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Additional file 9: Figure S1. Pedigrees linking the founder ‘Calville Rouge’ to all its offspring, over three generations. Cultivar names are in their short version (see Additional file 1: Table 1). The coloring of the name bars indicates the level of information known for the individual(s) in the pedigree: blue, individuals with both parents known; cream, individuals with one parent known; orange, unknown individual with both parents known; dark green, founders. Relationships are represented by black lines as the mother and the father cannot be identified with our data. The figure was drawn using data extracted from Additional file 8 and the Pedimap software [57]

To cope with increasing water scarcity, breeding programs targeting for more efficient crop water use are crucial. This requires comprehensive knowledge of plant responses to drought, including the regulation of water status (by stomatal closure) and water - use efficiency (the ratio of carbon gain to water use). These questions have been scarcely studied in fruit trees, yet are of major economic importance. A main limitation results from the lack of high throughput techniques to characterize the physiological responses of hundreds of trees in the field as required to perform genetic analyses. We screened the diversity of European apple tree responses to drought, by unique combination of hight hroughput and in planta measurements applied on two core - collections in Montpellier (France) and Bologna (Italy), respectively. A progressive soil water deficit was ensured and continuously monitored in both orchards, through summer irrigation withholding. In the whole collections (>250 varieties), a semi-empirical index (IPL index), computed from chlorophyll fluorescence measurements, was used as an indicator of leaf photosynthesis, whereas the variability of stomatal regulation and canopy structure was characterized by airborne imagery. The validity of high-throughput indices was assessed through fine measurements of water potential, stomatal conductance and photosynthesis on 6 varieties common to both collections. A large variability of IPL index was observed, with highly significant effects of the genotype and watering scenario (well-watered vs water stress). A genome wide association study (GWAS) was undertaken to identify the genomic regions controlling the variations detected. In parallel, the effect of interaction between Genotype and Environment (GxE) was dissected to highlight contrasted strategies of water use under drought across the varieties studied.

Acronyme de láffiliation = {INRA, INRA, INRA, , , INRA, , INRA, , , INRA, INRA}, Public visé = {Scientifique}, Type de lúnité = {UMR, UMR, UMR, , , UMR, , UMR, , , UMR, UMR}, Langue du titre = {eng}, Type dáctes = {Présentation orale}, Ville de lúnité = {Beaucouzé, Beaucouzé, Beaucouzé, , , Montpellier, , Montpellier, , , Beaucouzé, Beaucouzé, Laboratoire de lúnité = {UMR : Institut de Recherche en Horticulture et Semences, Beaucouzé, UMR : Institut de Recherche en Horticulture et Semences, Beaucouzé, UMR : Institut de Recherche en Horticulture et Semences, Beaucouzé, , , UMR : Amélioration Génétique et Adaptation des Plantes méditerranéennes et Tropicales, Montpellier, , UMR : Amélioration Génétique et Adaptation des Plantes méditerranéennes et Tropicales, Montpellier, , , UMR : Institut de Recherche en Horticulture et Semences, Beaucouzé, UMR : Institut de Recherche en Horticulture et Semences, Beaucouzé, Date de fin de l\'évenement = {2018-06-30; International audience; A number of European apple cultivars are old, some of them dating back to the Renaissance, Middle Ages or even earlier. Many other cultivars have been developed during subsequent times. In order to decipher the relationships that link some of these old cultivars, whole-genome SNP data (~ 250K) for over 1400 genotypes were analyzed to infer first-degree relationships and reconstruct pedigrees. We used simple exclusion tests based on a count of Mendelian error to identify up to a thousand potential parent-offspring duos, including 295 complete parent-offspring trios and a hundred duos that could be oriented. grand-parents for some missing parents could also be inferred. Combining all this information allowed us to reconstruct pedigrees (up to 6 generations) highlighting the central role of major founders such as ‘Reinette Franche’, ‘Margil’, and ‘Alexander’. Haplotypes were deduced from genotypic data and pedigrees, and used to measure haplotype sharing between supposedly unrelated cultivars, allowing investigating further links between them.To our knowledge, such a large analysis to reconstruct multigeneration pedigrees involving (very) old cultivars selected over such time has never before been performed in perennial fruit species.

Background: The amount and structure of genetic diversity in dessert apple germplasm conserved at a European level is mostly unknown, since all diversity studies conducted in Europe until now have been performed on regional or national collections. Here, we applied a common set of 16 SSR markers to genotype more than 2,400 accessions across 14 collections representing three broad European geographic regions (North + East, West and South) with the aim to analyze the extent, distribution and structure of variation in the apple genetic resources in Europe. Results: A Bayesian model-based clustering approach showed that diversity was organized in three groups, although these were only moderately differentiated (FST = 0.031). A nested Bayesian clustering approach allowed identification of subgroups which revealed internal patterns of substructure within the groups, allowing a finer delineation of the variation into eight subgroups (FST = 0.044). The first level of stratification revealed an asymmetric division of the germplasm among the three groups, and a clear association was found with the geographical regions of origin of the cultivars. The substructure revealed clear partitioning of genetic groups among countries, but also interesting associations between subgroups and breeding purposes of recent cultivars or particular usage such as cider production. Additional parentage analyses allowed us to identify both putative parents of more than 40 old and/or local cultivars giving interesting insights in the pedigree of some emblematic cultivars. Conclusions: The variation found at group and subgroup levels may reflect a combination of historical processes of migration/selection and adaptive factors to diverse agricultural environments that, together with genetic drift, have resulted in extensive genetic variation but limited population structure. The European dessert apple germplasm represents an important source of genetic diversity with a strong historical and patrimonial value. The present work thus constitutes a decisive step in the field of conservation genetics. Moreover, the obtained data can be used for defining a European apple core collection useful for further identification of genomic regions associated with commercially important horticultural traits in apple through genome-wide association studies. This work has been partly funded under the EU seventh Framework Programme by the FruitBreedomics project N°265582: “Integrated approach for increasing breeding efficiency in fruit tree crops”. Genotyping of the Spanish collection was partially funded by INIA, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (project grant no RF2004-008-C03-00). Genotyping of the Swiss collection was funded by the Swiss Federal Office for Agriculture. Genotyping of the French collection was funded by the FRB, ‘Fondation pour la Recherche sur la Biodiversité’. Initial genotyping of the UKNFC material was funded by the UK Depart for the Environment Food and Rural Affairs (Defra), grant GC0140. Providing of VNIISPK material (DNA isolation and delivery) have been done with support of Russian Scientific Fund, Project 14- 1600127. JU has been partially supported by an Early Stage Research Fellowship of the Institute of Advanced Studies (University of Bologna).

MareyMap plot of TxE linkage map. Vertical bars indicate the putative position of the centromere. The solid line represents the recombination rate plotted along the 8 pseudomolecules calculated using the cubic spline method. (PDF 236Â kb)

Anchoring of the peach scaffolds to the three genetic maps. Colored bars represent the 8 linkage groups: pink for PxF, purple for TxE and blue for CxA. WGS scaffolds were positioned in each pseudomolecule (Pp01 to Pp08) with the corresponding genetic markers and are depicted in three different colors (dark blue, pink and pale blue); genetic markers are in the same colors of the corresponding WGS scaffolds. The zero (0) denotes the six scaffolds placed with random orientation along the pseudomolecules. The asterisk (*) indicates the two scaffolds with random order. The crosshatch (#) indicates the two scaffolds with the wrong order in Peach v2.0 that need to be inverted in a future release. (PDF 495Â kb)

MareyMap plot of CxA linkage map. Vertical bars indicate the putative position of the centromere. The solid line represents the recombination rate plotted along the 8 pseudomolecules calculated using the cubic spline method. (PDF 233Â kb)

MareyMap plot of PxF linkage maps (including the F1 and recurrent parent maps). Vertical bars indicate the putative position of the centromere. The solid line represents the recombination rate plotted along the 8 pseudomolecules calculated using the cubic spline method. (PDF 405Â kb)

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