Functional Annotation of ANimal Genomes (FAANG) Project
— A coordinated international action to accelerate Genome to Phenome
USDA NIFA ARZT ARZT-1370520-R50-130 (2018-10-01~2023-09-30)
Objectives: Create and share data and technology to enhance the development and application of genomics, epigenomics, and systems biology in poultry.
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.
Additional Info: The consortium consist of 20 partners from nine European countries and represent both academia and industry.
EU Horizon Grant 817998 [€5,999,891] (2019-07-01~2023-06-30)
Objectives: GENE-SWitCH aims to deliver new underpinning knowledge on the functional genomes of two main monogastric farm species (pig and chicken) and to enable immediate translation to the pig and poultry sectors. We will characterize the dynamics (“switches”) of the functional genome from embryo (chicken) and fetus (pig) to adult life by targeting a panel of tissues relevant to sustainable production. New expression QTL data in pigs and existing high-resolution QTL data in chicken will be used for developing innovative genomic predictive models that integrate functional annotations, and these models will be validated in commercial pig and poultry populations. In addition, nutritional epigenetic data will allow evaluation of the influence of maternal diet on the epigenome of the pig fetus and whether such effects persist until post-weaning. These open-shared datasets will conform fully with FAANG standards and add valuable knowledge on genetic and epigenetic variation of functional elements to FAANG.
Additional Info: The consortium consists of 10 partners from nine European countries and represent both academia and industry.
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.
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)
USDA-NIFA GRANT12684524  (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.
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.
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.
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.
USDA NIFA Grant 2018-67015-27500 [$2,500,000] (2018-01-01~2020-12-31)
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.
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.
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.
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.
Grayson Jockey Club Foundation 2018-000-000 [$199,990] (2018-04-01~2020-03-31)
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.
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.
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
Grayson-Jockey Club Research Foundation Award #0000 [$199,177] (2016-04-01~2018-03-31)
Additional Info: There is a complementary support of $13,530 from the USDA NRSP-8 Equine Species Coordinator Funds.
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.
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)
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.
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
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