Biology subjects

Berard, A.

Publications and source records attributed to Berard, A..

13 recordsLinked to original sources

bioRxiv2026

Intensive pine plantation management shapes infectious agent communities in the generalist rodent Apodemus sylvaticus, with consequences for zoonotic hazard

Land use change is widely recognized as a major driver of emerging zoonotic diseases. Yet, while forest plantations are expanding worldwide, their consequences on the circulation of infectious agents in wildlife remain poorly understood. We investigated how native pine plantations and broadleaved habitats shape rodent-associated infectious hazard in the generalist wood mouse (Apodemus sylvaticus), in southwestern France. Using a multi-season survey, we screened 424 wood mice for a broad range of infectious taxa and compared infection probability and infected-host abundance among pine plantation edges, broadleaved hedgerows embedded within pine plantations and broadleaved forests. Using a combination of linear mixed model and joint species distribution modelling, we tested whether infectious hazard differed between pine plantations and broadleaved forests, whether broadleaved hedgerows shifted these patterns towards those observed in broadleaved forests, and how these habitat-related patterns varied across seasons. We detected 22 potentially infectious taxa, including nine recognized zoonotic bacteria. Season strongly influenced infectious patterns, while habitat effects were taxa and season dependent. In spring, pine plantation edges increased infection probability for Bartonella grahamii and Neoerhlichia mikurensis compared to broadleaved forest, but their strong negative effect on wood mouse abundance resulted in consistently lower infected-host abundance for most infectious taxa. Broadleaved hedgerows showed distinct and season-dependent patterns with infectious profiles resembling those of pine edges in spring, but with higher infectious hazard than both other habitats for several taxa in autumn. Our results highlight that habitat effects on infectious hazard cannot be inferred from infection probability alone. Pine plantations may reduce rodent-associated zoonotic hazard through their strong negative effect on host abundance, despite increasing infection probability for some agents. Forest diversification and restoration initiatives, such as broadleaved hedgerows here, may have unforeseen epidemiological consequences, underscoring the need to integrate disease ecology into forest management and restoration to anticipate variation in zoonotic risks, while maximizing ecological benefits.

ecology↗

bioRxiv2026

Development and application of SNP markers to facilitate DUS testing in tomato

Variety registration in Europe requires the evaluation of Distinction, Uniformity, and Stability (DUS) based on multi-environment trials and extensive phenotyping. The integration of molecular markers into DUS testing offers opportunities to increase efficiency and reduce costs, particularly in tomato (Solanum lycopersicum L.), a species characterized by rapid varietal turnover. We developed a high-density SNP genotyping resource targeting gene-rich regions across the tomato genome and applied it to a panel of 300 varieties registered over the past five decades. Temporal patterns of genetic diversity were assessed and compared with those observed in a collection of heirloom accessions predating 1970. Genome-wide association studies (GWAS) were conducted for 50 DUS traits to identify marker-trait associations and evaluate the potential of SNPs to complement phenotypic descriptors. Detected associations were compared with previously reported genes and quantitative trait loci (QTLs), enabling the validation of known loci and the identification of novel candidate genomic regions underlying trait variation. Finally, we assessed the discriminatory power of selected subsets of informative SNPs for variety distinction and grouping. Our results demonstrate the potential of integrating genomic and phenotypic data to enhance the robustness, resolution, and scalability of DUS testing in tomato.

Plant Biology↗

bioRxiv2026

Linkage and association mapping coupled with pan-genome analyses of Vat homologs reveal QTLs and alleles for aphid resistance in melon

Aphids threaten crop productivity through phloem feeding and the transmission of plant viruses. Aphis gossypii, in particular, is a widespread and damaging pest of worldwide cultivated melon. Resistance to its emerging CUC1 clone in Europe remains poorly characterized. Here, we dissected the genetic architecture of melon resistance to CUC1 using complementary traits that capture multiple stages of the aphid-melon interaction: plant attractiveness to aphids, acceptance, aphid colonization, and multiplication. Genome-wide association studies (GWAS) in a diversity panel of 174 accessions identified a quantitative trait locus (QTL) for attractiveness on chromosome 6, while analyses in a complementary panel of 212 accessions revealed QTLs for plant acceptance by aphids on chromosomes 3, 8, and 12. Colonization and multiplication traits further highlighted resistance QTLs on chromosomes 5 and 12, the latter supported by both SNP-based GWAS and bulk-segregant analysis. Pan-NLRome k-mer- and graph-based GWAS, together with Vat presence/absence association analyses, provided allele-level resolution of the QTL on chromosome 5, corresponding to the Vat region. Leveraging allelic diversity at this locus, we functionally characterized 20 Vat homologs with four R65aa motifs within their leucine-rich repeat (LRR) domain and demonstrated the capacity of 4R65aa-type Vat alleles to confer clone-specific resistance. Resistance-conferring alleles limited virus multiplication, such as Cucumber mosaic virus (CMV), when transmitted by five A. gossypii clones, including CUC1. Together, our results revealed multiple genetic determinants underlying quantitative resistance to the A. gossypii CUC1 clone in melon and highlighted the central role of Vat homologs in resistance to both A. gossypii and the viruses it vectors. These findings provide strategic targets for pyramiding resistance loci acting at different stages of the pest life cycle to enhance durable protection against these biotic threats.

genetics↗

bioRxiv2026

Broadleaved hedgerows as complementary habitats for small mammals in pine plantation landscapes

O_LIThe global decline of natural forests is accompanied by a rapid expansion of commercial tree plantations, which are expected to further increase to meet growing demand for wood products. However, planted forests generally support lower biodiversity than natural forests, particularly when monospecific and intensively managed. In this context, broadleaved hedgerows have been proposed as a nature-based solution to enhance biodiversity within conifer-dominated plantation landscapes. Such features may be especially beneficial for small mammals, including rodents and shrews, which are key contributors to forest ecosystem functioning. However, their effects on small mammal communities remain largely unquantified. C_LIO_LIHere, we assessed variation in small mammal communities among habitat types within a native pine plantation-dominated landscape in southwestern France. Using a multi-year, multi-season survey, we compared species richness and abundance among plantation edges, broadleaved hedgerows embedded within plantations and natural broadleaved forests. We further tested whether environmental descriptors of hedgerow sites influenced dominant species and whether seasonal and interannual demographic dynamics modified habitat-related patterns. C_LIO_LIPine plantation edges and broadleaved hedgerows supported lower small mammal species richness than natural broadleaved forests and were dominated by two habitat generalists, Apodemus sylvaticus and Crocidura russula. This pattern was driven by the near absence of the forest specialist Clethrionomys glareolus. Hedgerows did not increase species richness relative to plantations, but provided favourable habitat for A. sylvaticus, which was scarce in pine plantation, while supporting fewer C. russula. Variation in hedgerow structure and composition further influenced A. sylvaticus abundance, while seasonal and interannual rodent population dynamics modulated habitat-related differences. C_LIO_LIOur results indicate that intensively managed pine plantations act as environmental filters, excluding forest-associated small mammals. While broadleaved hedgerows benefited one species, their capacity to restore forest-specialist communities was limited without broader landscape-scale interventions. These findings highlight both the ecological benefits and constraints of edge-based habitat interventions and provide guidance for designing and evaluating biodiversity-oriented management in plantation landscapes. C_LI

ecology↗

bioRxiv2025

Identifying a Vaginal Microbiome-Derived Selective Antibiotic Metabolite via Microbiome Pharmacology Analysis

The vaginal microbiome plays a critical role in maintaining immune and epithelial homeostasis in the female reproductive tract. Bacterial Vaginosis (BV) is deleterious to female health, causing the loss of beneficial Lactobacillus species, overgrowth of anaerobic taxa, changes in vaginal pH, breakdown of protective mucins and epithelial barriers, and activation of the immune system. Treatment with gel-based antibiotics (Metronidazole or Clindamycin) resolves BV for 85% of patients, but 50% of those cases recur, indicating a need to identify strategies for overcoming antibiotic resistance and achieving a more durable response. Here, we developed a systems biology approach termed Microbiome Pharmacology Analysis to characterize the antibiotic potential of vaginal microbes, their metabolites and functions, via computational fusion of human cohort multi-omics and post-drug perturbation transcriptomic profiles. We focused on Clindamycin and Metronidazole as candidate drugs and screened 780 vaginal microbiome-drug mimicry candidates to identify candidate taxa and metabolites with antibiotic potential. We demonstrate experimentally that Lactobacillus crispatus-derived Hydroxyisocaproate (HICA) selectively kills Gardnerella vaginalis and that HICA enhances epithelial barrier integrity in a human vagina-on-a-chip system. Our work demonstrates the first use of Pharmacobiome Analysis, for discovering novel, selective antibiotic metabolites for BV with implications for charting the full pharmacologic potential of the vaginal microbiome.

microbiology↗

bioRxiv2025

Intra-specific NLR allelic diversity and genomic landscape for plant resistance association studies

The identification of nucleotide-binding domain leucine-rich repeat receptor genes (NLRs) across multiple accessions is essential to capture their genetic diversity within a plant species. Using Nanopore adaptive sampling and de novo assembly, we accurately reconstructed the NLR regions across 143 Cucumis melo accessions representing diverse botanical groups and geographical origins. NLR annotation evidenced diverse cluster architectures and unexpected variation in NLR content across accessions, leading to unsaturated allelic diversity curves. Using this diversity, we further proposed pan-NLRome graph- and k-mer-based genome-wide association studies (GWAS), which, using Fusarium wilt races 1 and 2 severity data, accurately identified Fom-1, Fom-2, and novel non-NLR candidates. Furthermore, we extended these approaches for the identification of a candidate gene for flaccid necrosis caused by zucchini yellow mosaic virus. Our study offers a comprehensive view of NLR diversity in melon, overcoming the limitations of single-reference analyses, and supporting future efforts in NLR-focused GWAS and resistance breeding.

genomics↗

bioRxiv2024

Nuclear and organelle genome assemblies of five Cucumis melo L. accessions, Ananas, Canton, PI 414723, Vedrantais and Zhimali, belonging to diverse botanical groups

The construction of accurate whole genome sequences is pivotal for characterizing the genetic diversity of plant species, identifying genes controlling important traits, or understanding their evolutionary dynamics. Here, we generated the nuclear, mitochondrial and chloroplast high- quality assemblies of five melon (Cucumis melo L.) accessions representing five diverse botanical groups, using the Oxford Nanopore sequencing technology. The accessions here studied included varied origins, fruit shapes, sizes, and resistance traits, providing a holistic view of melon genomic diversity. The final chromosome-level genome assemblies ranged in size from 359 to 365 Mb, with approximately 25x coverage for four of them multiplexed in half of a PromethION flowcell, and 48x coverage for the fifth, sequenced individually in another half of a PromethION flowcell. Contigs N50 ranged from seven to 15 Mb for all the assemblies, and very long contigs reaching sizes of 20-25 Mb, almost compatible with complete chromosomes, were assembled in all the accessions. Quality assessment through BUSCO and Mercury indicated the high completeness and accuracy of the assemblies, with BUSCO values exceeding 96% for all accessions, and Mercury QV values ranging between 32 and 47. We focused on the complex NLR resistance gene clusters to validate the accuracy of the assemblies in highly complex and repetitive regions. Through Nanopore adaptive sampling, we generated accurate targeted assemblies of these regions with a significantly higher coverage, enabling the comparison to our whole genome assemblies. Overall, these chromosome-level assembled genomes constitute a valuable resource for research focused on melon diversity, disease resistance, evolution, and breeding applications. Article SummaryThis study presents high-quality nuclear, mitochondrial, and chloroplast genome assemblies for five diverse melon (Cucumis melo L.) accessions, using Oxford Nanopore sequencing. The assemblies represent a broad spectrum of melon diversity, including differences in origin, fruit morphology, or resistance traits. The genomes, ranging from 359 to 365 Mb, were assembled at a chromosome level with high contiguity, and verified using different validation approaches. This study provides valuable insights for research on melon genetic diversity, disease resistance, and breeding applications. The genome data will be especially valuable for plant geneticists, breeders, and researchers working on crop improvement and resistance traits.

genomics↗

bioRxiv2024

Novel phages of Pseudomonas syringae unveil numerous potential auxiliary metabolic genes

Relatively few phages that infect plant pathogens have been isolated and investigated. The Pseudomonas syringae species complex is present in various environments, including plants. It can cause major crop diseases, such as bacterial canker on apricot trees. This study presents a collection of 25 unique phages genomes that infect P. syringae. These phages were isolated from apricot orchards with bacterial canker symptoms after enrichment with 21 strains of P. syringae. This collection comprises mostly virulent phages, with only three being temperate. They belong to 14 genera, 11 of which are newly discovered, and 18 new species, revealing great genetic diversity within this collection. Novel DNA packaging systems have been identified bioinformatically in one of the new phage species, but experimental confirmation is required to define the precise mechanism. Additionally, many phage genomes contain numerous potential auxiliary metabolic genes with diversified putative functions. At least three phages encode genes involved in bacterial tellurite resistance, a toxic metalloid. This suggests that viruses could play a role in bacterial stress tolerance. This research emphasises the significance of continuing the search for new phages in the agricultural ecosystem to unravel novel ecological diversity and new gene functions. This work contributes to the foundation for future fundamental and applied research on phages infecting phytopathogenic bacteria.

microbiology↗

bioRxiv2023

Nanopore adaptive sampling to identify the NLR-gene family in melon (Cucumis melo L.)

BackgroundNanopore Adaptive Sampling (NAS) offers a promising approach for assessing genetic diversity in targeted genomic regions. Herein, we design and validate an experiment to enrich a set of resistance genes in several melon cultivars as a proof of concept. ResultsWe showed that each of the 15 regions we identified in two newly assembled melon genomes (subspecies melo) were successfully and accurately reconstructed as well as in a third cultivar from the agrestis subspecies. We obtained a fourfold enrichment, independently from the samples, but with some variations according to the enriched regions. In the agrestis cultivar, we further confirmed our assembly by PCR. We discussed parameters that can influence enrichment and accuracy of assemblies generated through NAS. ConclusionsAltogether, we demonstrated NAS as a simple and efficient approach to explore complex genomic regions. This approach finally unlocks the characterization of resistance genes for a large number of individuals, as required for breeding new cultivars responding to the agroecological transition.

genomics↗

bioRxiv2020

Deciphering the genetic diversity of landraces with high-throughput SNP genotyping of DNA bulks: methodology and application to the maize 50k array

Genebanks harbor original landraces carrying many original favorable alleles for mitigating biotic and abiotic stresses. Their genetic diversity remains however poorly characterized due to their large within genetic diversity. We developed a high-throughput, cheap and labor saving DNA bulk approach based on SNP Illumina Infinium HD array to genotype landraces. Samples were gathered for each landrace by mixing equal weights from young leaves, from which DNA was extracted. We then estimated allelic frequencies in each DNA bulk based on fluorescent intensity ratio (FIR) between two alleles at each SNP using a two step-approach. We first tested either whether the DNA bulk was monomorphic or polymorphic according to the two FIR distributions of individuals homozygous for allele A or B, respectively. If the DNA bulk was polymorphic, we estimated its allelic frequency by using a predictive equation calibrated on FIR from DNA bulks with known allelic frequencies. Our approach: (i) gives accurate allelic frequency estimations that are highly reproducible across laboratories, (ii) protects against false detection of allele fixation within landraces. We estimated allelic frequencies of 23,412 SNPs in 156 landraces representing American and European maize diversity. Modified Rogers genetic Distance between 156 landraces estimated from 23,412 SNPs and 17 SSRs using the same DNA bulks were highly correlated, suggesting that the ascertainment bias is low. Our approach is affordable, easy to implement and does not require specific bioinformatics support and laboratory equipment, and therefore should be highly relevant for large-scale characterization of genebanks for a wide range of species.

genetics↗

bioRxiv2018

Sequence Imputation from Low Density Single Nucleotide Polymorphism Panel in a Black Poplar Breeding population

BackgroundGenomic selection accuracy increases with the use of high SNP (single nucleotide polymorphism) coverage. However, such gains in coverage come at high costs, preventing their operational implementation by breeders. Low density panels imputed to higher densities offer a cheaper alternative. Our study is one of the first to explore the imputation in a tree species: black poplar. About 1000 pure-breed Populus nigra trees corresponding to a subsample of the French breeding population were selected and genotyped with a 12K custom Infinium Bead-Chip. Forty-three of those individuals corresponding mostly to nodal trees in the pedigree were fully sequenced (reference), while the remaining majority (target) was imputed from 8K to 1.4 million SNPs using FImpute. Each SNP and individual was evaluated for imputation errors by leave-one-out cross validation in the training sample of 43 sequenced trees. Some summary statistics such as Hardy Weinberg Equilibrium exact test p-value, quality of sequencing, depth of sequencing per site and per individual, minor allele frequency, marker density ratio or SNP information redundancy were calculated. Principal component and Boruta analyses were used on all these parameters to rank the factors affecting the quality of imputation. Additionally, we characterize the impact of the relatedness between reference population and target population.\n\nResultsDuring the imputation process, we used 7,540 SNPs from the chip to impute 1,438,827 SNPs from sequences along the 19 Chromosomes. At the individual level, imputation accuracy was very high with a proportion of SNPs correctly imputed between 0.84 and 0.99. The variation in accuracies was mostly due to differences in relatedness between individuals. At a SNP level, the imputation quality strongly depended on genotyped SNP density and to a lesser extent on the original minor allele frequency. The imputation did not appear to result in an increase of linkage disequilibrium. The genotype densification not only brought a better distribution of markers all along the genome, but also we did not detect any substantial bias in annotation categories.\n\nConclusionsThis study shows that it is possible to impute low-density marker panels to whole genome sequence with good accuracy under certain conditions that could be common to many breeding populations.

genomics↗

bioRxiv2018

Quick and efficient approach to develop genomic resources in orphan species: application in Lavandula angustifolia

Next-Generation Sequencing (NGS) technologies, by reducing the cost and increasing the throughput of sequencing, have opened doors of research efforts to generate genomic data to a range of previously poorly studied species. In this study, we proposed a method for the rapid development of a large scale molecular resources for orphan species. We studied as an example Lavandula angustifolia, a perennial sub-shrub plant native from the Mediterranean region and whose essential oil have numerous applications in cosmetics, pharmaceuticals, and alternative medicines.\n\nWe first built a Maillette reference Unigene, compound of coding sequences, thanks to de novo RNA-seq assembly. Then, we reconstructed the complete genes sequences (with exons and introns) using a transcriptome-guided DNA-seq assembly approach in order to maximize the possibilities of finding polymorphism between genetically close individuals. Finally, we used these resources for SNP mining within a collection of 16 lavender clones and tested the SNP within the scope of a phylogeny analysis. We obtained a cleaned reference of 8, 030 functionally annotated genes (in silico annotation). We found up to 400K polymorphic sites, depending on the genotype analyzed, and observed a high SNP frequency (mean of 1 SNP per 90 bp) and a high level of heterozygosity (more than 60% of heterozygous SNP per genotype). We found similar genetic distances between pairs of clones, related to the out-crossing nature of the species, the restricted area of cultivation and the clonal propagation of the varieties.\n\nThe method propose is transferable to other orphan species, requires little bioinformatics resources and can be realized within a year. This is the first reported large-scale SNP development on Lavandula angustifolia. All this data provides a rich pool of molecular resource to explore and exploit biodiversity in breeding programs.

genomics↗

bioRxiv2018

A high-quality sequence of Rosa chinensis to elucidate genome structure and ornamental traits

Rose is the worlds most important ornamental plant with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Rose has a complex genome with high heterozygosity and various ploidy levels. Our objectives were (i) to develop the first high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short read sequencing, and anchoring to a high-density genetic map and (ii) to study the genome structure and the genetic basis of major ornamental traits.\n\nWe produced a haploid rose line from R. chinensis Old Blush and generated the first rose genome sequence at the pseudo-molecule scale (512 Mbp with N50 of 3.4 Mb and L75 of 97). The sequence was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features including the pericentromeric regions through annotation of TE families and positioned centromeric repeats using FISH. Genetic diversity was analysed by resequencing eight Rosa species. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and number of flower petals. A rose APETALA2 homologue is proposed to be the major regulator of petals number in rose. This reference sequence is an important resource for studying polyploidisation, meiosis and developmental processes as we demonstrated for flower and prickle development. This reference sequence will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae.

genomics↗