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Pig Genome Newsletter #051
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. 51 **************
* *
* <angenmap@db.genome.iastate.edu> *
* September 1, 2001 *
**************************************
+==========================================================================+
1. New Microsatellite Primers for Pig Diversity Research
2. Public Porcine Expressed Sequence Tagged (EST) Database
3. September 11 and A Personal Reflection
4. Plant and Animal Genome X
5. Upcoming Meetings
+==========================================================================+
New pig microsatellite diversity primers are available. This set of
primers was made in response to requests and suggestions concerning
pig diversity research and selected from markers across all 19 pig
chromosomes. These were suggested by several people and should work
nicely to study diversity in different breeds. There are a total of
50 pairs of primers, half of each primer pair is labeled with one of
the three fluorescent dyes (TET, HEX, and 6-FAM) in 5,000 pmoles
amounts. These primers were produced by Research Genetics. To date,
there are 11 sets of primers covering a total of 559 microsatellite
markers that have been made available through the USDA/CSREES Pig
Genome Coordination Program. More information on all sets of primers
can be found at the web site:
http://www.genome.iastate.edu/resources/fprimerintr.html. A Java
graphic view of fluorescent primers sets for microsatellite markers
has been created showing the relative linkage location
(http://www.genome.iastate.edu/resources/PrimerOnChr.html). A click
on the marker name in this graphic viewer will send a query to the
PigBase database and fetch detailed information on this marker. In
addition, there are a limited number of bags of the previous set X of
primers still available. For additional questions, please contact me
(mailto:mfrothsc@iastate.edu) or Dr. Yuandan Zhang
(ydzhang@iastate.edu).
o o o o o o o o o o o
A new public porcine expressed sequence tagged (EST) database, a set
of tools for EST analysis and web query tool for public access to
this database have all been developed. A consortium of five
institutions (Iowa State University, University of Missouri-Columbia,
University of Iowa, University of Nebraska and the National Center
for Genomic Resources) is developing extensive expressed sequence and
mapping data for cDNAs expressed in all major female reproductive
tissues. A total of 14,602 EST sequences derived from 20 libraries
(estrus or gestation for whole embryo, anterior pituitary
hypothalamus, ovary, uterus and term placenta) has been produced and
submitted to GenBank. Nucleotide similarities between the pig ESTs
and human genes were determined by BLAST analysis against 92,152
human UniGene sequences. A number of PERL scripts were written for
parsing the BLAST output and integrating it with a) human gene maps,
b) the PigBase database and c) pig-human comparative map information.
LocusLink, UniSTS and radiation hybrid (RH) map location were used to
order the putative human orthologs of pig ESTs on human chromosomes.
The pig-on-human comparative maps and homology between pig and human
chromosomes were then used to predict EST assignments on pig
chromosomes. For further information, please see the database which
is comprised of a number of tables covering the EST profile,
alignment similarity (between pig ESTs and human UniGene and between
pig ESTs and pig genes/loci sequences), human ortholog and
information on cytogenetic, linkage, and RH locations. Interactive
web query can be made by the public through using the EST database interfaces
(http://pigest.genome.iastate.edu). It is likely that public
EST data will be added to generate a more diverse pig EST database.
Visualized web presentation of putative human homology and predicted
pig maps of the pig ESTs is also in progress.
o o o o o o o o o o o
September 11 and a personal reflection. It is impossible for
civilized people not to shocked and saddened by the wholesale
destruction of lives and property by terrorists. It is likely that
like me, you may know someone who lost a loved one, but even if this
is not the case we have all been touched by the tragic and criminal
recent events. For your own personal health, take time to make a
special effort to be with family and friends and to work at
reclaiming the important things in life. Help others and find a
minute to smile and offer a friendly hand.
o o o o o o o o o o o
Are you going to San Diego for PAG?? Please see www.intl-pag.org/pag
for more information. Dr. Francis Collins, "Czar" of the Human
Genome Program at NIH, has agreed to give one of the plenary talks.
Other speakers include Ralph Greenspan on behavioral genetics, Tom
Blumdell on structure and function of the proteome, Steve Brown on
ENU mutagenesis in mice and Eric Green on comparative genome
sequencing. Several changes are on tap for next year. PAG-X will
again be at the Town & Country Convention Center in San Diego, CA,
next year running from Sat., Jan. 12, through Wed., Jan. 16. The
PAG-X meeting will include plant, animal and agricultural microbe
genomics all in one meeting. Also it is planned that a weekend-only
registration rate ($175) is available in addition to the usual
student ($225), non-profit ($425 early/$525), and industry ($550
early/$650) for full week registrations. Registration badges will be
required to participate in any workshop. As is the usual case the
swine committee will be meeting on Sunday January 13 of the meeting.
Jon Beaver, chair, has planned interesting swine sessions. Please
have your graduate student apply for the Neal Jorgensen Travel Award
for Swine before November 1 by sending a cover letter and abstract to
Max Rothschild at mfrothsc@iastate.edu.
o o o o o o o o o o o
Upcoming meetings (for more details see:
http://www.genome.iastate.edu/community/meetings.html) Plant and
Animal Genome X January 12-16, 2002 at the Town and Country
Convention Center, San Diego, CA. For information please contact D.
Sherago, Sherago International at darrins@scherago.com.
International Society of Animal Genetics, Göttingen, Germany, August
11-15, 2002. See http://www.gwdg.de/~bbrenig/ISAG2002.html for further
information.
7th World Congress of Genetics Applied to Livestock
Production, August 19-23, 2002, Montpellier, France. See
http://www.wcgalp.org for more information. Additional items can be
found at: http://www.agbiotechnet.com/calendar/index.asp.
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Contributions to Pig Genome Update 52 including short meeting announcements
are always welcome. Please send by December 10.
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
cc: Dick Frahm, CSREES and Caird Rexroad II, ARS
+==========================================================================+
U.S. PIG GENOME COORDINATION PROJECT
+-----------------------------------+
| Paid for by funds from the NRSP-8 | Web: http://www.genome.iastate.edu
| USDA/CSREES sponsored Pig Genome | Mailing list:
| Coordination Program | angenmap@db.genome.iastate.edu
+-----------------------------------+
+==========================================================================+
