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Pig Genome Newsletter #124
From: "Christopher K. Tuggle" <cktuggle@iastate.edu>
To: angenmap@animalgenome.org
Subject: US Pig Genome Newsletter #124
Date: Fri, 23 Sep 2016 14:03:12 -0500
Pig Genome Update # 124:
- PDF version is available at
http://www.animalgenome.org/pig/newsletter/pdf/No.124.pdf
- Web version is available at
http://www.animalgenome.org/pig/newsletter/No.124.html
- Plain text version is appended below:
P I G G E N O M E U P D A T E
_________________________________________________________________
A Periodic Newsletter of the U.S. Pig Genome Coordination Program
************** No. 124 **************
* *
* October 1, 2016 *
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1. Recent meetings summary- JAM 2016, ISAG 2016, FAANG Symposium,
Livestock Genomics 2016, Large Animal Genetic Engineering 2016
2. Update on new functional genomics project FAANG activities
3. Update on USDA-NIFA-AFRI
4. Reminder on PAG 2017 Midwest ASAS 2017 JAM 2017 registration deadlines
5. Upcoming additional meetings information
6. Update on projects supported by NRSP-8 funds - We want to hear from you
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1. Recent meetings summary
a. JAM 2016
The Joint Annual Meeting of the American Society of Animal Science, American
Dairy Science Association and Canadian Society of Animal Science was held
July 19-23, 2016 in Salt Lake City, UT (https://asas.org/meetings/jam-2016/home).
Breeding and Genetics sessions were coordinated by topic facilitating
interaction among scientists working with different species. Session topics
included Genomic Evaluation -- Methods, Genomic Evaluation -- Applications,
Selection for Improved Efficiency, Selection for Health and Fertility, and
Novel Traits and Selection Objectives, all of which included presentations
by pig geneticists. A highlight of the Breeding and Genetics program was
presentations on genetics of heat stress in pigs, which were presented in
the novel traits session and also in the Breeding and Genetics Symposium –
Resilience of Livestock to Changing Environments.
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b. Functional Annotation of Animal Genomes Symposium 2016
The FAANG Symposium was held on the day overlapping the two JAM and ISAG
meetings, July 23, 2016. Approximately 450 scientists from both the JAM and
ISAG communities attended this full-day Symposium. Seven world-class
speakers provided up-to-the-date information on the use of functional
annotation to explore human and model species genomes, early results on the
use of such data for understanding results from Genome-wide Association
studies, as well as new methods to assemble animal genomes. A description of
funded FAANG-associated projects was provided, as well as a summary of
progress made by the FAANG subcommittees. For example, the Animals, Samples,
and Assays committee has finalized protocols for sample collection as well
as several of the core assays. In addition, pipelines for data analysis have
been proposed by the Bioinformatics and Data Analysis committee. Finally,
the group discussed plans for the PAG 2017 and ISAG 2017 meetings. For the
latter, the group agreed to suggest to ISAG that FAANG speakers be
incorporated into three Workshops, Comparative and Functional Genomics,
Epigenetics, and especially into a renamed Genome Sequencing and Annotation
Workshop).
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c. ISAG 2016
The International Society of Animal Genomics meeting was held in Salt Lake
City, UT July 23-27, 2016. The local organizing committee, chaired by Clare
Gill of Texas A&M, did a great job and the venue and entertainment was
terrific. Four plenary sessions and many workshops were held. Workshops of
relevance to swine genomics included: Genetically Engineered Livestock;
Genetics of Immune Response and Disease Resistance; Comparative and
Functional Genomics; Domestic Animal Epigenetics; and the Pig Genetics and
Genomics Workshop. The latter included 9 talks covering genotype-phenotype
association, the porcine gut microbiome, the pig metabolome, regulatory
pathway analyses, as well as genome editing to create porcine models of
disease relevant to biomedicine.
The next meeting of ISAG will be in Dublin 16-21 July 2017. At the ISAG
business meeting, presentations for several possible 2019 locations were
also made, including: Toronto, Canada; Llieda Spain; and Piacenza, Italy.
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d. Livestock Genomics
This meeting is held every two years in Cambridge, UK, organized by the
European Molecular Biology Laboratory-European Bioinformatics Institute. The
meeting attracts European leaders in livestock genomics as well as some
speakers from around the globe. It is a smaller meeting with most attendees
providing a talk and/or a poster, thus providing excellent opportunities to
gain knowledge in livestock genomics thought leaders. Thirty-five talks were
presented at the meeting from14-16 September 2016. Several species-agnostic
bioinformatic tool presentations, and two roundtable discussions on data
genotype to phenotype and handling multiple genome assemblies were also
held.
Seven talks and several posters reported pig genome data. Chris
Tuggle presented a talk on the porcine blood transcriptome, including the
use of PacBio data from other tissues to validate these transcript
assemblies, which was supported by NRSP-8 (see below). Other swine-related
talks included a presentation by Elisabetta Giuffra on the FAANG projects in
the pig and other species, and Amanda Warr on the current status of the new
PacBio-based Genome Assembly of TJ Tabasco, which was the pig whose genome
sequence was reported in 2012. IMPORTANTLY, THERE WAS A CALL FOR ANYONE TO
SUBMIT DATA THAT COULD BE OF USE IN ANNOTATION OF THIS NEW GENOME ASSEMBLY
(SUCH AS RNAseq DATA) TO SUBMIT AS SOON AS POSSIBLE TO NCBI or ENA. THE
INTENT IS TO MAXIMIZE SUCH INFORMATION FOR THE GENOME ASSEMBLY ANNOTATION,
WHICH WILL BE DONE BY ENSEMBL OVER SEVERAL MONTHS; THIS WILL START SOON.
Several talks on linking porcine genotypes to phenotypes were also presented
by scientists from U. Llieda and U. Bologna. The pdf of the meeting program,
which includes the Abstracts of speakers and posters, is available here:
http://www.ebi.ac.uk/~streeter/livestock-2016/meeting-booklet.pdf. Slides of
talks should be available soon. Contact Ian Streeter (streeter@ebi.ac.uk)
for more information.
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e. Large Animal Genetic Engineering 2016
This new meeting was held in Bethesda, MD September 18-20, 2016, and was
organized by Utah State. Many very interesting projects on the use of pigs
as biomedical models were presented, including many individual gene
knockouts but also transgene insertions including some projects with up to 6
transgenes at one time for xenotransplantation. Controversy over the
timelines and throughput of FDA approvals of genetically
modified/genome-edited organisms for food consumption were a major topic,
which many felt was an impediment to using this promising new technology in
agricultural production. However, there was a clearly high level of
enthusiasm for CRISPR approaches to make dramatically rapid advances to
understand porcine physiological mechanisms. Plans were discussed to have a
repeat meeting in September of 2018 in Park City, Utah.
2. Update on new functional genomics project FAANG activities (beyond the
Special Symposium on FAANG held during JAM-ISAG).
As described in prior PG Updates, the FAANG Consortium has been organized
and held meetings. The following text is a summary of the activities of
FAANG since the last PG Update; for further information please see the FAANG
website (www.faang.org).
a) The meeting report of the GO-FAANG Workshop held in October 2015 was
accepted for publication. An e-copy of this paper by Tuggle et al. is
available at: http://www.ncbi.nlm.nih.gov/pubmed/27453069.
e) Responding to FAANG member requests, a new webpage has been developed to
provide information on new funding opportunities for FAANG related proposals
(available on FAANG website, member’s area page).
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3. Update on USDA-NIFA-AFRI
In July 2016, Dr. Lakshmi Matukumalli provided guidance to several members
of the genome community on the following. He indicated that AFRI Animal
Genome:Tools and Resources panel would like to see 4-6 proposals per species
submitted for FAANG-related projects, which would be scientifically
independent but would be complementary to each other and linked to the
overall goals of FAANG. The genome Coordinators were notified of this
suggestion and each group is handling any group discussion or coordination.
Chris Tuggle sent out a note to all members of the Swine Sub-committee and a
conference call is being scheduled with those interested. This will be an
important topic for the Subcommittee to discuss at the PAG 2017 meeting.
Dr. Matukumalli further indicated that the AFRI request for applications for
the yearly genome-oriented opportunities (Tools and Resources) is
anticipated to be released approximately early February, which is earlier
than last year. However, the intent by AFRI is to provide about 3 months
between the RFA release and the deadlines. Be sure to read and consider
applying for these opportunities! If a letter of support, including matching
funds from NRSP-8, would be useful, please let the Co-coordinators know
early in the process.
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4. Reminder on PAG 2017, Midwest ASAS-ADSA 2017, ASAS-CSAS 2017, ADSA 2017
meeting registration deadlines.
A reminder that the 25th Plant and Animal Genome Meeting
(http://www.intlpag.org/), will be held January 14-18, 2017 in San Diego CA
(as usual, location is the Town and Country Hotel). This meeting will
include the Swine Genome Subcommittee Workshop on January 14. The PAG25
early registration deadline is October 31, 2016 (see:
http://www.intlpag.org/2017/attend/registration-and-fees), and the abstract
submission deadline is October 28, 2016 (see:
http://www.intlpag.org/2017/abstracts/poster-submission).
The Midwest Section meeting of the ASAS and ADSA will be held March 13-15,
2017 in Omaha, NE. Registration for the Midwest ASAS-ADSA meeting will open
October 2016; (watch here for further details:
https://www.asas.org/membership-services/asas-sections/midwest-section/meetings.
) Midwest ASAS-ADSA 2017 abstracts are due by October 26, 2016. See
https://asas.confex.com/asas/mw17/cfp.cgi for more details.
Information on ASAS-CSAS 2017, to be held July 8-12, 2017 in Baltimore, MD
is available here: https://asas.org/meetings/annual-2017/home Lowest cost
registration deadline is February 9, 2017.
Information on ADSA 2017, to be held July 25-28 in Pittsburgh, PA is
available here: http://www.adsa.org/2017/
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5. Upcoming additional meetings information
Besides the meetings discussed above, there are many other meetings of
relevance to the genomics community over the next 6-12 months, see:
http://www.animalgenome.org/pig/community/meetings). As mentioned above, a
reminder that the ISAG community will hold their next meeting in July 2017,
not in 2018, to avoid the World Congress to be held in 2018. ISAG will then
go back to biannual year meetings in the future; continuing in 2019. The
location for the 2019 meeting is being discussed.
o o o o o o o o o o o
6. Update on projects supported by NRSP-8 funds- We want to hear from you!
Update on FAANG project: Dr. H. Zhou presented a poster summarizing the
FAANG project at the ISAG meeting. Please email Dr. Zhou at
hzhou@ucdavis.edu with any questions.
Update on High Density Genotyping: Two 96 sample assays have been processed
on the Affymetrix Axiom™ PigHD_V1 Array including samples representative of
the Yorkshire, Duroc, Landrace and Hampshire breeds in the US, and the
genotype data is currently being evaluated. Please contact Cathy Ernst
(ernstc@msu.edu) or Jack Dekkers (jdekkers@iastate.edu) with any questions.
Update on PacBio Isoseq Data analysis: Illumina and PacBio Isoseq data has
been received from Dr. Tim Smith for eight tissues. Error correction of the
latter has been completed for 4 tissues using the Illumina data. Additional
tissues and cell samples to be analyzed in the same way are being planned.
Please email Dr. Chris Tuggle (cktuggle@iastate.edu) or Dr. Tim Smith
(Tim.Smith@ARS.USDA.GOV) with any questions.
The swine genome coordinators are always glad to hear from NRSP-8 members
and other readers about ways that the coordination effort can be improved or
provide resources that are needed. If you have items of general interest to
the swine genetics and genomics communities that can be included in this
newsletter please share. Our issues are now planned for February 1 and
October 1 each year. Any contribution should be sent to the Coordinators one
week prior to these dates.
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Items for Pig Genome Update 125 can be sent to me by no later than December
15 please.
Joint Coordinators:
Christopher Tuggle Catherine Ernst
2255 Kildee Hall Anthony Hall, 474 S. Shaw Lane, Room 1205
Department of Animal Science Department of Animal Science
Iowa State University Michigan State University
Ames, IA 50011 East Lansing, MI 48824
Phone: 515-294-4252 Phone: 517-432-1941
Fax: 515-294-2401 Fax: 517-353-1699
Email: cktuggle@iastate.edu Email: ernstc@msu.edu
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Supported by Multi-State Research Funds to the National Research Service
Program (NRSP-8). National Animal Genome Research Program (NAGRP),
Lakshmi Matukumalli, NAGRP Director, NIFA, USDA
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Web: http://www.animalgenome.org/pig | Mail: angenmap@animalgenome.org
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