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Functional
Annotation of
ANimal
Genomes (FAANG) Project
— A coordinated international action to accelerate Genome to Phenome
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INRAE, Institut Agro, Brittany region & ANR ANR-CE20-EFFICACE [€400,000] 
(2019-03-01~2025-12-31)
Objectives: 1) Extend the ENSEMBL catalog by gathering different LNC resources (NCBI, NONCODE, ALDB, Fr-AgENCODE, LNC predicted from additional 356 RNA-seq data) 2) Investigate LNC conservation between chicken and mammals 3) Extract a gold standard LNC set 4) Atlas of tissue expression of LNC & protein coding genes (PCG) 5) Assess the genetic basis of intra-tissue LNC expression and PCG-LNC co-expression (200+ animals) in metabolic tissues with a focus on liver which will be related to lipid phenotypes, using RNA-seq, ATAC-seq, HiC and methylation profiles.
Project directors:
Primary contact: Sandrine.lagarrigue@agrocampus-ouest.fr Linked projects: FR-AgENCODE, GENE-SWitCH
Contact: Sylvain Foissac (sylvain.foissac@inrae.fr)
INRAE, Institut Agro, Brittany region 10^nRnaSeq [€130,000] (2020-01-06~2023-12-31)
Objectives: 1) Workflow for identifying SNP variants and genotypes from RNAseq data 2) Workflow for identifying cis-eQTL by Allele Specific Expression from RNAseq data 3) Explore cis-eQTL and short variants in protein-coding genes (PCG) and LNC in different populations.
Project directors:
Primary contact: Christophe.klopp@inrae.fr & Sandrine.lagarrigue@agrocampus-ouest.fr Linked projects: FR-AgENCODE, GENE-SWitCH
Contact: Sylvain Foissac (sylvain.foissac@inrae.fr)
EU Horizon Grant 815668 [€6,033,458] (2019-09-01~2023-08-31)
Objectives: The BovReg consortium will provide a comprehensive map of functionally active genomic features in cattle and how their (epi)genetic variation in beef and dairy breeds translates into phenotypes. we will generate functional genome data based on FAANG core assays from representative bovine tissues and newly established cell lines covering different ontological stages and phenotypes applying novel bioinformatic pipelines. We will establish detailed knowledge on traits related to robustness, health and biological efficiency in cattle. Data, knowledge and protocols will be deposited in European biological archives, aiming to set up and maintain a knowledge hub and establish gold standards. Our biology-driven genomic prediction tools will integrate biological knowledge on regulatory genomic variation into genomic selection schemes for local and global cattle populations.
Project directors:
Additional Info: The consortium consist of 20 partners from nine European countries and represent both academia and industry.
Contact: Christa Kuehn (kuehn@fbn-dummerstorf.de)
EU Horizon Grant 817923 [€6,000,000] (2019-05-01~2023-04-30)
Objectives: AQUA-FAANG will functionally annotate the genomes of all six fish species, employing standardized experimental assays and analysis pipelines defined by the FAANG initiative. AQUA-FAANG datasets will be shared and coordinated with other FAANG initiatives via the FAANG data coordination centre, and made available through the Ensembl genome browser. Functional assays will be used to study intermediate phenotypes and prioritise causative genetic variants in trait-associated genomic regions to accelerate selection of disease-resistant stocks. Functionally-enriched marker panels will be developed to improve accuracy of genomic selection.
Project directors:
Additional Info: Sigbjørn Lien, head of CIGENE, will be the coordinator of the project, with support from Daniel Macqueen from University of Edinburgh. The consortium consist of 24 partners from nine European countries and represent both academia and industry. (https://tinyurl.com/y2nvrbfo)
Contact: Sigbjorn Lien (sigbjorn.lien@nmbu.no)
USDA-NIFA 2020-67015-31175 [$500,000] (2020-04-01~2023-03-31)
Objectives: (1) Identify and annotate regulatory elements in chicken gut and reproductive tissues by integrating information from RNA-seq, ATAC-seq, and ChIP-seq; (2) Use lentiMPRA in a model cell line to functionally validate a set of enhancers; (3) Employ promoter capture Hi-C to identify target genes of enhancers. More importantly, this knowledge will greatly enhance precision genome selection, which will translate into significant improvements for US poultry producers and consumers.
Project directors:
Contact: Huaijun Zhou (hzhou@ucdavis.edu)
USDA-NIFA GRANT12684524 [$500,000] (2019-10-01~2022-09-30)
Objectives: 1) closing the reference genome assembly by utilizing long-read PacBio sequencing in combination with a previously generated BioNano whole-genome optical map and Dovetail-HiRise map of chromatin interactions. 2) annotate the reference genome for the coding and non-coding transcript-isoforms and alternative splicing, by full-length single-molecule sequencing. 3) annotate the genome for chromatin histone-modifications, chromatin accessibility, by integrating the RNA-seq, ATAC-seq, and ChIP-seq data across various tissues.
Project directors:
Contact: Mohamed (Moh) Salem (mosalem@umd.edu)
USDA-NIFA 0000-0000-0000 [$120,000] (2020-10-01~2022-09-30)
Objectives: To achieve sustainable genetic improvements of agricultural species, the expertise of a broad community of agricultural researchers must be engaged from both crop and livestock communities. This includes integrative disciplines such as life science, breeders, engineers, data scientists, economists, and social scientists. The overall objective of the Agriculture Genome to Phenome Initiative (AG2PI) is to assemble and prepare a transdisciplinary community to conduct AG2P research. This initiative will: - Develop a vision for AG2P research - Identify research gaps and opportunities - Foster early community solutions to these challenges and gaps - Rapidly disseminate findings to the broader community
Project directors:
Additional Info: AG2PI is a cooperative project involving 40+ institutions and/or organizations around the world with Scientific Board Members from institutions in multiple countries.
Contact: Christopher Tuggle (cktuggle@iastate.edu)
USDA NIFA Grant 2018-67015-27500 [$2,500,000] (2018-01-31~2022-01-31)
Objectives: (1) Generate detailed transcriptome information from a comprehensive set of cattle tissues. (2) Generate detailed chromatin state information from a comprehensive set of cattle tissues. (3) Integrate transcriptome and chromatin state datasets into readily accessible maps of functional elements in the bovine genome. (4) Demonstrate the utility of genome-wide functional maps for GWAS analysis.
Project directors:
Contact: Huaijun Zhou (Hzhou@ucdavis.edu)
USDA NIFA Grant 2018-67015-27501 [$2,500,000] (2018-01-01~2021-12-31)
Objectives: (1) Maximize functional annotation in healthy adult porcine tissues relevant to phenotypes important for genetic improvement; (2) Create functional annotation of important tissues during fetal development and the association of allele-specific expression with allele-specific chromatin modification; (3) Identify the functional components of the immune system as a resource for improving resilience in pigs; (4) Integrate all public and project data to develop a higher-order regulatory understanding of the porcine genome, including a predicted chromatin state map.
Project directors:
Contact: Christopher Tuggle (cktuggle@iastate.edu)
INRAE INRAE-SELGEN-2015b [€29,444] (2021-01-01~2021-12-31)
Objectives: 1) Improve the genome annotation of 4 livestock species by producing and analyzing RNA-seq data using 11 tissue samples from the FR-AgENCODE project (including the 3 original ones). 2) Investigate gene conservation between the 4 species. 3) Characterize the tissue specificity of protein-coding and non-coding genes.
Project directors:
Website: www.fragencode.org This project is an extension of the original FAANG pilot project FR-AgENCODE and runs with the remaining part of the original grant.
Contact: Sylvain Foissac (sylvain.foissac@inrae.fr)
USDA NIFA Grant 2018-67015-27499 [$1,000,000] (2018-10-01~2021-09-30)
Objectives: (1) Identify coding and long noncoding RNA transcripts in the chicken genome. (2) Identify promoter, enhancer, silencer and insulator elements in the chicken genome. (3) Characterize activity states and tissue specificity of cis-regulatory elements. (4) Map distal regulatory elements to their interacting target promoters.
Project directors:
Contact: Yvonne Drechsler (ydrechsler@westernu.edu)
USDA NIFA Grant 2019-67015-29340 [$500,000] (2019-04-01~2021-03-31)
Objectives: 1) From a USDA NRSP8-supported biobank of material from two, well-phenotyped Thoroughbred stallions, collect whole-genome sequence and across-tissue gene expression to define the transcriptome and identify DNA variation. 2) Define regions of genome regulation, including four histone modification marks and a genomic insulator in eight tissues of high priority collected from these two Thoroughbred stallions; correlate with whole-transcriptome data and delineate sex differences by comparing these data to that in hand from two Thoroughbred mares. 3) Identify tissue-specificity and across-individual variation in the epigenetic determination of centromere position and its association with markers of genome regulation while concurrently determining the role of non-centromeric CENP-A binding sites in genome function.
Project directors:
Contact: Jessica Petersen (jessica.petersen@unl.edu)
BBSRC Grant 0000-0000 [£543,722] (2016-01-11~2020-10-31)
Objectives: (1) Ensure high quality and rich supporting metadata to describe the project's animals, specimens, cell cultures and experimental assays by developing tools for the community to enrich and validate against FAANG metadata standards. (2) Develop the FAANG data portal (http://data.faang.org/) to provide a focused functional data resource from which researchers can explore, identify and download validated, richly described, high quality and comparable datasets for their genome to phenome research. (3) Provide a responsive helpdesk to the community, and promote and provide training on best practices in data management for the farmed and companion animal community.
Project directors:
Contact: Paul Flicek (flicek@ebi.ac.uk)
NSF Award 11456942 (2015-10-01~2020-09-30)
Objectives: The intent of this funding is to promote efforts leading to better understanding of the relationships between genome and phenome. This can take the form of sponsoring meetings and providing funds for travel. Current focus is on supporting FAANG and on improving our understanding of invertebrate genome to phenome relationships. Funding is limited to U.S institutions and citizens. No monies are provided for actual experimentation.
Project directors:
Contact: Carl Schmidt (schmidtc@UDel.Edu)
COST Action Award 15112 [$497000] (2016-04-13~2020-04-12)
Objectives: To facilitate the aims of the FAANG project through coordination, development of agreed standards for experiments, data and metadata, training and dissemination of standards and results.
Project directors:
Contact: Alan Archibald (alan.archibald@roslin.ed.ac.uk)
Grayson Jockey Club Foundation 2018-000-000 [$199,990] (2018-04-01~2020-03-31)
Objectives: n/a
Project directors:
Contact: Carrie Finno (cjfinno@gmail.com)
USDA-NIFA Grant 2016-10149 [$500,000] (2017-01-01~2019-12-31)
Objectives: 1) Develop a deep and robust dataset of transcribed elements in the sheep genome. 2) Develop a deep and robust dataset of transcription regulatory features of the sheep. 3) Annotation of the ovine genome reference assembly. 4) Provide ovine FAANG data and support to the public.
Project directors:
Acknowledgement: We would like to acknowledge the USDA NIFA for funding the “Ovine FAANG Project”. This project leveraged data from the preceding USDA NIFA 2013-00978, GRANT11298059 “Improving Reference Genomes for Agriculturally Important Animals”, and USDA NIFA 2013-00976 “Building the Sheep Genomes Database”. Additional support was provided by NRSP8 - National Animal Genome Research Program and USDA Meat and Animal Research Center. Furthermore, we would like to thank the International Sheep Genomics Consortium, AgResearch CORE funds and MBIE “Genomics for Production & Security in a Biological Economy” C10X1306 research grant for aligned co-funding.
Contact: Brenda Murdoch (bmurdoch@uidaho.edu)
USDA NIFA GRANT 12224584 [$460,384] (2017-01-01~2018-12-31)
Objectives: (1) Generate comprehensive and high quality experimental data for most transcripts expressed in bovine, pig and chicken tissues; (2) Integrate novel and current information to improve transcriptome annotation of bovine, pig, and chicken genomes, in a format readily available to the broader genome community
Project directors:
Contact: Pablo Ross (pross@ucdavis.edu)
Grayson-Jockey Club Research Foundation Award #0000 [$199,177] (2016-04-01~2018-03-31)
Objectives: (n/a)
Project directors:
Additional Info: There is a complementary support of $13,530 from the USDA NRSP-8 Equine Species Coordinator Funds.
Contact: Carrie Finno (cjfinno@gmail.com)
INRAE INRAE-SELGEN-2015 [€299,700] (2015-01-01~2017-12-31)
Objectives: As one of the first pilot projects of the FAANG initiative, the goal of the FR-AgENCODE project is to improve the functional annotation of 4 animal species: cattle, pig, chicken and goat. It includes the production and the analysis of mRNA-seq, sRNA-seq, ATAC-seq and Hi-C data on CD4/CD8 sorted T cells and liver samples from 2 males and 2 females of each species (Bos taurus, Sus scrofa, Gallus gallus and Capra hircus).
Project directors:
Reference: Foissac et al, 2019. Multi-species annotation of transcriptome and chromatin structure in domesticated animals. BMC Biol 17, 108 (2019). https://doi.org/10.1186/s12915-019-0726-5 Project web site: http://www.fragencode.org
Contact: Sylvain Foissac (sylvain.foissac@inrae.fr)
USDA NIFA Grant 2015-67015-22940 [$500,000] (2015-01-01~2017-12-31)
Objectives: (1) Annotate chromatin states corresponding to DNase hypersensitivity, four histone modifications, and one transcription factor; (2) Annotate promoters, enhancers, and silencers by integrating information from RNA-seq, DNAse-seq, and ChIP-seq against four histone modifications and one transcription factor; (3) Freely distribute all raw and annotated data via UCSC Genome Browser and Ensembl.
Project directors:
Additional Info: This is complementary funded with additional grants from Poultry, Swine and Cattle Genome Coordination fund ($86,500), from National Pork Board ($30,000), and from Aviagen Ltd ($20,000)
Contact: Huaijun Zhou (Hzhou@ucdavis.edu)
USDA NIFA Grant 2016-0070 [$17,500] (2016-03-01~2017-02-28)
Objectives: Provide avenue for further discussing collaborations on FAANG community and financial support for invited speakers, students and postdocs.
Project directors:
Contact: Huaijun Zhou (Hzhou@ucdavis.edu)
France-Berkeley Fund Grant 2016-0070 [$12,000] (2016-03-01~2017-02-28)
Objectives: Jointly develop standardized sampling protocols for the core “omics” FAANG assays
Project directors:
Contact: Huaijun Zhou (Hzhou@ucdavis.edu)
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