Biology subjects

de Miguel, M.

Publications and source records attributed to de Miguel, M..

6 recordsLinked to original sources

bioRxiv2026

Whole-genome sequencing data of a diverse grapevine germplasm collection maintained in Bordeaux, France

Grapevine (Vitis vinifera) is one of the worlds most economically important fruit crops and a model species for perennial fruit tree genetics and genomics. The extensive genetic diversity found in cultivated and wild Vitis species provides a valuable resource for studies of domestication, adaptation, trait evolution, and breeding. This article presents a standardized whole-genome variant dataset comprising 547 grapevine accessions maintained in the INRAE Bordeaux grapevine germplasm collection, including 397 domesticated V. vinifera cultivars and 150 wild Vitis accessions. Whole-genome sequencing data were generated at a target sequencing depth of approximately 20x, and sequence variants were identified using a standardized Genome Analysis Toolkit (GATK) workflow against the reference genome PN40024v4 (40X). Variant discovery was carried out simultaneously across the complete sample set to ensure consistent genotype calling. All accessions were sequenced using the same technology and processed using the same reference genome, sequence alignment, variant-calling, and filtering workflow to produce a standardized variant dataset comprising ca. 9.1M SNPs and 0.77M INDELs. The resulting VCF files provide a harmonized genomic resource that can be readily reused for studies of grapevine genetics, germplasm characterization, population genomics, comparative genomics, genome-wide association studies, and the development and benchmarking of bioinformatic methods. SPECIFICATIONS TABLE O_TBL View this table: org.highwire.dtl.DTLVardef@14f2b12org.highwire.dtl.DTLVardef@94b5acorg.highwire.dtl.DTLVardef@1232f80org.highwire.dtl.DTLVardef@1038e85org.highwire.dtl.DTLVardef@81ec71_HPS_FORMAT_FIGEXP M_TBL C_TBL VALUE OF THE DATAO_LIThis dataset provides whole-genome raw sequencing for 118 wild Vitis accessions originating from North America and Asia and a sequencing-derived variant data for these accessions and 429 Vitis vinifera cultivars and wild accessions from the INRAE Bordeaux germplasm collection, previously published by Dong et al. 2023[1]. The dataset captures genetic variation across a total of 547 grapevine accessions, including domesticated and wild grapevine germplasm using a common variant-calling pipeline, facilitating direct comparisons among accessions. C_LIO_LIThe inclusion of wild Vitis species together with cultivated grapevine accessions provides a resource for studies of grapevine diversity, domestication, phylogenetic relationships, and comparative genomics. The dataset enables the investigation of genetic variation across multiple Vitis species using a standardized set of genomic variants. C_LIO_LIThe variant call format (VCF) file can be reused for population genetics, phylogenetic analyses, genetic diversity assessments, introgression analyses, and the identification of genomic regions of interest. The dataset is compatible with widely used bioinformatics software and can be integrated with other publicly available grapevine genomic resources. C_LIO_LIThis dataset constitutes a genomic resource for grapevine breeding and conservation research. Researchers can use these data to identify genetic diversity in wild relatives, compare allelic variation between cultivated and wild germplasm, investigate candidate loci associated with traits of interest, and support the management and characterization of grapevine germplasm collections. C_LI

genomics↗

bioRxiv2026

Non-plastic gene expression underlies root phenotypes involved in drought adaptation in Vitis spp.

Drought is a major abiotic stress threatening plant productivity and agricultural sustainability, yet the molecular mechanisms underlying adaptive root responses to water deficit in the water use strategies continuum remain insufficiently understood, particularly in perennial crops. In this study, we explored drought responses in nine accessions belonging to three wild Vitis species (V. acerifolia, V. candicans, and V. doaniana) displaying variying drought-response strategies. Plants were subjected to moderate drought stress (40% soil water content) for three weeks under greenhouse conditions. By integrating physiological, metabolic, and transcriptomic analyses, we aimed to identify both conserved and species-specific mechanisms associated with drought adaptation. Differential expression analyses revealed a conserved core set of drought-responsive genes shared among species, including genes involved in abscisic acid signaling, reactive oxygen species detoxification, solute transport, and plant defense. In parallel, each species exhibited distinct transcriptional and metabolic signatures reflecting alternative adaptive strategies related to osmoregulation, and oxidative stress mitigation. Weighted gene co-expression network analysis (WGCNA) further revealed significant associations between constitutive, non-plastic gene expression and root phenotypic traits. Overall, our findings demonstrate that wild Vitis species rely on both conserved stress-responsive pathways and species-specific constitutive regulation to cope with drought stress. These results highlight the importance of root-associated traits and intrinsic regulatory networks in shaping drought adaptation and provide new targets for the development of drought-resilient grapevine rootstocks.

plant biology↗

bioRxiv2025

A higher load of deleterious mutations has a detrimental effect on tree growth in maritime pine

A high proportion of deleterious mutations in the genome is predicted to cause a reduction in fitness known as genetic load. In plants, most studies focus on how detrimental mutations increase as a consequence of population bottlenecks, for instance in cultivated species as a negative outcome of domestication or at the margin of species ranges. However, the actual adverse effect of genetic load on individual phenotypes remains little characterised, especially in wild plant species with large populations and long lifespans. We estimated genetic load based on genomic data in populations of the conifer maritime pine (Pinus pinaster, Ait.), and examined its association with phenotypic traits related to growth, phenology, and water-use efficiency measured under common garden conditions. Our results revealed a strong negative correlation between genetic load and tree height on the Mediterranean island of Corsica, thus suggesting a negative cumulative effect of deleterious mutations on tree growth at the regional scale. Our study is one of the first to experimentally demonstrate adverse phenotypic effects (reduced tree growth) of genetic load in a long-lived plant.

evolutionary biology↗

bioRxiv2021

Extreme climatic events but not environmental heterogeneity shape within-population genetic variation in maritime pine

How evolutionary forces interact to maintain quantitative genetic variation within populations has been a matter of extensive theoretical debates. While mutation and migration increase genetic variation, natural selection and genetic drift are expected to deplete it. To date, levels of genetic variation observed in natural populations are hard to predict without accounting for other processes, such as balancing selection in heterogeneous environments. We aimed to empirically test three hypotheses: (i) admixed populations have higher quantitative genetic variation due to introgression from other gene pools, (ii) quantitative genetic variation is lower in populations from harsher environments (i.e. experiencing stronger selection), and (iii) quantitative genetic variation is higher in populations from spatially heterogeneous environments. We used phenotypic measurements of five growth, phenological and functional traits from three clonal common gardens, consisting of 523 clones from 33 populations of maritime pine (Pinus pinaster Aiton). Populations from harsher climates (mainly colder areas) showed lower genetic variation for height in the three common gardens. Surprisingly, we did not find any association between within-population genetic variation and environmental heterogeneity or population admixture for any trait. Our results suggest a predominant role of natural selection in driving within-population genetic variation, and therefore indirectly their adaptive potential.

evolutionary biology↗

bioRxiv2020

Polygenic adaptation and negative selection across traits, years and environments in a long-lived plant species (Pinus pinaster Ait.)

A decade of association studies in multiple organisms suggests that most complex traits are polygenic; that is, they have a genetic architecture determined by numerous loci distributed across the genome, each with small effect-size. Thus, determining the degree of polygenicity and its variation across traits, environments and years is useful to understand the genetic basis of phenotypic variation. In this study, we applied multilocus approaches to estimate the degree of polygenicity of fitness-related traits in a long-lived plant (Pinus pinaster Ait., maritime pine) and to analyze how polygenicity changes across environments and years. To do so, we evaluated five categories of fitness-related traits (survival, height, phenology-related, functional, and biotic-stress response traits) in a clonal common garden network, planted in contrasted environments (over 12,500 trees). First, most of the analyzed traits showed evidence of local adaptation based on QST-FST comparisons. Second, we observed a remarkably stable degree of polygenicity, averaging 6% (range of 0-27%), across traits, environments and years. As previously suggested for humans, some of these traits showed also evidence of negative selection, which could explain, at least partially, the high degree of polygenicity. The observed genetic architecture of fitness-related traits in maritime pine supports the polygenic adaptation model. Because polygenic adaptation can occur rapidly, our study suggests that current predictions on the capacity of natural forest tree populations to adapt to new environments should be revised, which is of special relevance in the current context of climate change.

genetics↗

bioRxiv2019

Genetic basis of susceptibility to Diplodia sapinea and Armillaria ostoyae in maritime pine

Forest ecosystems are increasingly challenged by extreme events, e.g. drought, storms, pest and pathogenic fungi outbreaks, causing severe ecological and economical losses. Understanding the genetic basis of adaptive traits in tree species is of key importance to preserve forest ecosystems, as genetic variation in a trait (i.e. heritability) determines its potential for human-mediated or evolutionary change. Maritime pine (Pinus pinaster Aiton), a conifer widely distributed in southwestern Europe and northwestern Africa, grows under contrasted environmental conditions promoting local adaptation. Genetic variation at adaptive phenotypes, including height, growth phenology and susceptibility to two fungal pathogens (Diplodia sapinea and Armillaria ostoyae) and an insect pest (Thaumetopoea pityocampa), were assessed in a range-wide clonal common garden of maritime pine. Broad-sense heritability was significant for height (0.219), growth phenology (0.165-0.310) and pathogen susceptibility (necrosis length caused by D. sapinea, 0.152; and by A. ostoyae, 0.021) measured after inoculation under controlled conditions, but not for pine processionary moth incidence in the common garden. The correlations of trait variation among populations revealed contrasting trends for pathogen susceptibility to D. sapinea and A. ostoyae with respect to height. Taller trees showed longer necrosis length caused by D. sapinea while shorter trees were more affected by A. ostoyae. Moreover, maritime pine populations from areas with high summer temperatures and frequent droughts were less susceptible to D. sapinea but more susceptible to A. ostoyae. Finally, an association study using 4,227 genome-wide SNPs revealed several loci significantly associated to each trait (range of 3-26), including a possibly disease-induced translation initiation factor, eIF-5. This study provides important insights to develop genetic conservation and breeding strategies integrating species responses to biotic stressors.

genetics↗