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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.

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

Le projet « PRUNUS- Réalités et perspectives de l’écologisation en arboriculture fruitière » a été financé par le programme Pesticides* du ministère de l’environnement sur la période 2013-2015 avec pour objectif d’identifier les effets de verrouillage et les leviers de transition vers une écologisation des pratiques agricoles (réduction des pesticides) dans les vergers de pêchers et d’abricotiers de la basse Vallée du Rhône.

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International audience

Background Diseases caused by Pseudomonas syringae (Ps) are recognized as the most damaging factors in fruit trees with a significant economic and sanitary impact on crops. Among them, bacterial canker of apricot is exceedingly difficult to control due to a lack of efficient prophylactic measures. Several sources of partial resistance have been identified among genetic resources but the underlying genetic pattern has not been elucidated thus far. In this study, we phenotyped bacterial canker susceptibility in an apricot core-collection of 73 accessions over 4 years by measuring canker and superficial browning lengths issued from artificial inoculations in the orchard. In order to investigate the genetic architecture of partial resistance, we performed a genome-wide association study using best linear unbiased predictors on genetic (G) and genetic x year (G × Y) interaction effects extracted from linear mixed models. Using a set of 63,236 single-nucleotide polymorphism markers genotyped in the germplasm over the whole genome, multi-locus and multi-variate mixed models aimed at mapping the resistance while controlling for relatedness between individuals. Results We detected 11 significant associations over 7 candidate loci linked to disease resistance under the two most severe years. Colocalizations between G and G × Y terms indicated a modulation on allelic effect depending on environmental conditions. Among the candidate loci, two loci on chromosomes 5 and 6 had a high impact on both canker length and superficial browning, explaining 41 and 26% of the total phenotypic variance, respectively. We found unexpected long-range linkage disequilibrium (LD) between these two markers revealing an inter-chromosomal LD block linking the two underlying genes. This result supports the hypothesis of a co-adaptation effect due to selection through population demography. Candidate genes annotations suggest a functional pathway involving abscisic acid, a hormone mainly known for mediating abiotic stress responses but also reported as a potential factor in plant-pathogen interactions. Conclusions Our study contributed to the first detailed characterization of the genetic determinants of partial resistance to bacterial canker in a Rosaceae species. It provided tools for fruit tree breeding by identifying progenitors with favorable haplotypes and by providing major-effect markers for a marker-assisted selection strategy. Electronic supplementary material The online version of this article (10.1186/s12870-019-1631-3) contains supplementary material, which is available to authorized users.