AnGenMap

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From listmasteranimalgenome.org  Fri Sep  2 07:02:07 2016
From: "Alison Van Eenennaam" <alvaneenennaamucdavis.edu>
Postmaster: submission approved by list moderator
To: Multiple Recipients of AnGenMap <angenmapanimalgenome.org>
Subject: Bovine Genome Coordinators Newsletter September, 2016
Date: Fri, 02 Sep 2016 07:02:07 -0500

Bovine Genome Coordinators Newsletter

September, 2016
======================================================================
1. Bovine Genome Coordinator Newsletter
2. Update on Improvement of the bovine genome reference assembly
   – Juan Medrano
3. FAANG updates – Huaijun Zhou
4. Development and availability of Illumina functional chip
   – Jerry Taylor
5. Cattle genomic database update – Harvey Blackburn
6. PacBio + PBJelly improved genome reference has been submitted to
   GenBank
7. Cattle/Sheep/Goat/NRSP-8 Program at PAG XXV in San Diego
   – Jared Decker
8. Nominate students for the PAG XXIV Neal A. Jorgenson Graduate
   Student Travel Award
9. eBEEF (eBEEF.org) beef genetics/genomics community of practice
   with eXtension launched
10. NIFA updates - Lakshmi Kumar Matukumalli (lmatukumallinifa.usda.gov)
======================================================================

1. Cattle Genome Coordinators Newsletter

Welcome to this the Bovine Genome Coordinator Newsletter from Juan
Medrano, UC Davis (jfmedranoucdavis.edu) Bovine Genome Coordinator, and
co-coordinators Jerry Taylor, University of Missouri
(taylorjerrmissouri.edu), and Alison Van Eenennaam, UC Davis
(alvaneenennaamucdavis.edu). We hope to keep the Bovine Genome
Community informed of developments and activities of the Bovine Genome
Coordinators through this periodic newsletter. If you have any
informational items you would like distributed via this newsletter
please call Alison Van Eenennaam at (530) 752-7942, or Email
alvaneenennaamucdavis.edu.

Important priorities for NRSP8, as related to Bovine Genomics for the
next 5 years are:

1) Development of a significantly improved Dominette bovine reference
genome sequence assembly, including annotation and sequence variation
derived from other breeds of cattle
2) Development of a repository for large datasets of phenotype and
genomic data, and
3) Translation of genetic findings from NRSP8 and USDA AFRI-funded
projects into tangible deliverables for industry.

2.  The new bovine reference assembly ARS-UCD v0.1 – Juan Medrano
(jfmedranoucdavis.edu)

Tim Smith at USDA/MARC and Juan Medrano at UCDavis have generated
approximately 80X PacBio coverage of Dominette with funding from NRSP8
Coordinator Funds, USDA/MARC and donations from Neogene and Zoetis. A
FALCON de novo assembly was produced at PacBio, followed by scaffolding
with the recently developed Optical Map of Dominette, Dovetail Genomics
Chicago library/HiRise technology and a recombination map of 59K SNP.
Several iterations applying the scaffolding resources in different order
have been used in order to develop several versions of the assembly. The
current ARS-UCDv0.1 assembly consists of 640 contigs and 29 scaffolds,
representing 118 and 218-fold reduction in number, respectively,
compared with the UMD3.1 assembly that is made up of 75,618 contigs and
6337 scaffolds.  The improvement is reflected in contiguity, as the new
assembly has contig N50=11.7 Mb and scaffold N50=110 Mb, representing
120 and 17-fold improvement compared to UMD3.1 (contig N50=0.97Mb,
scaffold N50=6.4Mb).  Further, the ARS-UCDv0.1 assembly has contig
L50=66 and scaffold L50=10, with a maximum scaffold length of 211.2Mb
corresponding to bovine chromosome 1.
One of the assemblies has been chosen for continue refinement to
chromosome level with contributions from Sergey  Koren at NHGRI, Aleksey
Zimin at U. Maryland, Derek Bickhart at USDA/BARC, and Christian
Dreischer and Sebastian Schultheiss at Computomics. To support
annotation, full-length transcripts have been sequenced using the PacBio
Iso-Seq method from approximately 30 Dominette tissues. We expect to
approach chromosome-length contigs for many chromosomes, and believe
that the improvements in the cow assembly are substantial enough that it
is worth considering waiting for them for ongoing GWAS and WGR studies.
A public version of the new ARS-UCD assembly is expected to be ready
within the next 6 months.  Please address inquiries about the assembly
to either jfmedrano@ucdavis.edu, or tim.smithars.usda.gov.

3.  FAANG updates – Huaijun Zhou  (hzhouucdavis.edu)

As a part of the FAANG initiative, and with the support of both USDA
NIFA and NRSP8 Bovine Genome Coordinator funds, tissues were collected
from four (2 males and 2 females) 14 month Line 1 Herefords provided by
. The samples from eight tissues (Skeletal muscle, Liver, Adipose,
Spleen, Hypothalamus, Brain cortex/whole, Cerebellum, Lung) from the
males were processed for RNA-seq, ChIP-seq, and DNase-seq, and data will
be integrated to functionally annotate regulatory elements of the bovine
genome. There are additional tissues that were collected on the males
for which there is not yet funding secured to perform these assays
(pancrea, Heart, Trachea, Thyroid gland, Esophagus, Thymus, Skin,
Testis, Bone marrow, Blood, Cartilage, Duodenum, Jejunum, Ileum, Cecum,
Colon, Abomasum, Olfactory bulb etc.), and all these same tissues were
collected on the two females as well. To see the database of all of the
different tissues collected for bovine (and other livestock species) log
into the FAANG site (http://www.faang.org) and go to the working group
“Animals, Samples and Assays (ASA)” and under “Documentations” there is
a link “Sample Collection Schedules” which lists the samples collected
for the different species – as of 8/26/16 there were 692 buffalo, 318
cattle, 116 chicken, 89 goat, 143 horse, 338 pig, and 959 sheep samples.
Listed at this location is what type of animal the tissue came from
(genetic line, development stage, tissue), where the samples were
collected, and the number of different assays (e.g. RNA-profiling,
Histone Modification, transcription factor, open chromatin) that have
been/will be performed on that tissue. Those that are funded (A), or
included in a grant under review (B). With respect to bovine tissues
there are a number of groups from around the world (Australia, Canada,
France, Germany, USA) that have collected both dairy and beef tissues
samples listed on the spreadsheet there. It is recommended looking at
this public list to determine the work that is ongoing in FAANG, and to
possibly access samples for a new FAANG assay or propose a grant to
secure funding to analyze samples using an existing assay.    For more
information contact Huaijun Zhou at the UC Davis (hzhouucdavis.edu) who
is the PI on the USDA NIFA Foundational project.

4.  Development and availability of Illumina functional chip – Jerry
Taylor (taylorjerrmissouri.edu)

The University of Missouri in collaboration with GeneSeek have developed
an Illumina 250K Bead Infinium functional variant assay which we call
the GGP F250. This assay was developed with USDA NIFA funding which
supported whole genome sequencing for variant discovery and the
purchasing of sufficient numbers of chips to support the design. The
assay was designed using sequence data on over 400 individuals from
multiple taurine breeds and sequence data from the 1000 Bull Genomes
Project, dbSNP and indicine cattle were used to validate the loci
included in the design. The chip is focused on the detection of genic
variants likely to be functional in taurine cattle. The 250K beads were
allocated to 199K functional variants and 34K imputation SNPs found on
the BovineSNP50, BovineHD and GeneSeek Products. The assay has been used
to genotype 18,271 samples from the USDA NIFA supported “Bovine
Respiratory Disease CAP,” “Feed Efficiency” and “Heifer Fertility”
Projects and these samples were used to generate the GenomeStudio
cluster files.  Based on these samples 206,652 variants were
successfully clustered and of these 173,609 variants were variable and
had a call rate of at least 90%. Of these, 82,979 are amino acid
substitutions, 665 are coding indels, 2,017 are splice site variants,
44,358 are intronic and 18,009 are located in UTRs. The remaining 25,581
variants are not located within genes. The manifest is in the process of
being annotated and the annotation will be available within a few weeks.
The anticipated cost of the assay will be about $100 per sample
dependent on volume. Inquiries can be directed to Stewart Bauck at
GeneSeek (SBauckneogen.com).

5.  Cattle GRIN Genomics Database update – Harvey Blackburn
(Harvey.Blackburnars.usda.gov)

The Animal – GRIN Genomics Database was updated in 2015 and 2016. This
database will eventually contain several types of genomic information.
Currently the database contains SNP-chip data. Graduate students at
Colorado State University beta-tested the system by uploading genomic
data from various cattle projects and extracting information. NAGP staff
also uploaded genomic information from cattle and swine populations
maintained in the repository as part of the testing process. All of the
purebred boars in the NAGP collection have been SNP-chip genotyped and
these data are in this system. Efforts have also been ongoing to
interface the Animal-GRIN system with the Internet 2 effort which ARS as
a whole has been engaged in developing. Further web-interface work on
front-ends/back-ends is being completed to facilitate user requests. We
anticipate this system to be fully functional in 2017.

6. PacBio + PBJelly improved genome reference has been submitted to
GenBank - Kim Worley (kworleybcm.edu) reports that the Hereford
reference genome assembly has been improved using Pacific Biosciences
long read data and the PBJelly software (English, et al., 2012).  The
improved assembly, Btau_5.0.1, is available in GenBank and has been
annotated by RefSeq
(http://www.ncbi.nlm.nih.gov/...bly/GCF_000003205.7/).  The assembly
has a contigN50 of 276,285 kb.  The annotations include 21,514 protein
coding genes and 5,563 non-coding genes.

The long read data used for the improvement are available in the SRA
(http://www.ncbi.nlm.nih.gov/sra?
LinkName=biosample_sra&from_uid=3897382).

7.  Cattle/Sheep/Goat/NRSP-8 Program at Plant and Animal Genome XXIV
in San Diego –
          Jared Decker (DeckerJEmissouri.edu)
Poster Abstract Submission Deadline: October 28, 2016.

Jared Decker is seeking speakers for the PAG 2017Cattle/Sheep/Goat
workshop!  If you are interested, please contact Jared Decker:
DeckerJEmissouri.edu  with a tentative title of your presentation and a
brief description of your work by Monday October 3rd.  Speakers will be
chosen by Friday October 14th, 2016. Chosen speakers must be confirmed
before November 1st.  Deadline for workshop abstract submissions is
December 2, 2016.   Scientists at all career stages will be considered.

8.  Nominate students for the PAG XXIV Neal A. Jorgenson Graduate
Student Travel Award
Application Deadline: October 15, 2016

Up to two students will be selected to receive the Neal A. Jorgenson
Genome Travel Award by the Bovine Genome coordinators. This award
provides up to $1000 for travel expenses and registration provided for
graduate students in the USA to travel to and attend PAGXXIV. Look for
their posters at PAG XXIV, and depending upon their research topic and
the interest that it may generate their oral presentation may be
selected for presentation at one of the NRSP8 cattle workshops! Apply at
http://www.intlpag.org/...grants-jorgenson.pdf.


9.  eBEEF (eBEEF.org) beef genetics/genomics community of practice
with eXtension
http://www.eBEEF.org, eBEEF is the beef genetics/genomics community of practice
within eXtension (the interactive learning environment delivering
research-based information emerging from America's land-grant university
system). The mission of eBEEF is to foster a research and outreach
community, engage beef cattle producers and agricultural professionals
through training and publications, and support research and outreach
projects. eBEEF was developed in an attempt to consolidate information
about beef breeding and genetics into a single site rather than in the
disparate collection of sites that currently houses a lot of beef
genetics and genomics information, especially that associated with the
various USDA AFRI-funded  beef projects.

Beef cattle specialists from five land grant institutions (Dr. Darrh
Bullock, University of Kentucky; Dr. Jared Decker, University of
Missouri; Dr. Megan Rolf, Kansas State University; Dr. Matt Spangler,
University of Nebraska; Dr. Bob Weaber, Kansas State University; and Dr.
Alison Van Eenennaam; University of California – Davis) are participants
in eBEEF. The site contains factsheets, short frequently asked question
(FAQ) video clips, relevant conference recordings and webinars, a
YouTube channel, Twitter account, a blog and links to other useful beef
sites. Interested parties can sign up to join at eBEEF.org to receive a
quarterly email newsletter.

If you have any informational items you would like distributed via the
next bovine genome coordinator newsletter please call Alison Van
Eenennaam at UC Davis at (530) 752-7942, or Email
alvaneenennaamucdavis.edu.

10. NIFA updates - Lakshmi Kumar Matukumalli
(lmatukumallinifa.usda.gov)
I. NIFA Annual Report (https://nifa.usda.gov/pdf-version)
II. NIFA Leadership
• Director of NIFA: Dr. Sonny Ramaswamy (sramaswamynifa.usda.gov)
• Deputy Director of Institute of Food Production and
Sustainability (IFPS):
Dr Parag Chitnis (parag.chitnisnifa.usda.gov)
• Director of Division of Animal Systems: Dr. Adele Turzillo
(aturzillonifa.usda.gov)

III. NIFA Budgets, FFAR, and 2014-18 Farm Bill Updates:
• https://nifa.usda.gov/...d-budget-information
 For program priorities including upcoming challenge area priorities,
please read the explanatory notes.
•
https://nifa.usda.gov/...20House%20
and%20Senate%20Committee%20Table.pdf
• 2014-18 Farm Bill (Agricultural Act of 2014) Updates:
o Centers of Excellence (Sec. 7214 of Farm Bill)  This provision
is implemented since 2015 in competitive programs
o Commodity Boards Provision (Sec 7404 of Farm Bill):  This
provision is implemented since 2016 and some commodity boards provided
matching dollars. Please talk to the commodity boards pertaining to your
species of interest to enrol in the program and provide matching funds.
http://nifa.usda.gov/commodity-boards

o Foundation for Agricultural Research (http://foundationfar.org/)
is providing funds for new innovators and rapid responses. Feel free to
engage with the new FFAR team to discuss animal science priorities. FFAR
programs may also require industry matching funds.

IV. AFRI Competitive Programs
• In FY 2017 Agriculture and Food Research Initiative (AFRI) RFAs
are targeted for release in mid-February, 2017 and the submission
deadlines will likely be around mid-May, 2017. Most AFRI foundational
programs do not change significantly from year to year. Hence it can be
useful to see the program description and priorities in the previous
year RFAs in you are planning on submitting a proposal. The program
priorities in the challenge areas change year to year, please see the
budget explanatory notes (http://www.obpa.usda.gov/19nifa2017notes.pdf)
for the program area priorities most relevant to animal sciences such as
food security, food safety (Antimicrobial Resistance), water, and
climate change.
• AFRI Foundational Program  (FY 2016 $31M Total Funds for Animal
Programs)
http://www.nifa.usda.gov/...-and-food-
research-initiative-foundational-program

AFRI supports innovation in animal programs through multidisciplinary
programs such as nanotechnology, robotics, engineering, and economics.
To be successful in these programs it will be essential to build
partnership with your colleagues from other departments to jointly
develop new solutions to support animal agriculture.

In addition to these programs AFRI Foundational RFA has two programs to
address agricultural (animal) challenges:
“Critical Agricultural Research and Extension” (CARE) Program
      ($300,000; short-term, very applied science);
- Integrated Research and Extension Projects
- Develop and implement solutions to critical producer problems
associated with animal and crop production, protection, or product
quality. Emphasis will be placed on achieving results that can be
applied by the producer as quickly as possible following project
completion. Applications should include justification of why the issue
is critical and how project outcomes will rapidly impact the stakeholder
community. The project must include stakeholders.

“Exploratory” ($100,000; support transformative preliminary data)
- New and emerging innovative ideas that have high potential
impact;
- Application of new knowledge or new approaches to unsolved
challenges that have high potential impact;
- Tools required to have a paradigm shift in the field; and/or
- Rapid response to natural disasters and similar unanticipated
events.

V. Dual Purpose with Dual Benefit: Research in Biomedicine and
Agriculture Using Agriculturally Important Domestic Species – NIH and
NIFA have extended this joint program for an additional 3 years (2016 –
18).  Applications are submitted to NIH using the R01 funding mechanism
and reviewed at NIH’s Center for Scientific Review using special
emphasis review panels (including reviewers with expertise in
agricultural animals).  Applications must address one of the areas of
identified in the PAR; focus on a problem that is similar, if not
identical, in human health and animal agriculture; use an agricultural
animal as the model; and be justified in terms of relevance to human
health and animal agriculture.  Program contact is Dr. Mark Mirando
(mmirandonifa.usda.gov); next application deadline is September 27,
2016.
https://grants.nih.gov/...iles/PAR-16-366.html

VI. Ecology and Evolution of Infectious Disease - Funding
opportunity partnering NIFA, NSF, NIH, and the U.K. Biotechnology and
Biological Sciences Research Council.  Applications are submitted to and
reviewed at NSF with NIFA, NIH, & U.K. participation. NIFA provides a
minimum of $2.5 million each year.  Program contact is Peter Johnson
pjohnsonnifa.usda.gov; next application deadline is November 16, 2016.
NIFA awards to date: FY2013 (two US-UK Collaborative Research Awards:
Foot and Mouth Disease; and, Potato Virus); In FY2014, (one US-UK award
on Mycobacterial Diseases (Johne’s & Bovine Tuberculosis));
http://www.nsf.gov/...umm.jsp?pims_id=5269

VII. Veterinary Medicine Loan Repayment Program (VMLRP;
http://www.nifa.usda.gov/vmlrp) - $5 M (FY-15 enacted) and Veterinary Services
Grants Program ($2.5 M).  NIFA’s VMLRP administers competitively awarded
educational loan repayments incentivizing veterinarians to serve in
shortage situations in the food supply veterinary sector.  Up to $75,000
in loan repayments may be awarded for a minimum of 3 years of service in
shortage situations, and opportunities for competitive renewal awards
exist for those still carrying eligible educational debt after
completing the first three years of service. The Veterinary Services
Grants Program provides funding for equipment and educational activities
that enhances retention of veterinarians in rural areas that support
animal agriculture. Program contact is Dr. Gary Sherman;
vmlrp@nifa.usda.gov or vsgpnifa.usda.gov

VIII. Small Business Innovative Research (SBIR) program - $21.5 M:
Competitive Grants for qualified small businesses (< 500 employees);
Funded through set-aside formula (2.9% of all USDA extramural R&D
funds).  More than 70% of funds from NIFA, with remaining from ARS,
FSIS, APHIS, ERS, FAS and NASS.  Phase I and Phase II R&D projects with
commercial promise are supported.  Animal Production & Protection, is
one of ten programs.  Program Goals/Priorities are to develop
innovative, marketable technologies that will provide significant
improvement to: feed efficiency, safety and/or quality of end products,
animal health & well-being, productivity, and mitigate impact of
livestock on the environment.  Program Contact is Dr. Bob Smith
(rsmithnifa.usda.gov).

IX. Other competitive grant programs with opportunities for animal
and veterinary scientists
• Organic Agriculture Research and Extension Initiative (OREI)
• Organic Transitions
• Higher Education Challenge Grants (experiential student
learning; curriculum development; faculty development)
• Beginning Farmers and Ranchers Program
• Biotechnology Risk Assessment Grants (BRAG)
• AFRI Small and Medium-Sized Farms (see Ag Economics & Rural
Communities in AFRI Foundational RFA)
• 2016 Aquaculture Research Competitive Special Research Grants
X. Capacity Grant Programs: Distributions of Federal Appropriations
to State Agricultural Experiment (SAES), state Cooperative Extension
Systems (SCES), and Veterinary Colleges by formula; used by states to
address local or regional agriculture-related research, education and
extension needs:
A.  Hatch Capacity (formula) Grant Program: $244 M (FY-15 enacted) -
Supports agricultural/rural research across many discipline areas
(animals, plants, soil, water, food safety, climate change, bioenergy).
Funding distribution within each State is managed by the Director of the
SAES.
B. Smith Lever Capacity (formula) Grant Program: $300 M (FY-15 enacted)
- Supports Cooperative Extension education efforts across many
discipline areas (animals, plants, soil, water, food safety, climate
change, bioenergy, education).  Funding distribution within each State
is managed by the Director of the SCES.
C  Animal Health and Disease Research (AHDR) Sec. 1433 Capacity Grant
program; $4 M (FY-15 enacted) – These research dollars must be used for
animal health and disease research in agriculturally relevant species.
Funds are managed through the office of the Director of each SAES and/or
the Dean of the Veterinary school, or the Head of the Land Grant
University Veterinary Sciences department.

Multi-State Research Committees (MSRCs) and National Research Support
Projects (NRSPs): Facilitate gatherings of scientists sharing interest
in solving animal health and animal production challenges especially
important to specific states/regions (MSRCs) or the nation (NRSPs).
These regional committees and national projects are supported as a
specific apportionment (25% minimum) of the annual Hatch Capacity
appropriation.  For complete searchable listings and descriptions of
MSRCs and NRSPs, go to the National Information Management and Support
System (NIMSS).

XI. Stakeholder Input
• We recently concluded joint ARS-NIFA Animal Production
stakeholder Listening Sessions along with additional stakeholder inputs
through new co-digital platform. We are compiling the results and post
the report.

• Joint ARS-NIFA Aquaculture Genomics strategic workshop was held
at Auburn, AL. Meeting report from the workshop will be published
shortly. https://cws.auburn.edu/.../aquacultureworkshop

• Stakeholder webinar series on different topics pertaining to
Animal health are currently underway. Please register in your
interesting area/topic for providing inputs on program priorities. If
you cannot attend in person please send an email with your inputs to
animal.healthnifa.usda.gov with a subject line as one of the topics
from the webinar series.
https://nifa.usda.gov/...older-webinar-series

Inputs relating to NIFA programs are welcome at any time.  Comments
should be directed to the National Program Leader responsible for the
specific topic or program(s).

XII. Functional Annotation of Animal Genomes (FAANG)
Several FAANG related workshops were conducted recently and the
community has come up with a couple of white papers and action plan
describing the goals. I am glad to see that the coordination committee
has representation from many countries through-out the world. Although a
few pilot projects are already underway, now it is time to make the
vision articulated in the manuscripts into reality (submission of
multiple coordinated proposals for each of the major commodities?). The
Research Coordination Network (RCN) funded by NSF and the EU-COST
projects can enable engagement with researchers from agriculture other
animal communities. Engagement with other federal agencies with US
(USDA, NSF, NIH, and DOE) and outside US (EU, BBSRC, Genome Canada, INRA
and AnR France etc.,) is also important.
In addition the community can engage with the commodity boards and
private companies to raise matching funds that could be used to leverage
funding from NIFA commodity boards provision or through FFAR.Please
visit FAANG website or contact Chris Tuggle or one of the FAANG
coordinators for more details.  http://www.faang.org/bbs?s=go-faang.txt

XIII. Personnel Updates

National Program Leaders and Program Specialists, Division of Animal
Systems:

National Program Leaders:

Adele Turzillo  Division Director (202) 401-6158
aturzillonifa.usda.gov
Margo Holland Animal Health & Well-Being (202) 401-5044
mhollandnifa.usda.gov
Gene Kim Aquaculture (202) 401-1108 gene.w.kimnifa.usda.gov
Peter Johnson Animal Health & Well-Being (202) 401-1896
pjohnsonnifa.usda.gov
Charlotte Kirk Baer Animal Nutrition (202) 720 5280
cbaernifa.usda.gov
Lakshmi Matukumalli Animal Genomics (202) 401-1766
lmatukumallinifa.usda.gov
Mark Mirando Animal Nutrition, Growth & Repro. (202) 401-4336
mmirandonifa.usda.gov
Gary Sherman Veterinary Science & Medicine (202) 401-4952
gshermannifa.usda.gov
Bob Smith Veterinary Medicine (202) 401-4892
rsmithnifa.usda.gov
Steve Smith Animal Production Systems  (202) 401-6134
sismithnifa.usda.gov

Program Coordinator

Danielle Tack Animal Health Program Coordinator (202) 401-6802
danielle.tacknifa.usda.gov

Program Specialists:

Desiree Abrams Animal Systems (202) 401.5046 dabramsnifa.usda.gov
Max Mayeaux Aquaculture (202) 401-3352 mmayeauxnifa.usda.gov
Lisa Stephens Animal Protection & Biosecurity (202) 401-6438
lstephensnifa.usda.gov
 Davida Tengey        Animal Systems
(202) 401-1772
dtengeynifa.usda.gov NIFA updates - Lakshmi Kumar Matukumalli
(lmatukumallinifa.usda.gov)
XIV. NIFA Annual Report (https://nifa.usda.gov/pdf-version)
XV. NIFA Leadership
• Director of NIFA: Dr. Sonny Ramaswamy (sramaswamynifa.usda.gov)
• Deputy Director of Institute of Food Production and
Sustainability (IFPS):
Dr Parag Chitnis (parag.chitnisnifa.usda.gov)
• Director of Division of Animal Systems: Dr. Adele Turzillo
(aturzillonifa.usda.gov)

XVI. NIFA Budgets, FFAR, and 2014-18 Farm Bill Updates:
• https://nifa.usda.gov/...d-budget-information
 For program priorities including upcoming challenge area priorities,
please read the explanatory notes.
•
https://nifa.usda.gov/...20House%20
and%20Senate%20Committee%20Table.pdf
• 2014-18 Farm Bill (Agricultural Act of 2014) Updates:
o Centers of Excellence (Sec. 7214 of Farm Bill)  This provision
is implemented since 2015 in competitive programs
o Commodity Boards Provision (Sec 7404 of Farm Bill):  This
provision is implemented since 2016 and some commodity boards provided
matching dollars. Please talk to the commodity boards pertaining to your
species of interest to enrol in the program and provide matching funds.
http://nifa.usda.gov/commodity-boards

o Foundation for Agricultural Research (http://foundationfar.org/)
is providing funds for new innovators and rapid responses. Feel free to
engage with the new FFAR team to discuss animal science priorities. FFAR
programs may also require industry matching funds.

XVII. AFRI Competitive Programs
• In FY 2017 Agriculture and Food Research Initiative (AFRI) RFAs
are targeted for release in mid-February, 2017 and the submission
deadlines will likely be around mid-May, 2017. Most AFRI foundational
programs do not change significantly from year to year. Hence it can be
useful to see the program description and priorities in the previous
year RFAs in you are planning on submitting a proposal. The program
priorities in the challenge areas change year to year, please see the
budget explanatory notes (http://www.obpa.usda.gov/19nifa2017notes.pdf)
for the program area priorities most relevant to animal sciences such as
food security, food safety (Antimicrobial Resistance), water, and
climate change.
• AFRI Foundational Program  (FY 2016 $31M Total Funds for Animal
Programs)
http://www.nifa.usda.gov/...-and-food-
research-initiative-foundational-program

AFRI supports innovation in animal programs through multidisciplinary
programs such as nanotechnology, robotics, engineering, and economics.
To be successful in these programs it will be essential to build
partnership with your colleagues from other departments to jointly
develop new solutions to support animal agriculture.

In addition to these programs AFRI Foundational RFA has two programs to
address agricultural (animal) challenges:
“Critical Agricultural Research and Extension” (CARE) Program
      ($300,000; short-term, very applied science);
- Integrated Research and Extension Projects
- Develop and implement solutions to critical producer problems
associated with animal and crop production, protection, or product
quality. Emphasis will be placed on achieving results that can be
applied by the producer as quickly as possible following project
completion. Applications should include justification of why the issue
is critical and how project outcomes will rapidly impact the stakeholder
community. The project must include stakeholders.

Exploratory” ($100,000; support transformative preliminary data)
- New and emerging innovative ideas that have high potential
impact;
- Application of new knowledge or new approaches to unsolved
challenges that have high potential impact;
- Tools required to have a paradigm shift in the field; and/or
- Rapid response to natural disasters and similar unanticipated
events.

XVIII. Dual Purpose with Dual Benefit: Research in Biomedicine and
Agriculture Using Agriculturally Important Domestic Species – NIH and
NIFA have extended this joint program for an additional 3 years (2016 –
18).  Applications are submitted to NIH using the R01 funding mechanism
and reviewed at NIH’s Center for Scientific Review using special
emphasis review panels (including reviewers with expertise in
agricultural animals).  Applications must address one of the areas of
identified in the PAR; focus on a problem that is similar, if not
identical, in human health and animal agriculture; use an agricultural
animal as the model; and be justified in terms of relevance to human
health and animal agriculture.  Program contact is Dr. Mark Mirando
(mmirandonifa.usda.gov); next application deadline is September 27,
2016.
https://grants.nih.gov/...iles/PAR-16-366.html

XIX. Ecology and Evolution of Infectious Disease - Funding
opportunity partnering NIFA, NSF, NIH, and the U.K. Biotechnology and
Biological Sciences Research Council.  Applications are submitted to and
reviewed at NSF with NIFA, NIH, & U.K. participation. NIFA provides a
minimum of $2.5 million each year.  Program contact is Peter Johnson
pjohnsonnifa.usda.gov; next application deadline is November 16, 2016.
NIFA awards to date: FY2013 (two US-UK Collaborative Research Awards:
Foot and Mouth Disease; and, Potato Virus); In FY2014, (one US-UK award
on Mycobacterial Diseases (Johne’s & Bovine Tuberculosis));
http://www.nsf.gov/...umm.jsp?pims_id=5269

XX. Veterinary Medicine Loan Repayment Program (VMLRP;
http://www.nifa.usda.gov/vmlrp) - $5 M (FY-15 enacted) and Veterinary Services
Grants Program ($2.5 M).  NIFA’s VMLRP administers competitively awarded
educational loan repayments incentivizing veterinarians to serve in
shortage situations in the food supply veterinary sector.  Up to $75,000
in loan repayments may be awarded for a minimum of 3 years of service in
shortage situations, and opportunities for competitive renewal awards
exist for those still carrying eligible educational debt after
completing the first three years of service.
The Veterinary Services Grants Program provides funding for equipment
and educational activities that enhances retention of veterinarians in
rural areas that support animal agriculture. Program contact is Dr. Gary
Sherman; vmlrp@nifa.usda.gov or vsgpnifa.usda.gov

XXI. Small Business Innovative Research (SBIR) program - $21.5 M:
Competitive Grants for qualified small businesses (< 500 employees);
Funded through set-aside formula (2.9% of all USDA extramural R&D
funds).  More than 70% of funds from NIFA, with remaining from ARS,
FSIS, APHIS, ERS, FAS and NASS.  Phase I and Phase II R&D projects with
commercial promise are supported.  Animal Production & Protection, is
one of ten programs.  Program Goals/Priorities are to develop
innovative, marketable technologies that will provide significant
improvement to: feed efficiency, safety and/or quality of end products,
animal health & well-being, productivity, and mitigate impact of
livestock on the environment.  Program Contact is Dr. Bob Smith
(rsmithnifa.usda.gov).

XXII. Other competitive grant programs with opportunities for animal
and veterinary scientists
• Organic Agriculture Research and Extension Initiative (OREI)
• Organic Transitions
• Higher Education Challenge Grants (experiential student
learning; curriculum development; faculty development)
• Beginning Farmers and Ranchers Program
• Biotechnology Risk Assessment Grants (BRAG)
• AFRI Small and Medium-Sized Farms (see Ag Economics & Rural
Communities in AFRI Foundational RFA)
• 2016 Aquaculture Research Competitive Special Research Grants
XXIII. Capacity Grant Programs: Distributions of Federal Appropriations
to State Agricultural Experiment (SAES), state Cooperative Extension
Systems (SCES), and Veterinary Colleges by formula; used by states to
address local or regional agriculture-related research, education and
extension needs:
A.  Hatch Capacity (formula) Grant Program: $244 M (FY-15 enacted) -
Supports agricultural/rural research across many discipline areas
(animals, plants, soil, water, food safety, climate change, bioenergy).
Funding distribution within each State is managed by the Director of the
SAES.
B. Smith Lever Capacity (formula) Grant Program: $300 M (FY-15 enacted)
- Supports Cooperative Extension education efforts across many
discipline areas (animals, plants, soil, water, food safety, climate
change, bioenergy, education).  Funding distribution within each State
is managed by the Director of the SCES.
C  Animal Health and Disease Research (AHDR) Sec. 1433 Capacity Grant
program; $4 M (FY-15 enacted) – These research dollars must be used for
animal health and disease research in agriculturally relevant species.
Funds are managed through the office of the Director of each SAES and/or
the Dean of the Veterinary school, or the Head of the Land Grant
University Veterinary Sciences department.

Multi-State Research Committees (MSRCs) and National Research Support
Projects (NRSPs): Facilitate gatherings of scientists sharing interest
in solving animal health and animal production challenges especially
important to specific states/regions (MSRCs) or the nation (NRSPs).
These regional committees and national projects are supported as a
specific apportionment (25% minimum) of the annual Hatch Capacity
appropriation.  For complete searchable listings and descriptions of
MSRCs and NRSPs, go to the National Information Management and Support
System (NIMSS).

XXIV. Stakeholder Input
• We recently concluded joint ARS-NIFA Animal Production
stakeholder Listening Sessions along with additional stakeholder inputs
through new co-digital platform. We are compiling the results and post
the report.

• Joint ARS-NIFA Aquaculture Genomics strategic workshop was held
at Auburn, AL. Meeting report from the workshop will be published
shortly. https://cws.auburn.edu/.../aquacultureworkshop

• Stakeholder webinar series on different topics pertaining to
Animal health are currently underway. Please register in your
interesting area/topic for providing inputs on program priorities. If
you cannot attend in person please send an email with your inputs to
animal.healthnifa.usda.gov with a subject line as one of the topics
from the webinar series.
https://nifa.usda.gov/...older-webinar-series

Inputs relating to NIFA programs are welcome at any time.  Comments
should be directed to the National Program Leader responsible for the
specific topic or program(s).

XXV. Functional Annotation of Animal Genomes (FAANG)
Several FAANG related workshops were conducted recently and the
community has come up with a couple of white papers and action plan
describing the goals. I am glad to see that the coordination committee
has representation from many countries through-out the world. Although a
few pilot projects are already underway, now it is time to make the
vision articulated in the manuscripts into reality (submission of
multiple coordinated proposals for each of the major commodities?). The
Research Coordination Network (RCN) funded by NSF and the EU-COST
projects can enable engagement with researchers from agriculture other
animal communities. Engagement with other federal agencies with US
(USDA, NSF, NIH, and DOE) and outside US (EU, BBSRC, Genome Canada, INRA
and AnR France etc.,) is also important.

In addition the community can engage with the commodity boards and
private companies to raise matching funds that could be used to leverage
funding from NIFA commodity boards provision or through FFAR.

Please visit FAANG website or contact Chris Tuggle or one of the FAANG
coordinators for more details.  http://www.faang.org/bbs?s=go-faang.txt

XXVI. Personnel Updates

National Program Leaders and Program Specialists, Division of Animal
Systems:

National Program Leaders:

Adele Turzillo  Division Director (202) 401-6158
aturzillonifa.usda.gov
Margo Holland Animal Health & Well-Being (202) 401-5044
mhollandnifa.usda.gov
Gene Kim Aquaculture (202) 401-1108 gene.w.kimnifa.usda.gov
Peter Johnson Animal Health & Well-Being (202) 401-1896
pjohnsonnifa.usda.gov
Charlotte Kirk Baer Animal Nutrition (202) 720 5280
cbaernifa.usda.gov
Lakshmi Matukumalli Animal Genomics (202) 401-1766
lmatukumallinifa.usda.gov
Mark Mirando Animal Nutrition, Growth & Repro. (202) 401-4336
mmirandonifa.usda.gov
Gary Sherman Veterinary Science & Medicine (202) 401-4952
gshermannifa.usda.gov
Bob Smith Veterinary Medicine (202) 401-4892
rsmithnifa.usda.gov
Steve Smith Animal Production Systems  (202) 401-6134
sismithnifa.usda.gov


Program Coordinator

Danielle Tack Animal Health Program Coordinator (202) 401-6802
danielle.tacknifa.usda.gov

Program Specialists:

Desiree Abrams Animal Systems (202) 401.5046 dabramsnifa.usda.gov
Max Mayeaux Aquaculture (202) 401-3352 mmayeauxnifa.usda.gov
Lisa Stephens Animal Protection & Biosecurity (202) 401-6438
lstephensnifa.usda.gov
Davida Tengey Animal Systems (202) 401-1772 dtengeynifa.usda.gov

 
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