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Background: Comparative genomics studies are central in identifying the coding and non-coding elements associated with complex traits, and the functional annotation of genomes is a critical step to decipher the genotype-to-phenotype relationships in livestock animals. As part of the Functional Annotation of Animal Genomes (FAANG) action, the FR-AgENCODE project aimed to create reference functional maps of domesticated animals by profiling the landscape of transcription (RNA-seq), chromatin accessibility (ATAC-seq) and conformation (Hi-C) in species representing ruminants (cattle, goat), monogastrics (pig) and birds (chicken), using three target samples related to metabolism (liver) and immunity (CD4+ and CD8+ T cells)., Results: RNA-seq assays considerably extended the available catalog of annotated transcripts and identified differentially expressed genes with unknown function, including new syntenic lncRNAs. ATAC-seq highlighted an enrichment for transcription factor binding sites in differentially accessible regions of the chromatin. Comparative analyses revealed a core set of conserved regulatory regions across species. Topologically associating domains (TADs) and epigenetic A/B compartments annotated from Hi-C data were consistent with RNA-seq and ATAC-seq data. Multi-species comparisons showed that conserved TAD boundaries had stronger insulation properties than species-specific ones and that the genomic distribution of orthologous genes in A/B compartments was significantly conserved across species., Conclusions: We report the first multi-species and multi-assay genome annotation results obtained by a FAANG project. Beyond the generation of reference annotations and the confirmation of previous findings on model animals, the integrative analysis of data from multiple assays and species sheds a new light on the multi-scale selective pressure shaping genome organization from birds to mammals. Overall, these results emphasize the value of FAANG for research on domesticated animals and reinforces the importance of future meta-analyses of the reference datasets being generated by this community on different species.

The need to adapt to decrease farm vulnerability to adverse contextual events has been extensively discussed on a theoretical basis. We developed an integrated and operational method to assess farm vulnerability to multiple and interacting contextual changes and explain how this vulnerability can best be reduced according to farm configurations and farmers' technical adaptations over time. Our method considers farm vulnerability as a function of the raw measurements of vulnerability variables (e.g., economic efficiency of production), the slope of the linear regression of these measurements over time, and the residuals of this linear regression. The last two are extracted from linear mixed models considering a random regression coefficient (an intercept common to all farms), a global trend (a slope common to all farms), a random deviation from the general mean for each farm, and a random deviation from the general trend for each farm. Among all possible combinations, the lowest farm vulnerability is obtained through a combination of high values of measurements, a stable or increasing trend and low variability for all vulnerability variables considered. Our method enables relating the measurements, trends and residuals of vulnerability variables to explanatory variables that illustrate farm exposure to climatic and economic variability, initial farm configurations and farmers' technical adaptations over time. We applied our method to 19 cattle (beef, dairy, and mixed) farms over the period 2008-2013. Selected vulnerability variables, i.e., farm productivity and economic efficiency, varied greatly among cattle farms and across years, with means ranging from 43.0 to 270.0 kg protein/ha and 29.4-66.0% efficiency, respectively. No farm had a high level, stable or increasing trend and low residuals for both farm productivity and economic efficiency of production. Thus, the least vulnerable farms represented a compromise among measurement value, trend, and variability of both performances. No specific combination of farmers' practices emerged for reducing cattle farm vulnerability to climatic and economic variability. In the least vulnerable farms, the practices implemented (stocking rate, input use…) were more consistent with the objective of developing the properties targeted (efficiency, robustness…). Our method can be used to support farmers with sector-specific and local insights about most promising farm adaptations.

Genomic imprinting is an epigenetic mechanism by which alleles of some specific genes are expressed in a parent-of-origin manner. It has been observed in mammals and marsupials, but not in birds. Until now, only a few genes orthologous to mammalian imprinted ones have been analyzed in chicken and did not demonstrate any evidence of imprinting in this species. However, several published observations such as imprinted-like QTL in poultry or reciprocal effects keep the question open. Our main objective was thus to screen the entire chicken genome for parental-allele-specific differential expression on whole embryonic transcriptomes, using high-throughput sequencing. To identify the parental origin of each observed haplotype, two chicken experimental populations were used, as inbred and as genetically distant as possible. Two families were produced from two reciprocal crosses. Transcripts from 20 embryos were sequenced using NGS technology, producing ∼200 Gb of sequences. This allowed the detection of 79 potentially imprinted SNPs, through an analysis method that we validated by detecting imprinting from mouse data already published. However, out of 23 candidates tested by pyrosequencing, none could be confirmed. These results come together, without a priori, with previous statements and phylogenetic considerations assessing the absence of genomic imprinting in chicken.