Biology subjects

Zerjal, T.

Publications and source records attributed to Zerjal, T..

4 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↗

bioRxiv2025

Unravelling the genetic architecture of persistence in production, quality, and efficiency traits in laying hens at late production stages

BackgroundThe laying hen industry aims to extend production for the economic and environmental benefits it offers, while at the same time facing the challenges of declining egg production and quality in aging hens. To explore trait persistence, we studied 998 Rhode Island Red purebred hens from the Novogen nucleus. We recorded daily egg production from 70 to 92 weeks of age and measured individual feed intake twice a week for three weeks, starting at 70, 80, and 90 weeks, as well as body weight at the start and at the end of each feed intake recording period. Random regression models were used to study trait trajectories over time, and PCA and hierarchical clustering were applied to identify groups of hens based on estimated breeding values for the intercept and slope of traits trajectory. ResultsResults showed different aging trajectories among traits. Daily body weight variation, Feed conversion ratio, Haugh unit and yolk percentage showed persistence (i.e., stability) over the measured period. On the contrary, daily feed intake, residual feed intake, laying rate, egg mass, eggshell breaking strength and stiffness decreased over time, while body weight, mean egg weight and eggshell colour increased. To assess the feasibility of selecting for trait persistence, we estimated the genetic variance of the slope and its correlation with the intercept. We found that, for egg weight and eggshell colour, genetic variance of the slope was negligible, indicating that selection for persistence on these traits requires other means. On the contrary, the slope for other traits such as laying rate and residual feed intake showed significant additive genetic variance. Strong genetic correlations between trait estimates at different ages were also observed and heritabilities estimates were low to high depending of the traits and period. ConclusionThe study explores hens trait persistence from 70 to 92 weeks, suggesting potential for improved egg production persistence. Challenges arise from low genetic variances impacting the efficiency of the potential selection on persistence. Clustering analysis reveals distinctive response patterns to elongation of production and underlined that selecting for enhanced persistence of different traits will necessitate compromises in breeding goals.

genetics↗

bioRxiv2024

Molecular responses of chicken embryos to maternal heat stress through DNA methylation and gene expression

Climate change, with its repercussions on agriculture, is one of the most important adaptation challenges for livestock production. Poultry production is a major source of proteins for human consumption all over the world. With a growing human population, improving poultrys adaptation to environmental constraints becomes critical. Extensive evidence highlights the influence of environmental variations on epigenetic modifications. The aim of this paper is therefore to explore chickens molecular response to maternal heat stress. We employed Reduced Representation Bisulfite Sequencing (RRBS) to generate genome-wide single-base resolution DNA methylation profiling and RNA sequencing (RNA-seq) to profile the transcriptome of the brains of embryos hatched from dams reared under either heat stress (32 {degrees}C) or thermoneutrality (22{degrees}C). We detected 289 significant differentially methylated CpG sites (DMCs) and one differentially methylated region (DMR) between heat stressed and control groups. These DMCs were associated with 357 genes involved in processes such as cellular response to stimulus, developmental processes and immune function. In addition, we identified 11 genes differentially expressed between the two groups of embryos, and identified ATP9A as a target gene of maternal heat stress on offspring. This study provides a body of fundamental knowledge on adaptive mechanisms concerning heat tolerance in chickens.

genomics↗