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International audience; As perennial plants, fruit trees must cope, individually, with the fluctuating threat of multiple pathogens over the years. In this long-lasting battle for plant immunity, disease resilience is emerging as a key mechanism for tree survival and fitness. More fundamental research is required to improve our understanding of disease resilience mechanisms, which in turn could be particularly relevant for a more sustainable fruit production. As this approach is novel for that field, we propose i) a clear definition of resilience for fruit producing trees, ii) a methodology for studying its phenotypic components which requires repeated measures of “resilience biomarkers”, iii) to decipher the genetic architecture of resilience components, and iv) an innovative strategy based on high-throughput phenotyping and genomics for identifying resilient genotypes. All in all, disease resilience appears as a meaningful breeding perspective in a context of unprecedented plant protection restrictions.

International audience; Genomic selection (GS) is a breeding approach which exploits genome-wide information and whose unprecedented success has shaped several animal and plant breeding schemes through delivering their genetic progress. This is the first study assessing the potential of GS in apricot (Prunus armeniaca) to enhance postharvest fruit quality attributes. Genomic predictions were based on a F1 pseudo-testcross population, comprising 153 individuals with contrasting fruit quality traits. They were phenotyped for physical and biochemical fruit metrics in contrasting climatic conditions over two years. Prediction accuracy (PA) varied from 0.31 for glucose content with the Bayesian LASSO (BL) to 0.78 for ethylene production with RR-BLUP, which yielded the most accurate predictions in comparison to Bayesian models and only 10% out of 61,030 SNPs were sufficient to reach accurate predictions. Useful insights were provided on the genetic architectureof apricot fruit quality whose integration in prediction models improved their performance, notably for traits governed by major QTL. Furthermore, multivariate modeling yielded promising outcomes in terms of PA within training partitions partially phenotyped for target traits. This provides a useful framework for the implementation of indirect selection based on easy-to-measure traits. Thus, we highlighted the main levers to take into account for the implementation of GS for fruit quality in apricot, but also to improve the genetic gain in perennial species.

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R Markdown script for analyses and raw data presented in the Manuscript Moury et al. 2021, doi: https://doi.org/10.1101/2021.03.03.433745

International audience

Dormancy is a physiological state that plants enter for winter hardiness. Environmental-induced dormancy onset and release in temperate perennials coordinate growth cessation and resumption, but how the entire process, especially chilling-dependent dormancy release and flowering, is regulated remains largely unclear. We utilized the transcriptome profiles of floral buds from fall to spring in apricot (Prunus armeniaca) genotypes with contrasting bloom dates and peach (Prunus persica) genotypes with contrasting chilling requirements (CR) to explore the genetic regulation of bud dormancy. We identified distinct gene expression programming patterns in endodormancy and ecodormancy that reproducibly occur between different genotypes and species. During the transition from endo- to eco-dormancy, 1,367 and 2,102 genes changed in expression in apricot and peach, respectively. Over 600 differentially expressed genes were shared in peach and apricot, including three DORMANCY ASSOCIATED MADS-box (DAM) genes (DAM4, DAM5, and DAM6). Of the shared genes, 99 are located within peach CR quantitative trait loci, suggesting these genes as candidates for dormancy regulation. Co-expression and functional analyses revealed that distinctive metabolic processes distinguish dormancy stages, with genes expressed during endodormancy involved in chromatin remodeling and reproduction, while the genes induced at ecodormancy were mainly related to pollen development and cell wall biosynthesis. Gene expression analyses between two Prunus species highlighted the conserved transcriptional control of physiological activities in endodormancy and ecodormancy and revealed genes that may be involved in the transition between the two stages.

Genomic selection (GS) refers to a selection method which intends to assess individuals according to their genomic values using genome-wide dense markers. Particularly efficient in animal improvement strategies, opening interesting perspective in crops, it is already engaged in perennial species such as apple where, genetic gain was maximized for fruit quality traits quantitatively inherited by comparison with conventional breeding strategy. In the present work, GS was applied on a biparental apricot population (184 individuals) characterized over two consecutive years for phenology (blooming and maturity dates) and fruit quality traits (fruit weight, color, sugar nd acidity content, ethylene production). A ridge regression (RR-BLUP) modelling has been used. The performance of GS was assessed by cross validation using the accuracy defined as the correlation between true phenotypes values and the estimated ones. The effects of markers density and number, training set size and composition as well as the heritability of the investigated traits were evaluated on the accuracy of the model. The main results issued from the two years multi-annual modelling approach are showing that (i) genomic predictions are accurate even with a little number of markers (>100 markers), (ii) the accuracy increases with the training population’s size and with high heritability traits, (iii) and the optimization of the training set improves the performance of genomic selection model. To conclude, a clear interest exists in continuing the evaluation of the genomic selection in biparental apricot populations even for traits that are difficult to measure. The robustness of the approach needs to be tested both on other progenies and on a large set of genetic resources

Apricot, a highly valuable crop is threatened by the growing importance of bacterial canker caused by Pseudomonas syringae. Among the key factors able to control the disease, genetic improvement is a promising measure. The variability of susceptibility on branches and the characterization of genetic determinants through a genome wide association study were thus investigated on a core-collection.73 accessions were annually inoculated in the orchard with an aggressive strain of the bacterium for 4 years. Phenotypic data about the length of both external canker (lgc) and superficial browning (bs) of tissues were collected. The analysis displayed a highly environmental-dependent genetic variation with broad-sense heritabilities of lgc and bs reaching respectively 59% and 78% for the most severe year. Considering the two variance-maximizing years, genetic (G) and genetic x year (GxY) BLUP were predicted for each variable using a linear mixed model. Association analysis were performed with a 63,236 SNP set through both a multi-variate (GEMMA) and a multi-locus genome-wide analysis.By exploiting the between-years (multi-locus model on G and GxY terms) and between-phenotypes (multivariate model on lgc-bs G terms) correlations, 11 significant associations have been detected. Among them, two SNP impacting both lgc and bs expressions over the two studied years and explaining 41% and 31% of the total phenotypic variance were identified on chromosomes 5 and 6. A long-range linkage disequilibrium had been noticed between these two markers suggesting a co-selection effect. The associated SNP reported from this work will open up new opportunities for a Marker-assisted selection strategy.

Apricot, a highly valuable crop is threatened by the growing importance of bacterial canker caused by Pseudomonas syringae. Among the key factors able to control the disease, genetic improvement is a promising measure. The variability of susceptibility on branches and the characterization of genetic determinants through a genome wide association study were thus investigated on a core-collection.73 accessions were annually inoculated in the orchard with an aggressive strain of the bacterium for 4 years. Phenotypic data about the length of both external canker (lgc) and superficial browning (bs) of tissues were collected. The analysis displayed a highly environmental-dependent genetic variation with broad-sense heritabilities of lgc and bs reaching respectively 59% and 78% for the most severe year. Considering the two variance-maximizing years, genetic (G) and genetic x year (GxY) BLUP were predicted for each variable using a linear mixed model. Association analysis were performed with a 63,236 SNP set through both a multi-variate (GEMMA) and a multi-locus genome-wide analysis.By exploiting the between-years (multi-locus model on G and GxY terms) and between-phenotypes (multivariate model on lgc-bs G terms) correlations, 11 significant associations have been detected. Among them, two SNP impacting both lgc and bs expressions over the two studied years and explaining 41% and 31% of the total phenotypic variance were identified on chromosomes 5 and 6. A long-range linkage disequilibrium had been noticed between these two markers suggesting a co-selection effect. The associated SNP reported from this work will open up new opportunities for a Marker-assisted selection strategy.

National audience

International audience; Phenological traits, e.g. dormancy, are mechanisms by which perennial tree species have adapted to stressful conditions that are unfavorable for growth. While there are many mechanisms by which trees adapt and respond to stress, the phenylpropanoid pathway in particular is known to be associated with tree stress response. In this study, Prunus persica (peach) and P. armeniaca (apricot) were used as models to explore the relationship between phenylpropanoids and adaptive trait variation. Concentrations of eight phenylpropanoid intermediates were measured throughout dormancy in floral buds of trees that differed genotypically and phenotypically in chill requirement (peach) and bloom date (apricot). There was a significant interaction effect of time and genotype on the concentration of each of the compounds (mixed ANOVA, P < 0.05). Moreover, concentrations of the flavonoid aglycones, apigenin, kaempferol, and quercetin, dropped precipitously in high chill peach and late flowering apricot, around the endodormancy-ecodormancy transition and at the time when buds began to show signs of blooming (e.g. presence of sepals and petals). These results suggest a potential role of phenylpropanoid intermediates in mediating the resumption of growth and development following winter dormancy. A better understanding of tree responses to stress, will be critical for tree improvement programs aimed at identifying and breeding trees more suitable for rapidly changing environments.

Ce numéro comprend les articles issus du colloque de restitution Ecophyto Recherche « Des outils et des dispositifs pour éclairer les décisions, explorer les possibles et accompagner la transition vers des systèmes économes et multi-performants », qui s’est tenu à Saint-Malo, du 22 au 24 mars 2017; The Prunus project has explored the issue of sustainable orchards (re)design, through an integrative approach articulating the different dimensions of varietal choice, pest management strategies, and larger evolutions within the agrifood system (including not only the economic actors but also extension, research, public policies and consumers). It brought together sociologists, economists, agronomists and geneticists, as well as diverse stakeholders in a socio-historical analysis, farm surveys, and multi-actors workshops for the co-construction of varietal ideotypes. Our analyses show the impact of the constraints set by retailers and intermediaries, in a context of production calendar extension, on the innovation model (fruit ability to be transported and stored and fruit visual aspect), to the expense of environmental and farm viability criteria. Farm surveys show a large variability of practices observed in orchards producing similar levels of yield and suggest that a substantive reduction in pesticide use can be achieved in apricot production. New techniques but also references and exchange arenas should be developed to achieve this. Regarding varietal innovation and cultivars conception, we show that we need to develop multi-criteria approaches. Finally we how how multi-actors approaches help discussing the constraints and criteria of the diverse components of the agrifood system in an ecolologisation perspective; Le projet « Prunus » a exploré la question de la (re)conception de vergers « durables » au travers d’une approche intégrée prenant en compte à la fois le choix variétal, les conduites de cultures et les évolutions plus larges du système « agri-alimentaire » (filières, politiques publiques, recherche, conseil). Il a associé des chercheurs en sciences sociales, en agronomie et en génétique, ainsi que plusieurs acteurs de la filière autour d’une analyse socio-historique, d’enquêtes auprès des arboriculteurs, et enfin de séminaires de co-construction autour de l'innovation variétale. Nos analyses montrent l’impact des contraintes imposées par l’aval, dans un contexte d’allongement des calendriers de production, sur le modèle d’innovation variétale, aux dépens des possibilités de réduction d’intrants et même de la pérennisation du verger et des exploitations. Les résultats des enquêtes indiquent une grande variabilité des pratiques même pour des niveaux de production comparables, et un réel potentiel de réduction de l’utilisation des pesticides en production d’abricot. Il apparait nécessaire de développer de nouveaux leviers techniques mais aussi davantage de références et d’espaces d’échanges sur ces leviers. Le levier variétal reste majeur (notamment sur les maladies), mais il faut privilégier une approche multicritères et non plus le ciblage de caractères ponctuels dans l’innovation variétale. Nous montrons enfin l’intérêt des démarches multi-acteurs pour mettre en discussion les contraintes et critères des différents maillons du système

Le projet « Prunus » a exploré la question de la (re)conception de vergers « durables » au travers d’une approche intégrée prenant en compte à la fois le choix variétal, les conduites de cultures et les évolutions plus larges du système « agri-alimentaire » (filières, politiques publiques, recherche, conseil). Il a associé des chercheurs en sciences sociales, en agronomie et en génétique, ainsi que plusieurs acteurs de la filière autour d’une analyse socio-historique, d’enquêtes auprès des arboriculteurs, et enfin de séminaires de co-construction autour de l'innovation variétale. Nos analyses montrent l’impact des contraintes imposées par l’aval, dans un contexte d’allongement des calendriers de production, sur le modèle d’innovation variétale, aux dépens des possibilités de réduction d’intrants et même de la pérennisation du verger et des exploitations. Les résultats des enquêtes indiquent une grande variabilité des pratiques même pour des niveaux de production comparables, et un réel potentiel de réduction de l’utilisation des pesticides en production d’abricot. Il apparait nécessaire de développer de nouveaux leviers techniques mais aussi davantage de références et d’espaces d’échanges sur ces leviers. Le levier variétal reste majeur (notamment sur les maladies), mais il faut privilégier une approche multicritères et non plus le ciblage de caractères ponctuels dans l’innovation variétale. Nous montrons enfin l’intérêt des démarches multi-acteurs pour mettre en discussion les contraintes et critères des différents maillons du système, The Prunus project has explored the issue of sustainable orchards (re)design, through an integrative approach articulating the different dimensions of varietal choice, pest management strategies, and larger evolutions within the agrifood system (including not only the economic actors but also extension, research, public policies and consumers). It brought together sociologists, economists, agronomists and geneticists, as well as diverse stakeholders in a socio-historical analysis, farm surveys, and multi-actors workshops for the co-construction of varietal ideotypes. Our analyses show the impact of the constraints set by retailers and intermediaries, in a context of production calendar extension, on the innovation model (fruit ability to be transported and stored and fruit visual aspect), to the expense of environmental and farm viability criteria. Farm surveys show a large variability of practices observed in orchards producing similar levels of yield and suggest that a substantive reduction in pesticide use can be achieved in apricot production. New techniques but also references and exchange arenas should be developed to achieve this. Regarding varietal innovation and cultivars conception, we show that we need to develop multi-criteria approaches. Finally we show how multi-actors approaches help discussing the constraints and criteria of the diverse components of the agrifood system in an ecolologisation perspective

National audience