Biology subjects

Costes, E.

Publications and source records attributed to Costes, E..

6 recordsLinked to original sources

bioRxiv2025

Genomic insights into the local adaptation of spontaneously occurring populations of olive trees (Olea europaea ssp. europaea var. sylvestris) in the Mediterranean Basin

Living organisms are increasingly threatened by significant environmental changes, primarily driven by human-induced global alterations. Understanding and forecasting species adaptive responses to these environmental changes is therefore crucial for enhancing conservation efforts. In the Mediterranean Basin (MB), the average temperature is rising at a rate 20% faster than the global average, placing regional biodiversity at heightened risk. The study of local adaptation is thus particularly relevant. In the western MB, spontaneously occurring olive populations consist of both wild olives and admixed resulting of crop-to-wild gene flow. The wild is likely harbouring adaptive genetic variation shaped by local environmental pressures. In this study, we analysed target genomic sequencing data from spontaneously occurring populations (comprising both wild and admixed trees) as well as cultivated olive trees. We performed selective sweep and GEA analyses in wild olives to identify genomic regions associated with environmental variables. Our findings identified signatures of adaptation particularly associated with precipitation and temperature. Notably, admixed individuals retained many wild candidate SNPs in their genomes suggesting that they might retain a certain level of adaptation to their local environment. Those results are in line with recent studies suggesting hybrids could adapt more rapidly to novel environments than their parental populations. Key-words: Local adaptation, selective sweep detection, crop-to-wild gene flow, Olea europaea L., population genomics, genome-environment association

evolutionary biology↗

bioRxiv2024

Genome-wide association analysis of flowering date in a collection of cultivated olive tree

1.Flowering date in perennial fruit trees is an important trait for fruit production. Depending on the winter and spring temperatures, flowering of olive may be advanced, delayed, or even suppressed. Deciphering the genetic control of flowering date is thus key to help selecting cultivars better adapted to the current climate context. Here, we investigated the genetic determinism of full flowering date stage in cultivated olive based on capture sequencing data of 318 genotypes from the worldwide olive germplasm bank of Marrakech, Morocco. The genetic structure of this collection was organized in three clusters that were broadly attributed to eastern, central, and western Mediterranean regions, based on the presumed origin of genotypes. Flowering dates, collected over seven years, were used to estimate the genotypic best linear unbiased predictors, which were then analyzed in a genome-wide association study. Loci with small effects were significantly associated with the studied trait, by either a single- or a multi-locus approach. The three most robust loci were located on chromosomes 01 and 04, and on a scaffold, and explained 7.1%, 6.2%, and 6.5 % of the trait variance, respectively. A significantly higher accuracy in the best linear unbiased predictors of flowering date prediction was reported with Ridge-compared to LASSO-based genomic prediction model. Along with genomic association results, this suggests a complex polygenic determinism of flowering date, as seen in many other fruit perennials. These results and the screening of associated regions for candidate genes open perspectives for further studies and breeding programs targeting flowering date.

genetics↗

bioRxiv2023

Genomic evidence of genuine wild versus admixed olive populations evolving in the same natural environments in western Mediterranean Basin

Admixtures between wild animals and plants and their domesticated relatives are widely documented. This can have positive or negative impacts on the evolution of admixed populations in natural environments, yet the phenomenon is still misunderstood in long-lived woody species, contrary to short-lived crops. Wild olive Olea europaea L. occurs in the same eco-geographical range as domesticated olive, i.e. the Mediterranean Basin (MB). Moreover, it is an allogamous and anemophilous species whose seeds are disseminated by birds, i.e. factors that drive gene flow between crops and their wild relatives. Here we investigated the genetic structure of western MB wild olive populations in natural environments assuming a homogenous gene pool with limited impact of cultivated alleles, as previously suggested. We used a target sequencing method based on annotated genes from the Farga reference genome to analyze 27 western MB olive tree populations sampled in natural environments in France, Spain and Morocco. We also target sequenced cultivated olive tree accessions from the Worldwide Olive Germplasm Bank of Marrakech and Porquerolles and from an eastern MB wild olive tree population. We combined PCA, sNMF, pairwise Fst and TreeMix and clearly identified genuine wild olive trees throughout their natural distribution range along a north-south gradient including, for the first time, in southern France. However, contrary to our assumption, we highlighted more admixed than genuine wild olive trees. Our results raise questions regarding the admixed population evolution pattern in this environment, which might be facilitated by crop-to-wild gene flow.

evolutionary biology↗

bioRxiv2021

Unraveling the role of MADS transcription factor complexes in apple tree dormancy using sequential DAP-seq

BackgroundThe effect of global warming on dormancy and flowering patterns of crop trees threatens world-wide fruit production and food security. In Rosaceous tree species, it is believed that a group of genes encoding MADS transcription factors (TFs) controls temperature-mediated dormancy cycle. These genes are similar to SHORT VEGETATIVE PHASE (SVP) from Arabidopsis thaliana and referred as DORMANCY-ASSOCIATED MADS-BOX (DAM) genes. ResultsBy making use of apple tree (Malus x domestica) as a model for Rosaceous species, we have investigated the function of MADS TFs during the dormancy cycle. We found that MdDAM and other dormancy related MADS TFs form multimeric complexes with MdSVPa, and that MdSVPa is essential for the transcriptional complex activity. Then, for the first time in non-model plant species, we performed sequential DNA Affinity Purification sequencing (seq-DAP-seq) to define the genome-wide binding sites of these MADS TF complexes. Target genes associated with the binding sites were identified by combining seq-DAP-seq data with transcriptomics datasets obtained by the inducible glucocorticoid receptor expression system, and reanalyzing preexisting data related to dormancy cycle in apple trees. ConclusionWe have determined a gene regulatory network formed by MdSVPa-containing complexes that regulate the dormancy cycle in apple trees in response to environmental cues. Key genes identified with our genomic approach and the elucidated regulatory relationships provide leads for breeding fruit trees better adapted to changing climate conditions. Moreover, we provide novel molecular evidence on the evolutionary functional segregation between DAM and SVP proteins in the Rosaceae family.

plant biology↗

bioRxiv2019

Impact of within-tree organ distances on floral induction and fruit growth in apple tree: implication of carbon and gibberellin organ contents

In plants, organs are inter-dependent for growth and development. Here, we aimed to investigate the distance at which interaction between organs operates and the relative contribution of within-tree variation in carbohydrate and hormonal contents on floral induction and fruit growth, in a fruit tree case study. Manipulations of leaf and fruit numbers were performed in two years on Golden delicious apple trees, at the shoot or branch scale or one side of Y-shape trees. For each treatment, floral induction proportion and mean fruit weight were recorded. Gibberellins content in shoot apical meristems, photosynthesis, and non-structural carbohydrate concentrations in organs were measured. Floral induction was promoted by leaf presence and fruit absence but was not associated with non-structural content in meristems. This suggests a combined action of promoting and inhibiting signals originating from leaves and fruit, and involving gibberellins. Nevertheless, these signals act at short distance only since leaf or fruit presence at long distances had no effect on floral induction. Conversely, fruit growth was affected by leaf presence even at long distances when sink demands were imbalanced within the tree, suggesting long distance transport of carbohydrates. We thus clarified the inter-dependence and distance effect among organs, therefore their degree of autonomy that appeared dependent on the process considered, floral induction or fruit growth.

plant biology↗

bioRxiv2018

MuSCA: a multi-scale model to explore carbon allocation in plants

Background and aimsCarbon allocation in plants is usually represented at a specific spatial scale, peculiar to each model. This makes the results obtained by different models, and the impact of their scale of representation, difficult to compare. In this work we developed a Multi Scale Carbon Allocation model (MuSCA) that can be applied at different, user-defined, topological scales of a plant, and used to assess the impact of each spatial scale on simulated results and computation time.\n\nMethodsModel multi-scale consistency and behavior were tested by applications on three realistic apple tree structures. Carbon allocation was computed at five spatial scales, spanning from the metamer (the finest scale, used as a reference) up to 1st order branches, and for different values of a sap friction coefficient. Fruit dry mass increments were compared across spatial scales and with field data.\n\nKey ResultsThe model showed physiological coherence in representing competition for carbon assimilates. Results from intermediate values of the friction parameter best fitted the field data. For these, fruit growth simulated at the metamer scale (considered as a reference) differed from about 1% at growth unit scale up to 35% at first order branch scale. Generally, the coarser the spatial scale the more fruit growth diverged from the reference and the lower the obtained within-tree fruit growth variability. Coherence in the carbon allocated across scales was also differently impacted, depending on the tree structure considered. Decreasing the topological resolution reduced computation time up to four orders of magnitude.\n\nConclusionsMuSCA revealed that the topological scale has a major influence on the simulation of carbon allocation, suggesting that this factor should be carefully evaluated when using different carbon allocation models or comparing their results. Trades-off between computation time and prediction accuracy can be evaluated by changing topological scales.

plant biology↗