AnGenMap

Archived Post

From alvaneenennaamucdavis.edu  Thu Sep 24 22:52:45 2015
From: Alison Van Eenennaam <alvaneenennaamucdavis.edu>
Postmaster: submission approved by list moderator
To: Multiple Recipients of AnGenMap <angenmapanimalgenome.org>
Subject: Bovine Genome Coordinators' September 2015 Newsletter
Date: Thu, 24 Sep 2015 22:52:45 -0500

Thanks to all who participated on the Bovine Genome Coordinator conference
call on Wednesday.

Please find attached the September 2015 Bovine Genome Coordinators Newsletter
which covers the following topics.

Bovine Genome Coordinators Newsletter
September, 2015
=================================================================================
 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. Cattle/Sheep/Goat/NRSP-8 Program at PAG XXIV in San Diego - Stephanie McKay
 7. Nominate students for the PAG XXIV Neal A. Jorgenson Graduate Student Travel
    Award
 8. Annotation of bovine genome with the NLM controlled Medical Subject Headings
 9. PacBio + PBJelly improved genome reference has been submitted to GenBank
10. LIC  (New Zealand)  plans to sequence Holstein Friesian bull to 70x coverage
    using Pac Bio
11. eBEEF (eBEEF.org) beef genetics/genomics community of practice with
eXtension
    launched
12. Discussion of  other issues of concern/priorities for the bovine genome
    community
13. NIFA updates - Lakshmi Kumar Matukumalli (lmatukumallinifa.usda.gov)
=================================================================================

The Bovine Genome Coordinators:

*  Juan Medrano, UC Davis (jfmedranoucdavis.edu), Coordinator
*  Jerry Taylor, University of Missouri (taylorjerrmissouri.edu), Co-coordinator
*  Alison Van Eenennaam, UC Davis (alvaneenennaamucdavis.edu), Co-coordinator


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. Improvement of the bovine genome reference assembly - Juan Medrano
   (jfmedranoucdavis.edu)

Tim Smith at USDA/MARC and Juan Medrano at UC Davis have generated
approximately 83X PacBio coverage of Dominette with funding from NRSP8
Coordinator Funds, USDA/MARC, UC Davis and a donations from Zoetis. A PacBio
de-novo assembly will be generated, followed by scaffolding of contigs using
the recently generated Optical Map and Dovetail Genomics' Chicago
library/HiRise scaffolding approach made possible by a donation from
GeneSeek/Neogen. The assembly will be completed by December 2015. Most of
the PacBio data were shared with Aleksey Zimin who will generate a hybrid
Pac-Bio/Sanger assembly and a full PacBio only assembly. Aleksey has been
supported by USDA/NIFA for this project. In addition, Kim Worley at Baylor
who is also supported by USDA/NIFA has produced a PacBio+PBJelly Dominette
assembly that has been submitted to GenBank and data are available in SRA
(see item 9). This will result in the need to compare and merge the produced
assemblies to create one high quality Dominette reference genome. Annotation
of the assembly will follow. LIC in New Zealand are in the process of
generating a 70X PacBio Holstein assembly which will be publicly available
(see item 10).

A paper on the optical mapping of the bovine genome was recently published:
S. Zhou, S. Goldstein, M. Place, M. Bechner, D. Patino, K. Potamousis, P.
Ravindran, L. Pape, G. Rincon, J. Hernandez-Ortiz, J.F. Medrano and D.C.
Schwartz 2015. A clone-free, single molecule map of the domestic cow (Bos
taurus) genome. BMC Genomics 16(664):1. http://www.biomedcentral.com/
1471-2164/16/644

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

As a part of the FAANG initiative, recent effort supported by both USDA NIFA
and NRSP8 Bovine Genome Coordinator funds has kicked off. A variety of
tissues from 4 Line 1 Hereford (2 males and 2 females) have been collected
and processed by RNA-seq, ChIP-seq, and DNase-seq, and data will be
integrated to functionally annotate the bovine genome. 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 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
will first be used to genotype samples from the USDA NIFA supported "Bovine
Respiratory Disease CAP," "Feed Efficiency" and "Heifer Fertility" Projects.
This genotyping is expected to be completed by late November 2015 after
which we shall release the manifest and allele frequency data and the assay
will be generally available to the public. 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 primary structure of the Animal - GRIN Genomics Database has been
constructed and is operational. The development effort will include several
areas of genomic information. Graduate students at Colorado State University
have been uploading genomic data from various projects and extracting
information. NAGP staff have also uploaded genomic information from cattle
and swine populations maintained in the repository as part of the testing
process. Efforts have also been ongoing to interface the Animal-GRIN system
into the Internet 2 effort which ARS as a whole has been engaged in
developing. Further work on front-ends/back-ends is needed to better
facilitate user requests. We anticipate soliciting a broader use of the
database by early 2016.

6. Cattle/Sheep/Goat/NRSP-8 Program at Plant and Animal Genome XXIV in San
   Diego - Stephanie McKay (Stephanie.McKayuvm.edu)

   Poster Abstract Submission Deadline: October 30, 2015.

Stephanie MacKay is seeking speakers for the PAG 2016 Cattle/Sheep/Goat
workshop! If you are interested, please contact Stephanie McKay:
Stephanie.mckayuvm.edu with a tentative title of your presentation and a
brief description of your work by Monday October 5th. Speakers will be
chosen by Friday October 16th. Chosen speakers must be confirmed before
November 1st. Deadline for workshop abstract submissions is November 6,
2015. Scientists at all career stages will be considered.

7. Nominate students for the PAG XXIV Neal A. Jorgenson Graduate Student
   Travel Award

   Application Deadline: October 30, 2015

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/...genson.pdf.

8. Annotation of bovine genome with the NLM controlled Medical Subject
   Headings

G. Morata and collaborators at the University of Nebraska have recently
annotated the bovine genome with the NLM controlled Medical Subject Headings
(MeSH). MeSH is a collection of comprehensive life science vocabulary
containing clinical and biological annotations. Annotation and enrichment
analysis software packages have been released on the Bioconductor website.
This is the first effort to characterize the bovine genome with MeSH
annotations.

 [1] http://dx.doi.org/...86/s12859-015-0453-z
 [2] http://dx.doi.org/10.1111/age.12307

9. PacBio + PBJelly improved genome reference which has been submitted to
   GenBank - Kim Worley (kworleybcm.edu)

The nucleotide files are out:
http://www.ncbi.nlm.nih.gov/...FC04000000
The read data are available in the SRA (see below)
Whole genome sequencing of Bos taurus blood sample BTAU.HE-female
6 PACBIO_SMRT (PacBio RS II) runs: 980,892 spots, 9.3G bases, 30.8Gb downloads
Accession: SRX1123979
Whole genome sequencing of Bos taurus blood sample BTAU.HE-female
40 PACBIO_SMRT (PacBio RS II) runs: 6.5M spots, 37.9G bases, 127.4Gb downloads
Accession: SRX1123978
Whole genome sequencing of Bos taurus blood sample BTAU.HE-female
53 PACBIO_SMRT (PacBio RS II) runs: 8.7M spots, 52.9G bases, 177.9Gb downloads
Accession: SRX1123977
Whole genome sequencing of Bos taurus blood sample BTAU.HE-female
8 PACBIO_SMRT (PacBio RS II) runs: 1.3M spots, 13.8G bases, 44.7Gb downloads
Accession: SRX1123976
Whole genome sequencing of Bos taurus blood sample BTAU.HE-female
51 PACBIO_SMRT (PacBio RS II) runs: 8.3M spots, 28.1G bases, 97.6Gb downloads
Accession: SRX1123975

10. LIC (New Zealand) plans to sequence one Holstein Friesian bull to 70x
    coverage using PacBio

LIC would like to announce that LIC are working on a breed specific reference
for a high usage NZ Holstein Friesian bull. The assembly is planned as a 70x
coverage PacBio long read assembly and will be used to investigate the
influence of the physical reference in phasing, imputation, structural
variation detection and gene discovery for the NZ dairy population. LIC plans
to make the assembly publically available.

11. eBEEF(eBEEF.org)beef genetics/genomics community of practice with
    eXtension

A new website (eBEEF.org) dedicated to beef cattle genetics was launched at
the 2015 Beef Improvement Federation Conference. 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 six land grant institutions (Dr. Darrh Bullock,
University of Kentucky; Dr. Jared Decker, University of Missouri; Dr. Megan
Rolf, Oklahoma 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.

12. Discussion of other issues of concern/priorities for the bovine genome
    community - summary of points raised at Teleconference held on 9/23/201

There were many groups represented on the conference call. LIC noted they
would unlikely be finished with the Holstein assembly by the end of 2015.
Jim Reecy asked about when the Dominette assembly will be switched to the
reference. Kim Pruitt from NCBI confirmed there would be 3 Dominette
assemblies coming into play - need to know what the community wants to call
the reference sequence. Medrano said there would an attempt to merge the 3
reference assemblies. This will be done in collaboration with Aleksey Zimin.
The assembly has not been put together at this point. The X chromosome will
be part of the assembly - Dominette does not help with Y chromosome. Kim
Worley mentioned the Baylor draft Y chromosome assembly is available in
GenBank. Huaijun Zhou said they are working on 2 animals for FAANG on 8
important tissues. Jerry asked whether we should be working on tissues from
RNA seq from the reference animal. Jerry has RNA seq data on 17 tissues. The
assay requires isolated nuclei from fresh tissue and that is why can't use
tissues from Dominette herself. It was suggested that it is possible to do
CHIP-seq from frozen tissue - but nuclei for DNase-seq requires fresh
tissue. Kim from NCBI asked if these data would be submitted publically -
yes that is the plan. All will be entered into Bio Project. Jim Reecy said
you need to get more animals to really functionally annotate the genome - to
ask higher order questions. Fernando asked how to become involved - there is
a FAANG workshop in 2 weeks in DC (October 7-8), and also another workshop
in January. Go to http://www.faang.org/GO-FAANG and can sign up
for any of the working groups you want to. Question about the number of
genes in the design of the functional chip - Jerry can send a document
interested parties. Email Jerry Taylor if you would you like a copy of that
document (taylorjerrmissouri.edu). There was a question about the
repository being developed by Harvey Blackburn - it is unique in that there
is the ability to store biological samples. Stephanie McKay spoke about
inviting speakers at PAG - contact her if you would like to speak at PAG
(Stephanie.mckayuvm.edu). The Neal A. Jorgenson Graduate Student Travel
Award winner(s) may be asked to speak at PAG this year too. There was a
suggestion to send out invitations to try to ensure we have participation at
PAG. Lakshmi discussed NIFA update. See Item 13 below for a detailed
summary. Kim Worley said PacBio data are available for those interested in
obtaining those data - see item 9. Erdogan Memili from Mississippi State
University said he is interested in organizing the next Cattle/Sheep/Goat
workshop for PAG 2017. It was suggested he attend the Cattle community
business meeting at PAG in 2016 and become nominated to organize the 2017
sessions.

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.

13. NIFA updates - Lakshmi Kumar Matukumalli (lmatukumallinifa.usda.gov)

  I. NIFA Updates (http://www.nifa.usda.gov/...pdate.html)

 II. AnimalAwards2014:http://nifa.usda.gov/...ved-animal

III. NIFA Personnel Highlights
   o Director of NIFA: Dr. Sonny Ramaswamy (sramaswamynifa.usda.gov)
   o Deputy Director of Institute of Food Production and Sustainability
     (IFPS): Dr Parag Chitnis (parag.chitnisnifa.usda.gov)
   o Director of Division of Animal Systems: Dr. Adele Turzillo
     (aturzillonifa.usda.gov)

IV. NIFA Budgets and 2014-18 Farm Bill Updates:

  o Total enacted discretionary & mandatory FY-15 Appropriations:
    $1,435,007,000

  o President's proposed FY-16 Total discretionary & mandatory funding:
    $1,687,543,000
    - FY-2016 NIFA Explanatory Notes
    - AMR-dedicated funding proposed: $33 million in AFRI
    - Competitive capacity carve-outs: Hatch ($12.5M), Smith Lever ($4M),
      Evans-Allen ($2.5M)
  o 2014-18 Farm Bill (Agricultural Act of 2014) Updates:
  o Centers of Excellence (Sec. 7214 of Farm Bill), This new provision
    states that NIFA shall prioritize centers of excellence established for
    purposes of carrying out research, extension, and education activities
    relating to the food and agricultural sciences (as defined in section
    1404 of the National Agricultural Research, Extension, and Teaching
    Policy Act of 1977 (7 U.S.C. 3103)) for the receipt of funding for any
    competitive research or extension program administered by NIFA

  o Commodity Boards Provision. The 2014 Farm Bill (Section 7404) requires
    USDA to establish procedures and a timeline under which federal or state
    commodity boards can propose topics for funding under the Agriculture and
    Food Research Initiative (AFRI) Requests for Applications (RFAs). This
    new provision is implemented in 2016 for AFRI programs. Commodity boards
    can provide matching funds to AFRI programs ($150K to $2.5M). The due
    date for submissions is Sept 22nd. The commodity board priorities will be
    incorporated into AFRI RFAs and will be released soon after.
    http://nifa.usda.gov/commodity-boards

V. AFRICompetitivePrograms

In FY 2016 Agriculture and Food Research Initiative (AFRI) is implementing
commodity boards' provision. The RFAs will be released after reviewing and
incorporating Commodity board requests. (http://www.nifa.usda.gov/...plications).
AFRI foundational programs do not change
significantly from year to year. Hence it can be useful to see the last
year RFAs in you are planning on submitting a proposal.

1. Foundational Program: http://www.nifa.usda.gov/...al-program

   Animal Health & Disease:
   Tools and Resources - Immune Reagents of Agricultural Animals:
   Animal Well-Being:
   Animal Reproduction:
   Animal Nutrition, Growth and Lactation:
   Tools and Resources - Animal Breeding, Genetics and Genomics:
   Improving Food Safety:
   Engineering, Products, and Processes:
   Nanotechnology for Agricultural and Food Systems:
   Economics, Markets and Trade:
   Environmental and Natural Resource Economics:
   Small and Medium-Sized Farms:

Two new opportunities that began in FY2014 and are included again under
FY2015 Foundational Program:

-- "Critical Agricultural Research and Extension" (CARE) Program
  ($200,000; short-term, very applied science);
 o Integrated Research and Extension Projects
 o 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)
 1. New and emerging innovative ideas that have high potential impact;
 2. Application of new knowledge or new approaches to unsolved challenges
    that have high potential impact;
 3. Tools required to have a paradigm shift in the field; and/or
 4. Rapid response to natural disasters and similar unanticipated events.

AFRI Challenge area priorities change from year to year. Please check for
NIFA website for updates
 o FY 2016 Food Security Challenge: To be announced
 o FY2015 Food Safety Challenge: To be announced
 o FY2015 Food, Agriculture, Natural Resources and Human Sciences
   Education and Literacy Initiative (provides fellowships to
   undergraduate, predoctoral, and postdoctoral students in the
   agricultural sciences)
 o FY2015 Climate Change Challenge Area: To be announced
 o FY2015 Water Program Challenge: To be announced
 o Sustainable Bioenergy Challenge: To be announced

AFRI Foundational Programs in Animal Health & Production: Outcomes for FY 2015

Animal Health and Production and Animal Products ($27.8 million total program
funds)
--------------------------------------------------------------------
Program Area 	Program             Funding       Standard  Success
                Contacts           ($ million)    Awards 1   Rate
--------------------------------------------------------------------
Animal          Mark Mirando          $4.50          9        16%
Reproduction

Animal          Margo Holland,       $11.50         23        16%
Health and      Peter Johnson
Disease

Animal          Steve Smith           $6.60         13        16%
Nutrition,
Growth, and
Lactation

Animal          Lakshmi Kumar         $2.50          5        18%
Breeding,       Matukumalli
Genetics,
and Genomics

Animal          Peter Johnson         $1.50          3        18%
Well-Being
---------------------------------------------------------------------
1. Budgets ≤ $500,000 total (including indirect costs) for up to 5 years;
   excludes seed, sabbatical, equipment and conference awards.

VI. 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 as
PAR-13-204. 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 24, 2015. http://grants.nih.gov/...3-204.html

VII. 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 18,
2015. NIFA awards to date: FY2012 (one: IHNV); 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/...77&org=NSF

VIII. Veterinary Medicine Loan Repayment Program
      (VMLRP; http://www.nifa.usda.gov/vmlrp) - $5 M (FY-15 enacted).

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. This program
emphasizes addressing shortages in the private food animal veterinary sector,
however approximately 10% of awards may be made to veterinarians filling
shortages in veterinary public practice. Since 2010, over 245 veterinarians
have been matched to priority shortage situations nominated for inclusion in
this program by State Animal Health Officials (SAHOs; aka, State
Veterinarians). The FY-14 VMLRP cycle was completed in September, 2014 with
offers being made to 51 veterinarians from a total of 163 applicants. Program
contact is Dr. Gary Sherman; vmlrpnifa.usda.gov.

IX. 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).

X. Other competitive grant programs with opportunities for animal and
   veterinary scientists

 o Organic Agriculture Research and Extension Initiative (OREI)
 o Organic Transitions
 o Higher Education Challenge Grants (experiential student learning; curriculum
   development; faculty development)
 o Beginning Farmers and Ranchers Program
 o Biotechnology Risk Assessment Grants (BRAG)
 o AFRI Small and Medium-Sized Farms (see Ag Economics & Rural Communities in
   AFRI Foundational RFA)
 o 2015 Aquaculture Research Competitive Special Research Grants

XI. 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).

XII. Stakeholder Input

o An AFRI Stakeholder Listening Session is tentatively planned for 2015.
o Joint ARS-NIFA Aquaculture Stakeholder Listening Sessions and a catfish
  stakeholder meeting were held in 2013. Results from the listening sessions
  and meeting can be found on the ARS National Program 106 website at:
  http://www.ars.usda.gov/...ry%206.pdf
o Stakeholder input relating to any NIFA program is welcome at any time.
  Comments should be directed to the National Program Leader responsible for
  the specific program(s). Contact information for NPLs is located towards the
  end of each grant program's informational webpage.
o National Academies Report on "Critical Role of Animal Science Research in
  Food Security and Sustainability" The NAS Report released in 2015 identifies
  several major priorities in domestic agriculture that include Breeding
  technology and Genetics, Environmental changes, Animal health and Animal
  welfare. The report also advocates the use of systems approaches. NIFA is
  currently analyzing these recommendations closely.

XIII. Other Areas of Importance

Antimicrobial Resistance (AMR)

President Obama announced new initiatives to combat antimicrobial resistance
and increase research in developing new antimicrobials. The new initiatives
proposed include increasing USDA budget related to AMR. These increases will
also reflect in the NIFA's proposed budget for FY2016.
http://www.whitehouse.gov/...t-combat-a

eXtension Communities of Practice (CoPs)

The online Extension community has established several communities of practice
to bring together researchers and extension professionals to share the latest
research results that can help farmers. http://about.extension.org/...criptions/

Researchers are encouraged to participate/support Extension activities, share
educational material, and even develop new CoPs.

DAIReXNET meets the educational and decision-making needs of dairy producers,
allied industry partners, Extension employees, and consumers with science-
based information and learning opportunities about the dairy industry.

eBEEF (eBEEF.org) is the beef genetics/genomics community of practice within
eXtension. More information can be found at http://www.ebeef.org.

International Collaborations
International researchers can be Co-Project Director's on NIFA grants and
receive funds via subcontracts.

USDA (NIFA) + UK(Biotechnology & Biological Sciences Research Council-BBSRC)
Partnership

In 2014, NIFA AFRI Animal Health and Disease and Veterinary Immune Reagents
did a pilot program with the UK-BBSRC offering a joint competitive program
where each agency funds researchers in their respective countries. 5 awards
were announced (News release). A US-UK meeting was held this summer to discuss
the continuation of this program.

Binational Agricultural Research Development & Development Fund (BARDD: US-
Israel) is encouraging collaborations between US and Israel scientists in
several challenge areas including Food Security
http://www.bard-isus.com/local.aspx?fid=69

Functional Annotation of Animal Genomes (FAANG)
The US-EU Animal Biotech taskforce scientific committee held a meeting at
Plant and Animal Genome 2014 to highlight the need for functional annotation
of animal genomes. (AgENCODE). Activities to establish standards and
facilitate international collaborations were discussed.

A group of researchers are hosting a fall 2015 meeting in Washington DC area
(October 7 and 8) to bring together and engage with USDA, NSF, NIH, & other
federal agencies, along with international funding agencies in the area of
animal sciences research. Please contact Chris Tuggle at Iowa State University
for more details. http://www.faang.org/GO-FAANG

XIV. 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    (202) 401-4336
                    & Repro.
                    mmirandonifa.usda.gov
Danielle Tack       Animal Health Program       (202) 401-6802
                    Coordinator
                    danielle.tacknifa.usda.gov
Gary Sherman        Veterinary Science &        (202) 401-4952
                    Medicine
                    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 Specialists:

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


 
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