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International audience; Genotypic variations in fruit tree architectural and functional traits have been reported but their genetic bases and the existence of common geneticdeterminants have rarely been investigated in wide genetic diversity. We made use of innovative in-eld high-throughput phenotyping on anassociation panel of 241 genotypes to quantify architectural and functional traits on 4-years old apple trees. T-Lidar technology was used for estimatingarchitectural traits (number of branches, tree height, STAR…), airborne thermal and multispectral imagery for assessing canopy temperature (a proxyof transpiration rate) and vegetation indices (NDVI, MCARI2, GNDVI). This dataset was complemented with yield-related traits (number of fruits, averagefruit weight). We explored genome wide associations on 16 traits with high density (275K) genotypic data. GWAS was run with a multi-locus mixedmodel using genetic kinship matrix and assuming different thresholds for SNP signicance: (i) the Bonferroni correction (Bonfth, -logpval > 6.7), (ii) acorrection based on an estimated number of independent SNPs (Bonfcor, -logpval > 5.7) and (iii) value based on common practices (-logpval = 5).Signicant SNPs with -logpval > 5 were detected for most traits with a number of them displaying -logpval above Bonfcor and above Bonfth. One to foursignicant SNPs were identied by variable with a proportion of variance explained by each SNP ranging from 6% to 14% and the total proportion ofvariance explained by all signicant SNPs exceeding up to 30% for the number of branches, STAR, MCARI2, number of fruit and crop load. SNPscontrolling different traits were detected on LG9 (height, STAR, volume) and LG13 (volume, MCARI2, NDVI, GNDVI). Analyses of the LD between SNPsallowed determining possible colocations within regions. Notably, some signicant SNPs were localized in genomic regions previously reported as QTLsfor similar traits in bi-parental population. This suggests their robustness and encourages further investigations.

International audience; Although more than 10.000 apple cultivars have been documented worldwide, modern commercial apple production is dominated by only a fewcultivars. Broadening the genetic diversity used in breeding programs thus appears as a necessity in order to reduce the vulnerability resulting fromgenetic uniformity. In this context, the identication of genetic resources that contain favourable alleles absent or rare in elite material is of primaryimportance for breeders. Harnessing this genetic diversity will probably require several generations of crosses starting from genetic resources, so thatparents carrying the identied favourable alleles are ready to be used in breeding programs. In order to effciently transfer these alleles, we propose touse genomic selection, a breeding approach that aims to estimate the breeding value of selection candidates using only genetic markers information.To do so, apple genetic resources (i.e. old varieties), elite material and hybrids between them have been genotyped and phenotyped so that predictionequations can be developed in order to evaluate the potential of genetic resources. As a preliminary step, these equations were built using data fromeither elite material or genetic resources and prediction accuracies were assessed and compared. To further improve the choice of the individuals usedto build the model, various optimisation algorithms were also used before estimating these accuracies. Given the differences in allele frequencies andlinkage disequilibrium patterns between the two datasets, the predictive ability of these models is expected to differ. One way to account for the differences is to combine these datasets and to use models that allow the estimation of population-specic effects. We will discuss the assets of suchan approach and how it could be effective to evaluate selection candidates. The obtained results should help us identify breeding strategies intendedto effciently transfer interesting alleles from genetic resources into elite material.

Resumen del trabajo presentado a la 10th Rosaceae Genomics Conference (RGC), celebrada de forma virtual del 9 al 11 de diciembre de 2020.

International audience; Finding new solutions to reduce the use of pesticides is a major challenge to move towards productive fruit orchards respectful of the environmentand human health. Breeding of new varieties naturally resistant to pathogens and pests has long been used, but the rapid overcome of geneticresistances is often observed. Induction of resistance by exogenous agents called Plant Resistance Inducers or PRI holds great potential for plantprotection, but their performance in the eld remains variable. The present project explores the added value of combining genetic and inducedresistances in apple for an efficient and sustainable control of apple scab (Venturia inaequalis)and re blight (Erwinia amylovora).For both diseases, protection tests were carried out on a F1 mapping progeny from the cross between two partially resistant genotypes, ‘TN10-8’ and‘Fiesta’, to evaluate the interaction between genetic resistances (QTLs) and PRI-induced resistance. The whole population (~260 individuals) wasphenotyped for scab and re blight resistance under articial inoculation performed two days after pretreatment with acibenzolar-S-methyl (Bion®,Syngenta; a salicylic acid analog) or water (control). The population was also genotyped with the Illumina 20K SNP array.The rst results support the hypothesis of an additive behavior when combining resistance QTLs and PRI effect. Five QTLs have been detected for scabresistance likewise for re blight. Most QTLs detected in PRI-treated population were detected in control population, and PRI treatment appears to onlyslightly modulate QTL allelic effects, except for one QTL in re blight.Molecular mechanisms involved in both, treated and untreated situations are under investigation thanks to gene expression (qPCR) and metabolomic(LC-MS) analyses to better characterize the combination of intrinsic (genetic) and induced resistance at various time after PRI-treatment andinoculation.

International audience; Genomic selection has the potential to increase the efficiency of breeding programs in perennial crops. In apple, genomic predictions have been reported only in a limited number of studies and to our knowledge genomic selection is hardly applied. The very first step to build up an efficient genomic selection program is to develop an experimental design with adequate plant material to test predictions. In apple, this is now made possible with the joint efforts of the European FruitBreedomics Consortium in developing the apple REFPOP, a population dedicated to genomic predictions and genome wide association analyses, along with appropriate genotyping and phenotyping tools. Here, we present the long-term genomic selection apple project built around the apple REFPOP. This population is composed of 570 replicated genotypes planted in six countries and was phenotyped for the first time in 2018 at all six sites for yield, phenology and fruit quality traits. Phenotyping for these and additional traits will be repeated in the coming years. Genotyping data were available through FruitBreedomics for most of the genotypes and were obtained with the combination of a medium, 20K SNP array, and the high-density Axiom® Apple487K SNP Affymetrix array via imputation. We provide insights into the genetic features of the apple REFPOP with a specific focus on linkage disequilibrium and structural patterns. By combining several phenotypic variables recorded across countries and years and high-density genotyping, our goal is to use the apple REFPOP as a training population to predict the potential of applied populations in multiple environments and for multiple traits. To face the increasing complexity of the data collected, machine learning methods will be tested. Finally, we also discuss different strategies to calibrate and implement genomic prediction models into modern, climate-ready breeding programs. This work is partially funded by the EU-H2020 project N°817970 INVITE

International audience; A wealth of previously unknown pedigree information has been generated for apple (Malus × domestica) through recent publications and through an ongoing pedigree identification project using SNP array data. This information has been postulated to be useful in a number of ways for germplasm collections and breeding programs. For example, pedigree information is an important part of genetic characterization of material in germplasm collections. Germplasm collections often seek to preserve cultivars that currently lack commercial relevance but have regional or historical significance or are phenotypically interesting. Pedigree information is often limited on such material. With pedigree information, an accurate genetic structure of these collections can be conveyed to breeders who wish to incorporate novel germplasm into new cultivars.

Despite the availability of whole genome sequences of apple and peach, there has been a considerable gap between genomics and breeding. To bridge the gap, the European Union funded the FruitBreedomics project (March 2011 to August 2015) involving 28 research institutes and private companies. Three complementary approaches were pursued: (i) tool and software development, (ii) deciphering genetic control of main horticultural traits taking into account allelic diversity and (iii) developing plant materials, tools and methodologies for breeders. Decisive breakthroughs were made including the making available of ready-to-go DNA diagnostic tests for Marker Assisted Breeding, development of new, dense SNP arrays in apple and peach, new phenotypic methods for some complex traits, software for gene/QTL discovery on breeding germplasm via Pedigree Based Analysis (PBA). This resulted in the discovery of highly predictive molecular markers for traits of horticultural interest via PBA and via Genome Wide Association Studies (GWAS) on several European genebank collections. FruitBreedomics also developed pre-breeding plant materials in which multiple sources of resistance were pyramided and software that can support breeders in their selection activities. Through FruitBreedomics, significant progresses were made in the field of apple and peach breeding, genetics, genomics and bioinformatics of which advantage will be made by breeders, germplasm curators and scientists. A major part of the data collected during the project has been stored in the FruitBreedomics database and has been made available to the public. This review covers the scientific discoveries made in this major endeavour, and perspective in the apple and peach breeding and genomics in Europe and beyond., This work has been funded under the EU seventh Framework Programme by the FruitBreedomics project No. 265582: Integrated Approach for increasing breeding efficiency in fruit tree crops (http://www.fruitbreedomics.com/).

International audience

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.

Apple and Pear diverged from each other between 5.4 and 21.5 MYA and are believed to share a common genome duplication event between 35 and 50 MYA (Velasco et al. 2010, Wu et al. 2012). Size differences have been observed between the Apple and Pear genomes which are estimated at 527Mb (Pyrus x Bretschneideri Rehd) and 700Mb (Malus x Domestica Borkh) respectively (Wu et al. 2013, Li et al. 2016). The difference in genome size has been accounted for primarily by the proliferation of transposable elements, with the gene space thought to be fairly similar between the two species (Wu et al. 2012). Comparative genomics of the lineage has however, been hampered by the fragmented nature of the reference assemblies. A new chromosome scale assembly was recently produced (Daccord et al. 2017) and now also a chromosome scale assmble of the European Pear (this study), which shows strong collinearity with Apple, greatly facilitating the comparative study of these genomes.

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).