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Functional
Annotation of
ANimal
Genomes (FAANG) Project
— A coordinated international action to accelerate Genome to Phenome
|
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)
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)
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)
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)
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)
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