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Pig Genome Newsletter #100
From: "Rothschild, Max F [AN S]" <mfrothsc@iastate.edu>
To: angenmap@animalgenome.org
Subject: US Pig Genome Newsletter #100
Date: Dec, 31 Dec 2009 11:34:57 -0600
Pig Genome Update # 100:
- PDF version is available at
http://www.animalgenome.org/pigs/newsletter/pdf/No.100.pdf
- Web version is available at
http://www.animalgenome.org/pigs/newsletter/No.100.html
- Plain text version is appended below:
P I G G E N O M E U P D A T E
__________________________________________________________________
A Bimonthly Newsletter of the U.S. Pig Genome Coordination Program
************** No. 100 **************
* *
* <angenmap@animalgenome.org> *
* January 1, 2010 *
***************************************
===========================================================================
1. Pig Genome Update reaches the century mark!
2. First draft sequence of the pig genome was announced at the recent Pig
Genome III meeting
3. Communication, Collaboration, and Leveraging the goal of federal funds
4. This pig gene went to market - an industry perspective
5. Pigs as humans?
6. Dreaming of San Diego and PAG?
7. National Swine Improvement federation meeting was recently held in
Nashville, TN
8. The 2009 International Porcine reproductive and respiratory syndrome
9. Help exists for Genetic Line Preservation and Use
10. Upcoming meetings ( 7 items )
11. Pig Genome Update Newsletters are distributed electronically through
AnGenMap
12. Refunding of the NRSP8 requires some help from each of you
===========================================================================
Happy Holidays and New Year to you, your families and colleagues!!
Pig Genome Update reaches the century mark! It seems hard to believe
that this publication has now been published for over 13 years. A lot
has happened in the "pig genome business" and I feel especially proud to
have worked with those of you in the community who have not only
contributed to the effort but have helped to move forward the science of
genomics of livestock species. It seems premature to predict what the
next 5 or even 10 years will produce in opportunities, challenges or
discoveries but one thing is clear is that we have, as a community,
accomplished a great deal and we owe thanks to many people. In this
special issue I have asked for a few contributions from people from
science, government and industry who have different viewpoints of the
progress made. These items are listed below.
o o o o o o o o o o o
First draft sequence of the pig genome was announced at the recent Pig
Genome III meeting at the Sanger institute. We owe a big thanks to all
the many contributors, and all those within the field that have helped
at Sanger and around the world to get us to that point. A total of 160
attendees came to this historic meeting where speakers presented updates
on several subjects related to the sequencing effort and plans for the
future. The deadline has passed for new clones to enter the sequencing
pipeline. However, some new clones are being identified as a possible
resource for future sequence gap closure. These identified BACs
currently stand at ~150 and have been identified using physical map and
sequence information. All chromosomes are over 90% sequenced taking the
genome to 95.72% from 16,974 sequenced clones. About 94% of the genome
is at the "Improved" status (15720 clones). There is 123Mb of finished
quality data within the 2.994Gb currently available. Sanger will
continue with chromosome X/Y sequencing - chromosome X clones sequenced
in the genome project will be finished and the map will continue to be
refined using a fosmid library too. Sanger has produced a chromosome Y
fosmid library which is currently being fingerprinted. This will be used
to select up to 1100 fosmid clones for sequencing and finishing. This
work is funded by BBSRC. In collaboration with TGAC (Norwich, UK) the
remaining BAC clones which have been selected from the fingerprint map
will be pooled and sequenced on the Illumina platform. A further x10
coverage of Duroc sow DNA will be produced on the Illumina platform to
be combined with the BGI data and assembled (also in collaboration with
TGAC). Automatic annotation will continue to be provided by Ensembl.
Another annotation jamboree is to be organized in 2010 (kindly provided
by Carol Churcher and Richard Clark).
o o o o o o o o o o o
Communication, Collaboration, and Leveraging the goal of federal funds.
It's hard to believe that 100 issues of the bimonthly Pig Genome Update
have been published! Way back in 1993, the USDA National Animal Genome
Research Program was established and supported by off-the-top Hatch
formula funds. Much has changed with regard to funding research in
animal genomics and the future of funding for animal genomics will
undoubtedly continue to change as the world recovers from the current
economic recession, as new zoonotic diseases such as H1N1 emerge, and
as pork producers deal with competing demands on corn and soybeans for
feeds and fuels. What hasn't changed is the importance of <B>communication,
coordination, and leveraging of resources</B> and these are the major
impacts of the bimonthly Pig Genome Update from an administrative point
of view. <B>Communication</B> including timely dissemination of funding
opportunities, changes in policies and procedures at the USDA-NIFA
(CSREES), and upcoming conferences are a regular feature of the
bimonthly Pig Genome Updates. In addition, all of this information (and
more) is archived on a user-friendly website http://www.animalgenome.org/pigs.
<B>Coordination</B>...of scientists to participate
in multi-state research projects, replication of experiments at
different research stations, and the opportunity to provide stakeholder
input on how best to spend limited funding to generate resources for the
pig genomics research community have resulted in extremely valuable
genomics tools for pigs (e.g., genetic maps, QTL maps and databases,
primers and probes, a 13,000 element oligo microarray, and a 60,000 SNP
chip). <B>Leveraging of resources</B> a relatively small amount of
off-the-top Hatch formula funds invested in the Pig Genome Coordination
Program have resulted in several NRI, AFRI, and National Pork Board grants
to independent investigators as well as larger grants to teams of
investigators to sequence the swine genome, develop a SNP-based
genotyping platform, and address issues related to the genetics of swine
health and disease. As we look to the future the new NIFA
administrators are emphasizing focus, scale, and impact as well as
increased funding for competitive grants. Thus, another 100 issues of
the bimonthly Pig Genome Update will likely be needed for effective
communication between scientists and federal funding agencies as well as
coordination of the pig genome research community as we move toward
implementing whole genome selection and marker-assisted management
strategies in pork production systems. We owe a tremendous thanks to
our Coordinator for volunteering to serve as the Pig Genome Coordinator
nonstop since 1993 (kindly provided by Dr. Deb Hamernik).
o o o o o o o o o o o
This pig gene went to market - an industry perspective. The meeting at
Hinxton to celebrate the "completion" of the pig genome sequence was a
great opportunity to reflect on how far we have come since our lab
cloned a repeat sequence from the pig Y chromosome to enable us to
evaluate semen sexing in the late 80's. Commercial semen sexing still
remains to be cracked for the pig, but the Y chromosome is going to
yield more information in the coming months as my old Cambridge
collaborators take it through targeted sequencing. The results will
provide new insight into sex chromosome evolution and may even help
understand the potential to change the sex ratio and take me back to the
beginning again. It would have been difficult to believe then that we
would, within 20 years, be able to search for any sequence of interest
from our desks and put it to work. We were about to start hunting for
the "halothane" gene and begin to think about candidate gene approaches
utilizing the first results being generated from our model species, man
and mouse. It was a relatively slow process with lots of false starts or
dead ends and industry geneticists had a relatively short list of
targets. Molecular biology was only expected to have a role in helping
identify "major genes" such as the mutation causing porcine stress
syndrome (and pale soft exudative meat) or the dominant white color -
the list was short. However, at that time results from tomatoes pointed
some of us towards "quantitative trait loci" and the potential for a new
approach to pig improvement. The PiGMaP project began in 1991 and
included the development of the statistical tools as well as beginning
the mapping of QTLs in the pig. Fittingly, many of those pioneering this
international collaboration were at Hinxton. Then in 1994 researchers
presented results showing an association between a polymorphism in the
estrogen receptor locus and litter size in pigs kicking off renewed
industry interest in the search for DNA markers that could help make
faster progress for "difficult to measure" traits. Progress has definitely
been slower than we had hoped, one of my current colleagues often reflects
on how optimistic, or was it deluded, we were to think we could do it with
such limited tools. However, all of the major pig breeding companies are
already using DNA markers within their programs and they continue to embrace
the opportunity presented by the new high throughput tools such as the
Porcine 60K Beadchip: one of the by-products generated by the Pig Genome
Sequencing Consortium. Remarkably this provides a SNP genotype at
something like one ten thousandth of the cost of the first commercial
marker test introduced in 1991. Much still needs to be done but the
genomic tools are not the hurdle nowadays, it is the development of the
phenotypes required to exploit them which is the next issue to consider.
It was pleasing to see how the community is rising to the challenge and
investigating traits such as disease susceptibility, sow longevity, and
even maternal infanticide (sow aggression). Congratulations everyone on
setting the standard for collaboration and delivery (kindly submitted by
Graham Plastow).
o o o o o o o o o o o
Pigs as humans? Much of the emphasis to sequence the pig genome came
from agriculture, as the pig is a very important source of protein as
food for the world's population. But the pig has another great, but
often underappreciated value, i.e. that of a scientific model for
humans. The National Institutes of Health spends millions of dollars
each year extramurally on research based on the pig. Why? Because the
pig not only has a size and physiology similar to humans, but as we
continue to learn it also has a genome that is similar to humans. The
pig is an excellent model for things like cardiovascular disease,
cutaneous pharmacology, ophthalmology, obesity, etc., and pigs are
considered as a possible source of organs for xenotransplantation. Even
without a completed genome genetic modification of pigs has moved
forward as transgenes have been added to create pigs that produce
pharmaceuticals such as human coagulation factors VIII and FIX, other
transgenes have been added to create disease models like retinitis
pigmentosa and Alzheimer's Disease. Genes have been knocked out to
develop pigs for xenotransplantation or create pigs with cystic
fibrosis. Previously, if a genetic modification was to be made in the
pig the basic genetic information had to first be assembled. Now with a
draft of the genome a researcher that wants to knockout or knockin a
gene can immediately access the genomic information for the pig and
begin building the necessary constructs. The sequence of the pig's
genome is so important that if the pig genome sequencing project did not
move forward the pig would have become a second-class species to the
biomedical community. Now the pig will remain an important component of
understanding human health (kindly submitted by Randall S. Prather).
o o o o o o o o o o o
REGULAR NEWS ITEMS
Dreaming of San Diego and PAG? Warmer weather and great meetings are
just around the corner. See http://www.intl-pag.org/ for more
information. Scheduled PAG XVIII plenary speakers include Eric Schadt,
Peter Raven, Howard Jacob, Evan Eichler, Joanne Chory, Robb Fraley and
Vicki Chandler. It promises to be a great meeting. Cathy Ernst
(ernstc@msu.edu) is organizing the Swine workshop for January 9.
o o o o o o o o o o o
National Swine Improvement federation meeting was recently held in
Nashville, TN. Attended by nearly 75 people, the meeting included a
special session devoted to genetic markers, genomic selection and
opportunities for the future. Featured speakers were Mark Boggess, USDA
ARS, Sally NorthCutt, American Angus Association and Alan Mileham, PIC.
Other speakers also presented early SNP chip data. The proceedings
should be available in the near future.
o o o o o o o o o o o
The 2009 International Porcine reproductive and respiratory syndrome
(PRRS) Symposium was held December 4-5, 2009 in Chicago. PRRS is the
most economically significant disease of swine in the U.S. and
worldwide. The PRRS Symposium brings together scientists involved in all
aspects of PRRS research; researchers, students, swine health
specialists, and pork producers. This year over 280 scientists from 25
countries attended the meetings that included 2 keynote talks, the first
by Juergen Richt, Kansas State Univ., on "Swine Influenza and the Need
for Rationally Designed Vaccines" and the second by Tomasz Stadejek,
National Veterinary Research Institute, Poland, on "Genetic diversity of
PRRSV - global emergence and evolution." There were an additional 16
talks selected from the 97 submitted abstracts that were all presented
as posters [a 23% increase over 2008]. The abstracts covered viral
structure, design of infectious clones, host-virus interaction,
vaccines, immunity, genetic resistance, ecology and viral elimination
strategies. The Proceedings of the 2009 PRRS Symposium will be posted on
the website www.prrssymposium.org. Next year's meeting will be held
December 3-4, 2010 in Chicago. An association trial aimed at resistance
to initial PRRSV infection, supported in part by the Pig Genome
Coordinator is well underway. (kindly submitted by Joan Lunney).
o o o o o o o o o o o
Help exists for Genetic Line Preservation and Use. The USDA ARS
National Animal Germplasm Program (NAGP) can serve as a way to preserve
your research lines. NAGP has the ability to freeze semen, and other
tissues, and securely store it long term. These resources are available
to preserve research lines either to capture genetic variation at phases
during the project, freeze the foundation population as an example, or
to preserve material from lines that are being terminated. So, if you
are interested in preserving any of your genetic lines, contact either
Terry Stewart (tstewart@purdue.edu, 765-494-0138), chairman of the swine
species committee or Harvey Blackburn (Harvey.Blackburn@ars.usda.gov,
970/495-3268). For parties interested in maintaining ownership of the
material there is the option of establishing a material transfer
agreement with USDA/ARS. NAGP can also be a source of genetic material
for genomic studies in all the economic species. To learn more NAGP and
the extensive material already in the collection, visit the NAGP web
site at http://www.ars.usda.gov/Main/docs.htm?docid=16979 (kindly
submitted by Terry Stewart).
o o o o o o o o o o o
Upcoming meetings (see:
http://www.animalgenome.org/pigs/community/meetings.html)
Tenth International Long-oligonucleotide Microarray Workshop, Jan. 3-8,
2010, U. of Arizona, Tucson, AZ. For further details and to register,
please contact David Galbraith (galbraith@arizona.edu) or Georgina
Lambert (georgina@cals.arizona.edu).
Plant & Animal Genome Conference, PAG XVIII, Jan. 9-13, 2010, Town &
Country Hotel, San Diego, CA. Information available at http://www.intl-
pag.org/ and see above.
Advances in Genome Biology & Technology meeting, Feb. 24-27, 2010, Marco
Island, FL. See www.agbt.org for more info.
Animal Genomics for Animal Health International Symposium, 31 May - 2
June 2010, at the Maison de la Chimie, Paris France, See
https://colloque.inra.fr/agah2010/ for more info.
International Society of Animal Genetics conference will take place in
Edinburgh (UK), July 26-30, 2010. For details see
http://www.isag.org.uk/society/conferences.asp
The 9th World Congress on Genetics Applied to Livestock Production
(WCGALP), Aug. 1-6, 2010, Leipzig, Germany. For more details visit
http://www.wcgalp2010.org/.
The 9th International Veterinary Immunology Symposium, August 16-20,
2010, Tokyo, Japan For more details visit http://9th-ivis.jtbcom.co.jp.
Pig Genome Update Newsletters are distributed electronically through
AnGenMap, the Animal Genome Discussion Group
(http://www.animalgenome.org/community/discuss). Previous
newsletters are at
http://www.animalgenome.org/pigs/newsletter/index.html.
Coordinator updates can also be found
http://www.animalgenome.org/pigs/community/NRSP8/. Please provide your
input as the Swine Genome Coordinator is always glad to hear from NRSP-8
members and other readers about ways that we can improve the
coordination effort or provide resources that are needed and with which
we may be able to help. Also, let us know if you have items of general
interest to include in this Newsletter.
Refunding of the NRSP8 requires some help from each of you. We are
continually asked what the coordinators money does. Many of you have
received reagents, arrays, SNP chip and some of this has been augmented
by funds from coordinator activities. Please send by December 1, 2009
to mfrothsc@iastate.edu any grant titles and dollar amounts for the past
3 years for any project helped by reagents, tools and bioinformatics in
part supplied by the Pig genome Coordination program.
<> <> <> <> <> <> <> <> <> <> <>
Items for Pig Genome Update 101 can be sent to me by no later than February 15
please.
Max Rothschild
U.S. Pig Genome Coordinator
2255 Kildee Hall, Department of Animal Science
Iowa State University
Ames, Iowa 50011
Phone: 515-294-6202, Fax: 515-294-2401
mfrothsc@iastate.edu
http://www.animalgenome.org/pigs/
cc: Muquarrab Qureshi, CSREES and Caird Rexroad II, ARS
===========================================================================
U.S. PIG GENOME COORDINATION PROJECT
+-----------------------------------+
| Supported by USDA/NIFA NRSP-8 | Web: http://www.animalgenome.org/pig
| National Animal Genome Research | Mail: angenmap@animalgenome.org
| Program |
+-----------------------------------+--------------------------------------
