Periodic Reporting for period 2 - GENE-SWitCH (The regulatory GENomE of SWine and CHicken: functional annotation during development) Reporting period: 2021-01-01 to 2022-06-30 Summary of the context and overall objectives of the project Achieving sustainable farmed animal productions requires the ability to use of an animals’ genomic information to predict its characteristics in specific environments (i.e. ‘genotype-to-phenotype’ or ‘G2P’). GENE-SWitCH contributes to the FAANG (Functional Annotation of Animal Genomes) initiative and is a founder partner of EuroFAANG (https://eurofaang.eu) a coordinated European effort - successfully established in RP1 and growing with more projects joining - that aims to unravel the connection between the genetic make-up of an animal and the observable physical and physiological traits. Since July 2019, the GENE-SWitCH consortium works to deliver new underpinning knowledge on the functional genomes of two main monogastric farm species (pig and chicken, two foremost sources of meat), and to enable its immediate translation to the pig and poultry sectors. The project has three main and interconnected objectives and is structured in eight work packages (WP) (see Figure). Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far W P1 aims to establish a collection of cryopreserved tissues and to perform the core molecular assays required for the functional annotation of the pig and chicken genomes. Extensive functional genomics information has been produced for a panel of seven tissues across three developmental stages, i.e. early and late organogenesis (embryos/foetuses) and newborn animals. These tissues have been characterized by several assays-by-sequence (described below), with about 50 terabytes of raw sequence data uploaded to the FAANG data portal (https://data.faang.org/home) under the GENE-SWitCH tag. WP2 analyses the data from these molecular assays to characterize the transcriptional and regulatory dynamics of both genome across development and to deliver comprehensive genome annotation maps. When the sequence data are aligned to the reference pig and chicken genome sequences they allow the identification of the functional elements within the genome. RNA-seq, sRNA-seq and Iso-seq data allow the identification of genes, both those encoding proteins and non-coding genes, and the RNA transcripts are the primary gene product. ATAC-seq data allow the identification of open regions of chromatin, whilst the whole genome and reduced representation bisulfite sequence (WGBS and RRBS respectively) allow the identification of methylated bases within the genome. ChIP-seq data allow the identification of genome regulatory sequences that are bound by key proteins like histone marks and finally promoter capture Hi-C data allow the identification of promoter and enhancer interactions at a genome-wide scale. . In WP2 we have developed software, modified existing software tools, to analyse these sequences, and have deposited all software in public repositories. We have undertaken the primary analysis of the RNA-seq, sRNA-seq, Iso-seq, ATAC-seq, WGBS and RRBS data and placed the results in the public sequence databases. We have released a first wave of improvements to the public annotation of the pig and chicken genomes. For the chicken we have annotated three reference genome sequences – one representation of broiler type chickens, one representative of layer type chickens and finally the latest revision of the ancestral Red Jungle Fowl reference genome. WP3 focusses on coordination, standardisation and integration of the wealth of the FAANG data generated by GENE-SWitCH. A new specialised and streamlined data submission process was developed, in particular to support the submission of new data not seen before in FAANG on embryos/foetuses and maternal diets. Moreover, EuroFAANG coordinates and sets the priorities of the necessary interoperability development for data, protocol and analysis sharing to enable future cross-project comparative analyses in Europe. The GENE-SWitCH FAANG sub portal displays all of the data generated by GENE-SWitCH, with new customised ways for scientists to query and interact with the wealth of generated data (https://data.faang.org/projects/GENE-SWitCH). WP4 aims to extend genomic prediction models, both Bayesian and machine learning, to exploit the new annotation maps of pig and chicken generated in GENE-SWitCH. The performance of these models has been evaluated with early available data, showing some marginal improvements in prediction accuracy. QTLs in chicken have been fine-mapped based on a powerful advanced intercross line, and eQTL in pigs have been generated from expression data in three tissues obtained from 300 pigs. These pig expression data will be used as phenotypes in the so-called level 1 validation of the developed models, while the eQTL and fine-mapped QTL will be used in the so-called level 2 validation of the developed models using commercial populations. WP5 is the exploratory “diet X epigenetics” study experiment of GENE-SWitCH. There is increasing evidence that SCFAs (Short Chain Fatty Acids) produced by microbial fermentation of non-digestible dietary fibre have effects on host physiology beyond the gut including host metabolic responses in liver and muscle. The functional and epigenetic effects of high fibre maternal diets on liver and skeletal muscle of piglets and foetuses, using a low fibre diet as a control, are being investigated by RNA-seq and ATAC-seq. The current results indicate that SCFAs have small but significant epigenetic effects on relevant functional pathways in skeletal muscle and liver. WP6 aims to design and implement the communication, dissemination and training activities of GENE-SWitCH. All the planned activities have been successfully implemented in this reporting period, as reported in the GENE-SWitCH website and the social dissemination channels of the project. WP7 has ensured a constant monitoring of the project progress, with assistance to WP leaders and meetings organized. WP8 has ensured compliance with the ethics and animal experimentation requirements. Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far) Considerable progress has been made in this second third of the project, with more scientific papers published or in advanced preparation stage and several outreach, dissemination and training activities implemented. The primary analyses of sequence-by-assay data are almost complete (pending the completion and submission of ChIP-seq data), integrative analyses have started, and the first Ensembl Regulatory Builds of the pig and chicken genomes are on the way. Increased connections have established between all WPs to make use of the new genome annotations. Large scale powerful datasets from commercial populations are being prepared to evaluate the potential of the new prediction models that incorporate the functional genomic annotations for animal breeding practice. The results of the diet X epigenetics study are very promising, and we anticipate that the final finding will be important for the welfare of pigs, also with implications for human health in utero and early life. The innovative presentation developments for the FAAG Data Portal and genome browsers will support scientists understanding of the way a livestock animals genome interacts with the environment and the mechanisms by which these effects induced by environment can be transmitted across generations. Ultimately, the key new datasets and results generated by GENE-SWitCH, coupled to the increased potential of dissemination and outreach ensured by EuroFAANG, will contribute to enhance the sustainability of farmed animal production and to ensure European food security. Related documents RP2_Publishable summary image.jpg
