Biology subjects

Eynard, S. E.

Publications and source records attributed to Eynard, S. E..

6 recordsLinked to original sources

bioRxiv2026

Genetic determinism and inheritance of differential DNA methylation profiles across three successive generations in quail.

Environmental exposures can induce epigenetic modifications that persist across generations, potentially contributing to the transmission of environmentally-induced phenotypes. However, the extent to which such persistence of molecular changes are maintained independently of genetic mechanisms remains unclear. In this study, we investigated the evolution and genetic determinism of DNA methylation (DNAm) variation across three successive generations of Japanese quails (G0 to G2) belonging to two epilines, defined according to whether their female ancestor had received genistein supplementation (epi+) or not (epi-). Using reduced representation bisulfite sequencing (RRBS), we characterised CpG methylation patterns and identified differentially methylated cytosines (DMCs) and regions (DMRs) between control and genistein-supplemented epilines. Out of 112,745 CpG sites analysed, no DMCs or DMRs were detected between epilines in the first generation following exposure (G0), whereas 621 DMCs (36 DMRs) were identified in G1, and 1,381 DMCs (101 DMRs) in G2. Despite this progressive increase of differential methylation sites, mean differences in methylation rate between epilines were globally small. Similarly, genome-wide genetic differentiation between epilines was very limited. Overall, SNP-based heritability of DNA methylation was 0.19 indicating that genetic variation accounted for only a small part of the global variation of DNAm levels. By contrast, DNAm at differentially methylated CpG sites was extensively under genetic control, with a mean SNP-based heritability > 0.5, and meQTL analysis further identified significant associations between SNPs and methylation levels. Together, these results indicate that local DNAm differentiation in quail is under substantial genetic regulation, while the limited genetic differentiation between groups suggests that genetic variation alone can not fully explain the progressive accumulation of methylation differences following an ancestral exposure to genistein. These results support DNAm as a plausible molecular candidate mechanism in the multigenerational response to environmental exposure and highlight the complex interplay between genetic and epigenetic regulations in the inheritance of phenotypes.

genomics↗

bioRxiv2025

Transgenerational transmission of an environmental modification in quails: changes in phenotypic variance components across three generations

BackgroundWhile epigenetic variations can contribute to shaping phenotypic diversity, it can be challenging to isolate and quantify the portion of trait variability under non-genetic influence. In this study we compared the phenotypic responses for different traits of two epilines of Japanese quails (Coturnix japonica) across three generations, using a large sample size. These epilines were built in parallel following (epi +), or not (epi -), an initial genistein ingestion in the ancestors diet and were maintained to harbour a similar genetic structure. ResultsLinear models were fitted to extract the fraction of variance allocated to multiple factors such as family, sex and epiline. The latter was found to be significantly associated with body weight. The contribution of the epiline to phenotypic variability progressively increased from the first generation (G0) to the last (G2), leading - for example in body weight at slaughter - to an average difference for adult males and females in G2 of 9 grams and 14 grams respectively, between epi + offspring and controls (epi-). ConclusionsAlthough these findings suggest genetic drift, they could also reveal a possible transgenerational effect of the initial diet disruption. The analysis of other phenotypes displayed rare significant effects of the epiline. This innovative experimental design offered a unique opportunity to better understand the evolution of phenotypic variability and the parameters constituting it across three generations following or not an environmental change.

genetics↗

bioRxiv2024

Sequence-based genome-wide association studies reveal the polygenic architecture of Varroa destructor resistance in Western honey bees Apis mellifera

Honey bees, Apis mellifera, have experienced the full impacts of globalisation, including the recent invasion by the parasitic mite Varroa destructor which has become one of the main causes of colony losses worldwide. Despite its lethal effects, some colonies have developed defence strategies conferring colony resistance and, assuming non-null heritability, selective breeding of naturally resistant bees could be a sustainable way to fight infestations. Here we report on the largest genome-wide association study performed on honey bees to understand the genetic basis of multiple phenotypes linked to varroa resistance. This study was performed on whole genome sequencing of more than 1,500 colonies belonging to different ancestries and combined in a meta-analysis. Results show that varroa resistance is polygenic. A total of 60 genetic markers were identified as having a significant impact in at least one of the tested populations pinpointing several regions of the honey bee genome. Our results also support strategies for genomic selection in honey bee breeding.

genetics↗

bioRxiv2023

The black honey bee genome: insights on specific structural elements and a first step towards pan-genomes

BackgroundThe actual honey bee reference genome, HAv3.1, was produced from a commercial line sample, thought to have a largely dominant Apis mellifera ligustica genetic background. Apis mellifera mellifera, often referred to as the black bee, has a separate evolutionary history and is the original type in western and northern Europe. Growing interest in this subspecies for conservation and non-professional apicultural practices, together with the necessity of deciphering genome backgrounds in hybrids, triggered the necessity for a specific genome assembly. Moreover, having several high-quality genomes is becoming key for taking structural variations into account in pan-genome analyses. ResultsPacific Bioscience technology long reads were produced from a single haploid black bee drone. Scaffolding contigs into chromosomes was done using a high-density genetic map. This allowed for a re-estimation of the honey recombination rate, over-estimated in some previous studies, due to mis-assemblies resulting in spurious inversions in the older reference genomes. The sequence continuity obtained is very high and the only limit towards continuous chromosome-wide sequences seem to be due to tandem repeat arrays usually longer than 10 kb and belonging to two main families, the 371 and 91 bp repeats, causing problems in the assembly process due to high internal sequence similarity. Our assembly was used together with the reference genome, for genotyping two structural variants by a pan-genome graph approach with Graphtyper2. Genotypes obtained were either correct or missing, when compared to an approach based on sequencing depth analysis, and genotyping rates were 89 and 76 % for the two variants respectively. ConclusionsOur new assembly for the Apis mellifera mellifera honey bee subspecies demonstrates the utility of multiple high-quality genomes for the genotyping of structural variants, with a test case on two insertions and deletions. It will therefore be an invaluable resource for future studies, for instance including structural variants in GWAS. Having used a single haploid drone for sequencing allowed a refined analysis of very large tandem repeat arrays, raising the question of their function in the genome. High quality genome assemblies for multiple subspecies such as presented here, are crucial for emerging projects using pan-genomes.

genomics↗

bioRxiv2021

From group to individual - Genotyping by pool sequencing eusocial colonies

BackgroundEusocial insects play a central role in many ecosystems, and particularly the important pollinator honeybee (Apis mellifera). One approach to facilitate their study in molecular genetics, is to consider whole colonies as single individuals by combining DNA of multiple individuals in a single pool sequencing experiment. Such a technique comes with the drawback of producing data requiring dedicated analytical methods to be fully exploited. Despite this limitation, pool sequencing data has been shown to be informative and cost-effective when working on random mating populations. Here, we present new statistical methods for exploiting pool sequencing data of eusocial colonies in order to reconstruct the genotype of the colony founder, the queen. This leverages the possibility to monitor genetic diversity, perform genomic-based studies or implement selective breeding. ResultsUsing simulations and honeybee real data, we show that the methods allow for a fast and accurate estimation of the genetic ancestry, with correlations of 0.9 with that obtained from individual genotyping, and for an accurate reconstruction of the queen genotype, with 2% genotyping error. We further validate the inference using experimental data on colonies with both pool sequencing and individual genotyping of drones. ConclusionIn this study we present statistical models to accurately estimate the genetic ancestry and reconstruct the genotype of the queen from pool sequencing data from workers of an eusocial colony. Such information allows to exploit pool sequencing for traditional population genetics, association studies and selective breeding. While validated in Apis mellifera, these methods are applicable to other eusocial hymenoptera species.

genomics↗

bioRxiv2021

Complex population structure and haplotype patterns in Western Europe honey bee from sequencing a large panel of haploid drones

Honey bee subspecies originate from specific geographic areas in Africa, Europe and the Middle East. The interest of beekeepers in specific phenotypes has led them to import subspecies to regions outside of their original range. The resulting admixture complicates population genetics analyses and population stratification can be a major problem for association studies. As a typical example, the case of the French population is studied here. We sequenced 870 haploid drones for SNP detection and identified nine genetic backgrounds in 629 samples. Five correspond to subspecies, two to isolated populations and two to human-mediated population management. We also highlight several large haplotype blocks, some of which coincide with the position of centromeres. The largest is 3.6 Mb long on chromosome 11, representing 1.6 % of the genome and has two major haplotypes, corresponding to the two dominant genetic backgrounds identified.

genetics↗