaken in Prunus davidiana, a wild species related to peach. An interspecific F1 population of Prunus persica var. Summergrand × P. davidiana clone P1908 was scored for resistance (aphid colony development and foliar damage) and 17 aphid feeding behaviour traits monitored by means of the electrical penetration graph technique. Seven resistance QTLs were detected, individually explaining 6.1–43.1% of the phenotypic variation. Consistency was shown over several trials. Nine QTLs affecting aphid feeding behaviour were identified. All resistance QTLs except one co-located with QTLs underlying aphid feeding behaviour. A P. davidiana resistance allele at the major QTL was associated with drastic reductions in phloem sap ingestion by aphids, suggesting a phloem-based resistance mechanism. Resistance was also positively correlated with aphid salivation into sieve elements, suggesting an insect response to restore the appropriate conditions for ingestion after phloem occlusion. No significant QTL was found for traits characterising aphid mouthpart activity in plant tissues other than phloem vessels. Two QTLs with effects on aphid feeding behaviour but without effect on resistance were identified. SSR markers linked to the main QTLs involved in resistance are of potential use in marker-assisted selection for aphid resistance. Linking our results with the recent sequencing of the peach genome may help clarify the physiological resistance mechanisms.

A European Integrated Project, untitled 'ISAFRUIT',has been engaged in January 2006. It deals with the improvement of fruit consumption by the consumers under both objectives: the optimization of the quality of the row products, and the optimization of the cultural practices. The project involves 40 Research Institutes and 20 Companies issued from 14 European countries and two associated countries. Within the whole project, a work package (6.1) is dedicated to the study of the genetics of fruit quality and health properties. It is subdivided in six main tasks, among them two concerning peach and apricot quality attributes have been already engaged: Task 1 - Identification and mapping of candidate genes for fruit quality in saturated maps of peach and apricot. Task 3 - QTLs analysis of fruit quality. Six research laboratories are involved in theses parts of the project based on the analysis of four Prunus progenies of 120 hybrid each, two apricot progenies cultivated in Avignon (Fr) and Bologna (It), and two peach progenies cultivated in Avignon and Bordeaux (Fr). Fruit quality characterization is based on (i) physical measurements (fruit weight, colour, firmness), (ii) biochemical measurements (refractometric index, titratable acidity) and (iii) on a fine metabolic profiling based on 1H RMN 1D, targeting the major metabolites, associated with a phenolic compounds characterization by HPLC. The related datasets will be joined with the genetic map under saturation for localising the associated QTLs. A particular attention will be paid to the co-linearity between species.

Sharka disease is now recognised as the most economically detrimental virus disease in stone-fruit worldwide and numerous breeding programs that aim to select new cultivars resistant to PPV are under progress. For apricot, an important source of resistance has been identified in 'Stark Early Orange', a North-American cultivar. It has been used at INRA Avignon for the apricot PPV breeding program and for a rootstock-breeding program aimed at PPV resistance. For peach, P. davidiana is the only known source for resistance; it has been widely used for introducing PPV resistance into the closely related P. persica genome. Several progenies derived from these resistance sources were developed for these programs at the INRA Avignon as well as the associated genetic maps. Additionally, a number of resistance genes were cloned at the INRA Bordeaux and assigned to these maps. These progenies segregate for the PPV resistance and phenotypic evaluations were performed under contrasting environmental conditions including different PPV strains in order to explain the inheritance of the trait and map the loci involved in the resistance. This work was carried out by a group of researchers working in different fields of activities focused on PPV resistance and we propose in this paper an overview of the main findings.

A complex, polygenic resistance to Plum pox virus (PPV) was previously described in a wild peach‐related species, Prunus davidiana clone P1908. In the current study, an analysis of quantitative trait loci (QTL) was performed on an F2 population comprising 99 individuals obtained by selfing the F1 individual #40 of an interspecific cross between susceptible nectarine cv. Summergrand and the resistant P. davidiana clone P1908. Six QTL were identified using both parametric and non‐parametric methods of detection, individually explaining 5–28% of the phenotypic variance. The total phenotypic variation explained ranged from 29 to 58%. Alignment of the genetic map of the F2 cross with the P. davidiana parent map showed consistency of QTL over generations, with three of the six QTL co‐localizing at the 1‐LOD interval and another one at the 2‐LOD interval. Two of the QTL were mapped onto linkage group one, where resistance to PPV was previously mapped in apricot. Development and mapping of new microsatellite markers linked to candidate genes revealed a striking co‐localization of three of the detected QTL with gene copies coding for eukaryotic translation initiation factors eIF4E and eIF(iso)4G. As co‐localization of one QTL with candidate gene eIF(iso)4E was previously reported in the F1 population, the results reported here strongly reinforce the idea that components of the eukaryotic translation initiation complex are correlated with resistance to PPV in P. davidiana P1908.

For several years, INRA has been developing a peach [Prunus persica (L.) Batsch] breeding program aimed partly at diversification. The selection objectives are more especially to create new varieties of peaches and flat nectarines better adapted to the needs of the French and European markets, as well as providing new canning peach varieties better suited to the constraints of the canning industry. Taking into account the interest of the Spanish market for these two fruit types, a trial was settled at IRTA (Lleida) to evaluate their agronomic potential of production in the pedo-climatic conditions of Catalonia, potentially favorable to these cultivars of medium chilling requirements. The results obtained in Spain and in France for several characteristics of the fruit (skin color, flesh firmness, size, juice traits: degrees Brix and acid total Meq/100 ml) and of the tree (type of pruning, flowering season, thinning, production level, ripening dates) are presented. They concern mainly two yellow flat nectarines, 'Mesembrine' cov and 'Oriola' cov, protected under the trademark 'Platerine'(R); three yellow flat peaches, 'Oriane' cov, 'Ornella' cov, and 'Ordigan' cov; and four original canning peach cultivars, 'Fergold' cov, 'Fercluse' cov, 'Ferlot' cov, and 'Exp 7040' cov. Their interest and performance are discussed in comparison to reference varieties. All these cultivars developed by INRA are edited in France by CEP INNOVATION.

We evaluated the possibility of using ecophysiological models to describe genetic variations observed in a population, identify QTLs (Quantitative Trait Loci) for the model parameters and combine QTLs and ecophysiological models. This approach was applied to peach quality observed in an advanced backcross between Prunits persica (L.) Batsch and Prunus davidiana. The ecophysiological model predicts fruit and stone dry and fresh masses and total sugar concentration in relation to environmental conditions. A preliminary study was conducted to select relevant parameters among the 40 parameters of the models. In a first step these parameters were estimated experimentally for nearly 130 individuals of the population and independent data were acquired to test the predictive quality of the model. In a second step, model analysis allowed us to identify the genotypic key-parameters. In a third step, QTL analysis resulted in the description of a model of genetic control of these parameters which predicts the parameter values for any genotype according to the alleles present at each locus of interest. To combine ecophysiological and genetic models, we replaced in the ecophysiological model the measured values of the parameters by the values predicted by the genetic model. Twelve genotypic parameters, involved in identified ecophysiological processes, appeared essential. QTLs for the twelve parameters were detected and co-locations between QTLs for quality traits and QTLs for parameters were observed. The combined model was satisfactory. Results of this study were considered in order to discuss the interest of such an approach for selection and biological understanding.

Plum pox virus (PPV), the causative agent of sharka disease in Prunoideae, is one of the most serious problems affecting stone fruit production in Europe and America. Resistance to PPV was previously described in a Prunus davidiana clone, P1908, and introduced into peach (Prunus persica) genotypes. Genetic resistance to PPV displays a complex pattern of quantitative inheritance. An analysis of quantitative trait loci (QTLs) for resistance was performed on an F1 interspecific peach population obtained from a cross between the susceptible nectarine cultivar Summergrand and P. davidiana. The hybrids were graft-inoculated with PPV in duplicate following a classical procedure. The incidence of infection was evaluated four times, over two vegetative cycles, by symptom observation and enzyme-linked immunoadsorbent assays (ELISA). Restriction of systemic downward movement of the PPV virus was also evaluated by testing the susceptible rootstocks. Using both analysis of variance and non-parametric tests, six genomic regions involved in PPV resistance were detected. Depending on the scoring data considered, between 22 and 51% of the phenotypic variance could be explained by the quantitative model. One QTL, located in the distal region of linkage group 1, maps in a genomic region that is syntenic to the location of a resistance gene previously identified in the apricot cv. Goldrich. Some QTLs appeared to be temporally specific, reflecting the environmental dependence of PPV-resistance scoring. Candidate gene fragments were amplified by PCR, isolated and mapped on the peach interspecific linkage map. We report here the co-localization of three analogues of virus resistance genes with two distinct genomic regions linked to PPV resistance in P. davidiana.

Plant-derived recombinant human insulin-like growth factor precursor prohormone IGF-1B caused differentiation of human neuroblastoma cell lines SH-SY5Y M. Panahi, X. Cheng, Z. Alli, R. Sardana, M. Callaghan, J. Phipps, I. Altosaar 21–31 QTLs for powdery mildew resistance in peach × Prunus davidiana crosses: consistency across generations and environments M. Foulongne, T. Pascal, F. Pfeiffer, J. Kervella 33–50

The green peach aphid, Myzus persicae, is one of the most serious pests of peach and nectarine in the southern Europe. Peach germplasm has been screened to identify sources of resistance and initiate breeding programmes. The clone P1908 of the wild species Prunus davidiana confers partial resistance to M persicae, that results in deteriorated aphid life history traits. A progeny (SxD progeny), derived from a cross between P 1908 and a nectarine cultivar, was used to construct a genetic linkage map of P. davidiana and to evaluate resistance to M persicae. For several evaluations of aphid resistance performed in various conditions, the SxD peach hybrids were partitioned into two categories according to their resistance score. Two consecutive molecular markers located on linkage group 3, i.e. the RAPD marker Q06-350 and the RFLP marker AG50A, were most strongly associated with aphid resistance, indicating that a factor of resistance located in this genomic region was segregating in the SxD progeny. To increase our understanding of the physiological process that alters suitability of P1908 as a host plant for M. persicae, we investigated the effect of the factor of resistance previously detected on the feeding response of the aphid. The aphid probing behaviour was recorded with the Electrical Penetration Graph (EPG) technique on the SxD peach hybrids. Then we compared EPG parameters of M persicae feeding on the hybrids with the allele associated with resistance (allele 1) and on the hybrids with the allele associated with susceptibility (allele 0) at marker Q06-350. On the hybrids carrying allele 1, aphids produced significantly less continuous phloem sap ingestion than on the hybrids carrying allele 0. They also produced more phases of salivary secretion into the sieve element. These results suggest that the factor of resistance detected in P1908 may be linked to a phloem seating system of the plant in response to injury of the sieve tubes by the aphid stylet, that would prevent aphid from sustained sap uptake.

A breeding programme has been undertaken to introgress a polygenic resistance to powdery mildew from P. davidiana clone P1908 into peach. The first step of the selection process was based on phenotypic data. Five interspecific hybrids between P1908 and Summergrand peach cultivar have been chosen for their good level of resistance to powdery mildew and each one was the starting point for backcross breeding schemes. The efficiency of this selection strategy was assessed in the light of molecular data (map and QTL detection) collected later on. Three alternative scenarios were compared by Monte-Carlo simulations: 1) random selection of F1 hybrids, 2) selection on phenotypic data, 3) selection on molecular markers. Simulations were performed in agreement with the genetic structure of the experimental population and the linkage mapping data available. For the selection of resistance loci, the selection with molecular markers appeared to be more efficient than the phenotypic selection, that itself was more efficient than random selection. Additional information about the genetic control of the resistance, collected after the selection step demonstrated the importance of preserving wild alleles over the whole genome. Because of this, the 3 scenarios were tested in reverse compared to their efficiency for the selection of resistance loci. When little is known about the QTLs controlling the character to be introgressed, which seems to be the case in fruit breeding, molecular markers could be used to monitor both the selection of target loci and the preservation of wild alleles on the rest of the genome.

The genetic relationships between several genitors used in peach breeding programmes, including two commercial peach cultivars [Prunus persica (L.) Batsch], six peach seed-propagated rootstocks and six accessions of related wild species including Prunus mira, Prunus kansuensis and Prunus davidiana, were studied using 28 SSR markers. The total number of alleles revealed by SSR analysis varied from 3 to 9 with an average of 6.2. The level of heterozygosity ranged from 5% to 58% and was much higher in wild species (27%) than in peach genotypes (16%). Low levels were found in seed-propagated rootstocks 'Bailey', 'Pamirskij 5 ' and 'Rubira (respectively 3.7, 3.8, and 8%) and for autogamous wild species P. kansuensis and P. mira (respectively 4 and 5%). At the opposite, the highest values (from 32 to 58%) were found in allogamous wild species Prunus davidiana. Cluster analysis of these data emphasized the distinction between the peaches and wild-related species, according to their geographical origin. Polymorphism between these two groups reached 85%. Moreover, a total of 89 and 65 alleles were specific to wild species and peach respectively, whereas only 19 were common to both germplasms. Wild species closely related to Prunus persica thus appear as an interesting source of variability for peach. These results provide a soundbasis to manage breeding programmes.

Powdery mildew, caused by Sphaerotheca pannosa var. persicae is one of the most important diseases in European peach orchards. Quantitative trait loci controlling powdery mildew resistance were detected using three related F1, F2 and BC2 populations derived from the cross between the resistant parent P. davidiana clone P1908 and the susceptible peach cultivar Summergrand. Powdery mildew resistance of each population was evaluated under natural exposure, in several locations and over several years. Thirteen QTLs were detected. For nine of them, the favourable allele came from the resistant parent. Five QTLs were consistently detected across the three populations. The F1 hybrid used to produce F2 and BC2 populations had not inherited the favourable allele from P1908 for QTL detected on LG3 and LG8 in F1 population. QTLs were not detected in the corresponding regions in F2 and BC2 populations. In two other genomic areas, significant substitution effects between P1908 alleles were evidenced in the F1 population, but the favourable allele came from Summergrand in the F2 and BC2 populations. Analysis of phenotypic data suggested an important qualitative change in the distribution of powdery mildew resistance after 1996, confirmed by QTL analysis. Indeed, a dramatic decrease of the effect of the major QTL previously detected on LG6 was observed after 1996, while the QTL on LG8 was increasingly involved in the control of powdery mildew resistance. Consequences for peach breeding strategies to improve powdery mildew resistance are discussed.

The potential for introgression of Prunus davidiana, a wild species related to peach, was evaluated with respect to problems of non-Mendelian segregation or suppressed recombination which often hamper breeding processes based on interspecific crosses. Three connected (F1, F2 and BC2) populations, derived from a cross between P. davidiana clone P1908 and the peach cultivar Summergrand were used. The intraspecific map of P. davidiana already established using the F1 progeny was complemented, and two interspecific maps, for the F2 and BC2 progenies, were built with a set of markers selected from the Prunus reference map. With the molecular data collected for the F2 map construction, regions with distorted marker segregation were detected on the genome; one third of all loci deviated significantly from the expected Mendelian ratios. However, some of these distorted segregations were probably not due to the interspecific cross. On linkage group 6, a skewed area under gametic selection was most likely influenced by the self-incompatibility gene of P. davidiana. Using anchor loci, a good colinearity between the three maps built and the Prunus reference map was demonstrated. Comparative mapping also revealed that homologous recombination occurred normally between P. davidiana and the Prunus persica genome. This confirmed the closeness of the two species. Higher recombination rates were generally observed between P. davidiana and P. persica than between Prunus amygdalus and P. persica. The consequences for plant breeding strategy are discussed. The three maps of the F1, F2 and BC2 progenies provide useful tools for QTL detection and marker-assisted selection, as well as for assessing the efficiency of the peach breeding scheme applied to introgress P. davidiana genes into peach cultivated varieties.