Funding Sources

US institutions must be PD; foreign components are allowed.

See program A1201 Animal Breeding and Functional Annotation of Genomes especially, although other programs may be relevant to FAANG goals. Important changes from previous year (from Lakshmi Matukumalli) (i) Given the NIFA relocation this is joint RFA is for both FY 2019 and FY 2020. (ii) The program deadlines vary across different programs. However for the programs related to Animals (Reproduction, Nutrition, Health, and Genomics) the deadlines are Fiscal Year 2019: Thursday, July 11, 2019 (5:00 p.m. Eastern Time) Fiscal Year 2020: Thursday, March 12, 2020 (5:00 p.m. Eastern Time) Letter of Intent is not solicited for these programs. (iii) Conference/Workshop funding requests can now be submitted throughout the year and there are no deadlines. (iv) The A1201 program takes into consideration the new Animal Genome Blueprint https://www.frontiersin.org/articles/10.3389/fgene.2019.00327/full and has expanded the scope of the proposals requested in this program that includes Breeding "A1201 - Animal Breeding and Functional Annotation of Genomes". Please read the RFA carefully for more guidance and let me know if you have questions. Here are some highlights. - All projects developing new genomics tools or resources will be submitting their proposal to this program. - Quantitative genetics methods proposals as well as projects that use enhanced breeding across all traits or breeding for specific trait (for example "implementing genome selection in catfish for disease and production traits", - "swine breeding for resistance to improve resistance to xxx disease" or - "beef cattle breeding to improve feed efficiency" are to be submitted to the A1201 program. (v) Please note that the RFA has a new section for inter-disciplinary programs a. Agricultural Innovation through Gene Editing b. Agricultural Microbiomes c. Critical Agricultural Research and Extension (CARE) d. Food and Agriculture Cyberinformatics Tools (FACT) e. Inter-Disciplinary Engagement in Animal Systems (IDEAS) f. Tactical Sciences for Agricultural Biosecurity Each of these programs have different deadlines and LOI requirements. Please read the RFA carefully. (vi) The new farm bill has changed the indirect costs for the projects. The overall indirect costs allowed for the project including the subcontracts is now limited to a maximum of 30%. Please contact the relevant program leaders for each of these programs for questions. Please note that all the AFRI program RFAs are now released. For more information visit https://nifa.usda.gov/afri-request-applications.

Genome Canada funds can only be awarded to individuals affiliated with one or more of the following types of organizations: Canadian universities and affiliated institutions including research hospitals and research institutes Not-for-profit organizations (including community or charitable organizations) with an explicit research mandate Canadian non-federal government departments or agencies Although led by Canadian researchers these projects do support (and indeed encourage) international collaboration.

Projects funded through this competition must focus on using genomic approaches to address challenges and opportunities of importance to Canada’s agriculture/agri-food and/or fisheries/aquaculture sectors. Topics of applied research that could be addressed include, but are not limited to, the following: increasing production efficiency, yield, and agronomic performance; genomics based approaches that reduce and/or mitigate abiotic and biotic stress in plants and animals; improving the health of crops, livestock, and fish through increased resilience to disease, pests and invasive species, along with more accurate diagnostic tests; reducing the environmental footprint of crop, livestock and aquaculture production systems through decreased water, fertilizer and pesticide use, reduced GHG emissions, and improved fish feed, resulting in improved sustainability; managing and reducing antimicrobial resistance in livestock and aquaculture - proposals are encouraged to include a one-health perspective (i.e., the collaborative efforts of multiple disciplines working locally, nationally and globally to achieve the best health for people, animals and our environment) but the main focus should be on livestock or aquaculture.

Research, Education or Extension Projects Eligible applicants for single-function Research, Education or Extension Projects include: a) State Agricultural Experiment Station; b) colleges and universities (including junior colleges offering associate degrees or higher); c) university research foundations; d) other research institutions and organizations; e) Federal agencies, f) national laboratories; g) private organizations or corporations; h) individuals who are U.S. citizens, nationals, or permanent residents; and i) any group consisting of two or more entities identified in a) through h). Eligible institutions do not include foreign and international organizations.

There are several AFRI Foundational programs that will accept projects related to FAANG. Because of the specific dates for A1541 Food and Agriculture Cyberinformatics Tools (FACT), this notice is for A1541 only. This program area priority focuses on data science to enable systems and communities to effectively utilize data, improve resource management, and integrate new technologies and approaches to further U.S. food and agriculture enterprises. The program encourages university-based research as well as public and private partnerships. There are many challenges associated with data in agriculture and food production. NIFA stakeholders identified at least a dozen issues that are critical to address: data infrastructure and management; applications and use of data; entities affected by data; creation, collection, provenance, and characteristics of data; training, programs, student, and knowledge needs around data; principles, and protocols associated with data; team, community, and public/private aspects of data; data producers, engineers, scientists, and researchers of data; public, corporate, and commercial entities' roles in data; privacy, security, confidentiality, and quality data; biological and interoperable data systems; bibliometrics, altmetrics, text and data mining; and data sharing, repositories, and analysis. The program will support projects that examine the value of data for small and large farmers, agricultural and food industries, and gain an understanding of how data can impact the agricultural supply chain, reduce food waste and loss, improve consumer health, environmental and natural resource management, affect the structure of U.S. food and agriculture sectors, and increase U.S. competitiveness. Applications for research or integrated projects must address one of the following priorities: # Design and Implementation o Build scalable data infrastructure and management systems o Conceptualize Open Data FAIR principles: Findable, Accessible, Interoperable, and Re-usable for all experimental and research data o Develop standards and best practices with other government and international organizations # Analysis o Develop data-integration and data-quality tools to improve analytic capability o Design and implement new algorithms and methods for depicting massive data # Technologies o Connect multiscale data o Bridge real-time distributed and parallel data systems o Create new methodologies and frameworks for tracking and processing data o Identify new approaches to data archiving and sharing # Applications and Human-Technology-Data Interactions o Examine scientific implications and practical aspects of how agricultural data and computer systems are accessed, designed, and used to improve human-human, human-technology, and human-decision experiences o Integrate visualization with statistical methods and other analytic techniques in order to support discovery and analysis o Engage students and professionals, teams, universities and public/private sectors o Develop decision-support tools that use diverse data sources and Big Data analytics modeling short-term impacts of various factors to create best value to the U S agricultural enterprise Applications for Coordinated Innovation Networks should: o Foster a cohesive, multi-disciplinary community that addresses bottlenecks in critical areas (e.g., high-throughput phenomics; systems modeling, access and integration of data from technologies like sensors and drones; smart cities); o Identify innovative and synergistic activities that prioritize needs and develop data standards for efforts in critical areas; o Bring together researchers (for research projects) or research, education, and/or extension (for integrated projects) communities working on multiple aspects of a data-supported problem into one multi- disciplinary network to collectively advance the field; o Include robust representation of public and commercial entities from relevant disciplines (e.g., geneticists, physiologists, engineers, informaticians, modelers, economists, social scientists, extension professionals and stakeholders); o Promote collaboration among research and education communities, both domestic and international, to leverage and facilitate sharing of expertise and resources; and o Develop and maintain effective networking strategies for connecting the public and private sector, students, and the media to foster interest and societal engagement. For additional resources on FACT including frequently asked questions, see the FACT page. https://nifa.usda.gov/program/fact.

Award grants may be made to State agricultural experiment stations; colleges and universities; university research foundations; other research institutions and organizations; Federal agencies; national laboratories; private organizations or corporations; individuals who are U.S. citizens, nationals, or permanent residents; or any group consisting of two or more of the aforementioned enti ties. Applications from scientists at non -U.S. organizations will not be accepted. Award recipients may subcontract to organizations not eligible to apply, provided such organizations are necessary for the conduct of the project.

USDA National Institute of Food and Agriculture (NIFA) is participating, effective immediately, in PAR-17-482 "Comparative Genomics Research Program" -- https://grants.nih.gov/grants/guide/pa-files/PAR-17-482.html. NIFA invites application for research developing comparative approaches that can be used to understand genome structure and function and the relationship between genomic features and phenotypes. NIFA will support studies that enable the use of a diverse array of species to advance our ability to improve genome annotations that complements Functional Annotation of Animal Genomes (FANNG) efforts or understand basic biological processes related to health and disease of agriculturally important animals, as well as studies that develop novel analytical tools and resources for the comparative genomics research community. Who is eligible to apply: Award grants may be made to State agricultural experiment stations; colleges and universities; university research foundations; other research institutions and organizations; Federal agencies; national laboratories; private organizations or corporations; individuals who are U.S. citizens, nationals, or permanent residents; or any group consisting of two or more of the aforementioned entities. Applications from scientists at non-U.S. organizations will not be accepted. Request For Applications: https://nifa.usda.gov/sites/default/files/rfa/Comparative-Genomics- Notice.pdf Apply For Grant: https://www.grants.gov/web/grants/view- opportunity.html?oppId=297339 Posted Date: Wednesday, June 6, 2018 Closing Date: Wednesday, June 5, 2019 Other Due Dates: See National Institutes of Health (NIH) National Human Genome Research Institute (NHGRI) comparative genomics program solicitation for details Submission Deadline for New Proposals : October 5, 2018, Feb 5, 2019, and June 5, 2019 Submission Deadline for Revised Proposals: November 5, 2018, March 5, 2019, and July 5, 2019 Funding Opportunity Number: PAR-17-482 https://grants.nih.gov/grants/guide/pa-files/PAR-17-482.html Estimated Total Program Funding: $3,000,000 Lakshmi Kumar Matukumalli National Program Leader, Animal Breeding, Genetics and Genomics National Institute of Food and Agriculture, USDA E- mail: lmatukumalli@nifa.usda.gov Office: 202-401-1766 Cell: 202-841-6009 http://www.nifa.usda.gov.

see page 69 of the pdf at the URL below. Expected that members of at least three EU countries or associated countries are involved.

18 million Euro available; expect to fund three proposals. The following is exerpted from the program announcement pdf found at the URL below. SFS-30-2018-2019-2020: Agri-Aqua Labs Specific Challenge: Agriculture and aquaculture are increasingly knowledge-intensive sectors that need to be supported by advances in basic science domains in tandem with translational research. This nexus between basic and applied research requires specific openings for testing ideas and their potential application in plant and animal production, both terrestrial and aquatic. Recent developments in genomic selection have revolutionised animal breeding and resulted in significant gains in production efficiency of animals. However, our understanding of the biological mechanisms underpinning traits remains limited. Most phenotypes, in particular for traits related to health, biological efficiency and robustness, are complex and a major goal of biological research is to use genome information to predict such complex outcomes. Scope: Proposals should address only one of the following sub-topics: A. [2018]: Understanding the genome of farmed animals, its expression and translation into traits (RIA) For the purpose of sub-topic A, the terms animal and farm apply to both terrestrial and aquatic animals. Research activities should generate experimental data to map out what part of farmed animal genomes are active (whether coding or regulatory), and under which circumstances, characterise the resulting phenotypes and assess how phenotypes are affected by genetic and epigenetic changes. Bioinformatic analyses should support identification of these functional and structural elements in genomes, and enable the development of tools for genotype to phenotype prediction. Work should also help to develop or extend terminologies (ontologies) to describe, represent and standardize annotation. Proposed projects should target one or more farmed animal species with high-quality genome assemblies (in particular cows, chicken, pigs, sheep, salmon and other relevant species), focussing on specific tissue panels, and address correlations between normal and abnormal situations. They may target different physiological and developmental stages and different breeds within the same species, where this brings added value to the understanding of the genotype to phenotype relationship. As regards genome annotation, the proposed projects should use FAANG70 metadata standards and core assays and coordinate with other projects in order to minimise overlaps. The data should be submitted to relevant European biological data archives in accordance with these standards to ensure they are available to the whole community (EMBL-EBI71). The proposed projects should develop and test, where appropriate, innovative tools to measure related phenotypes, including intermediate phenotypes. Activities may include biomarkers and their proxies, as well as sensors, together with ways to record related phenotypes at population level (whether reference populations or not). Proposals should include a task to cluster with other projects financed under this topic. 70 http://www.faang.org/index 71 http://data.faang.org.

Research, Education or Extension Projects Eligible applicants for single-function Research, Education or Extension Projects include: a) State Agricultural Experiment Station; b) colleges and universities (including junior colleges offering associate degrees or higher); c) university research foundations; d) other research institutions and organizations; e) Federal agencies, f) national laboratories; g) private organizations or corporations; h) individuals who are U.S. citizens, nationals, or permanent residents; and i) any group consisting of two or more entities identified in a) through h). Eligible institutions do not include foreign and international organizations.

There are several programs within AFRI Foundational RFA that will accept FAANG-related proposals. For those listed below, the above deadline applies, and NO letter of intent is required. Interested parties should read the full RFA to obtain information about all opportunities, however. An Repr A1211 An Health and Dis A1221 An Well-Being A1251 An Growth and Lactation A1231 Tools and Reagents: Immune Reagents A1223 Tools and Reagents: Animal Breeding Genetics and Genomics A1201.

See https://grants.nih.gov/grants/guide/pa-files/PAR-17-482.html#_Section_III._Eligibility Both US and foreign entities are eligible to apply; foreign components are eligible as well. Program is scheduled to continue through January 8, 2021.

NHGRI invites applications for research developing comparative approaches that can be used to understand genome structure and function and the relationship between genomic features and phenotypes. This program supports studies that enable the use of a diverse array of species to advance our ability to understand basic biological processes related to human health and disease, as well as studies that develop novel analytical tools and resources for the comparative genomics research community.

US institutions must be PD; foreign components are allowed.

Development of community genetic and genomic tools and resources, including software, experimental protocols and breeding methods, which can be applied to advance basic biology and improve animal health and production. Tools and resources may focus on: - Novel quantitative genetic methods including selection theory and modeling; or - Bioinformatics, cyber-infrastructure and databases for high-throughput genotyping,sequencing, and phenotyping. Program Area Priority Additional Information This Program Area Priority is limited to the development of tools and resources. Applications that apply genomic variation (e.g., selecting within a breed for a specific trait of interest) and relevance to function and phenotype for improved animal health or production, conventional/classical animal breeding, breed development, or applied quantitative genetics should be directed to Program Area Priorities 1, 2, 3, or 4 identified above. See program A1201 (Tools and Resources-Animal Breeding, Genetics and Genomics)and A1202 (Annotation of Agricultural Animal Genomes).

1) Research Projects Eligible applicants for Research Projects include:1) State Agricultural Experiment Station; 2) colleges and universities (including junior colleges offering associate degrees or higher); 3) university research foundations; 4) other research institutions and organizations; 5) Federal agencies, 6) national laboratories; 7) private organizations or corporations; 8) individuals who are U.S. citizens, nationals, or permanent residents; and 9) any group consisting of 2 or more entities identified in 1) through 8). Eligible institutions do not include foreign and international organizations. 2) Integrated Projects Eligible applicants for Integrated Projects include: 1) colleges and universities; 2) 1994 Land-Grant Institutions; and (3) Hispanic-serving agricultural colleges and universities. 1) Research Projects Eligible applicants for Research Projects include:1) State Agricultural Experiment Station; 2) colleges and universities (including junior colleges offering associate degrees or higher);.

**Be aware** The deadline listed is for one program described below; there are EARLIER deadlines for other programs. Several specific Programs may be relevant to FAANG related research. The most likely Program for FAANG projects is Tools and Resources - Animal Breeding, Genetics and Genomics Program Area Priority code #A12101, as they specifically mention FAANG in the research priorities list. The deadline is August 3, 2016 Tools and Resources - Animal Breeding, Genetics and Genomics Program Area Priority – Development of community genetic and genomic tools and resources, including software, experimental protocols and breeding methods, which can be applied to advance basic biology and improve animal health and production. Tools and resources may focus on: • Improvement of genome assembly; • Novel quantitative genetic methods including selection theory and modeling; or • Functional annotation of animal genomes (FAANG). Program Area Priority Additional Information: • This Program Area Priority is limited to the development of tools and resources. Proposals that apply genomic variation (e.g., selecting within a breed for a specific trait of interest) and relevance to function and phenotype for improved animal health or production, conventional animal breeding, breed development, or applied quantitative genetics should be directed to Program Area Priorities 1, 2, 3, or 4 identified above. • Projects related to FAANG must follow the guidelines developed by the FAANG community for selecting animals, tissues, assays, experimental protocols, data sharing and data analysis (http://www.faang.org/). Applicants should address major knowledge gaps and avoid duplication of efforts.

1862 Land-Grant Institutions, 1890 Land-Grant Institutions, 1994 Land-Grant Institutions, For-profit Organizations Other Than Small Businesses, Hispanic-Serving Institutions, Individuals, Native American Tribal Orgs, not Federally recognized Tribal Governments, Nonprofits with 501(c)(3) IRS status, other than Institutions of Higher Ed, Nonprofits without 501(c)(3) IRS status, other than Institutions of Higher Ed, Other or Additional Information (See below), Private Institutions of Higher Ed, Small Business, State Agricultural Experiment Stations, State Controlled Institutions of Higher Ed.

The goal of this Program Area Priority is to develop locally adapted crop cultivars and/or animal breeds that contribute to rural economic development and prosperity while enhancing regional and national resilience and food security. Projects are expected to lead to the development of cultivars and/or animal breeds that are able to resist or tolerate biotic and/or abiotic threats to production, enhance diversity and resilience of production systems, and maintain or enhance nutritional value. Projects should address the needs and challenges identified by producers and consumers. Proposals may include crops, animals, or a combination of both. Projects that develop tools and resources to enable discovery and advance breeding of crops and/or animals with strong potential to meet the program goals are encouraged. This program will support the development and use of high-throughput genomic technologies, phenomics, and advanced computational informatics to (i) produce varieties and breeds with improved resilience to climate change, drought, and extreme weather; (ii) increase protection of agricultural crops and food animals from disease and pests; and (iii) enhance nutritional composition for improved human health. In addition, development of new tools and technologies for high-throughput phenotyping in food crops and animals will be accelerated by leveraging breeding and phenomics expertise through research Coordination Networks.

Universities and Colleges - Universities and two- and four-year colleges (including community colleges) accredited in, and having a campus located in, the US acting on behalf of their faculty members. Such organizations also are referred to as academic institutions. Non-profit, non-academic organizations: Independent museums, observatories, research labs, professional societies and similar organizations in the U.S. associated with educational or research activities. Consortia of only the eligible organizations listed above.

The proposal deadlines shown above are for the EDGE track; the Core track (smaller proposals) have different deadlines shown in the website below. I think FAANG should look into the EDGE track. I would be interested in helping develop a plan for a LOI. CKT The Division of Integrative Organismal Systems (IOS) supports research aimed at understanding why organisms are structured the way they are and function as they do. Proposals should focus on organisms as a fundamental unit of biological organization. Principal Investigators (PIs) are encouraged to apply systems approaches that will lead to conceptual and theoretical insights and predictions about emergent organismal properties. Areas of inquiry include, but are not limited to, developmental biology and the evolution of developmental processes, nervous system development, structure, and function, physiological processes, functional morphology, symbioses, interactions of organisms with biotic and abiotic environments, and animal behavior. Proposals are welcomed in all of the core scientific program areas supported by the Division of Integrative Organismal Systems. Proposals may be submitted to the two tracks described in this solicitation. All investigator-initiated proposals submitted to the Core track of this solicitation must now be invited based on merit review of preliminary proposals. There is a single submission deadline with a limit of 2 preliminary proposals per investigator per year as PI or Co-PI in response to the Core track of this solicitation. Please see the GPG for definition of roles for PI and Co-PI. There are no limits on the number of proposals you can participate on as collaborator. These PI/Co-PI limits do not apply to full proposals submitted to the EDGE track of this solicitation, which has no PI or Co-PI limits on number of proposals submitted. The PI/Co-PI limits apply only to the preliminary proposals submitted to the Core track of this solicitation and do not pertain to proposals submitted in response to other NSF solicitations. Unsolicited full research proposals are no longer accepted into the IOS Core Programs. Full proposals submitted on a single deadline to the EDGE track of this solicitation do not require prior submission of a preliminary proposal. A Letter of Intent is required before submission of a full proposal to the EDGE track of this solicitation.