Pig Genome Update No. 85

July 1, 2007

  1. The Biology of Genomes Meeting was held at Cold Spring Harbor May 8-12th
  2. The Symposium on Epistasis held May 31 to June 3 at Iowa State University
  3. The CSREES-USDA NC-1004 meeting was held June 22-23 at North Carolina
    State University

  4. The Swine Genome Sequencing Workshop was recently held in St. Croix
  5. SNP chip under discussion
  6. Improvements to the Animal QTLdb have recently been made
  7. The new pig oligo arrays are here and can be ordered
  8. Upcoming meetings ( 6 items )

The Biology of Genomes Meeting was held at Cold Spring Harbor May 8-12th to present and discuss recent findings in the area of genome analysis. Numerous new approaches to genomic studies are showing us that DNA still contains a lot of surprises. For example, the diversity of organisms that live in the oceans and in our own mouths is absolutely amazing. There are thousands if not millions of new genes to be discovered. Several talks focused on whole genome analysis studies designed to elucidate genes involved in human diseases. Furthermore, with the advent of new high-throughput genome sequencing technologies, new avenues for genome analysis will come on-line shortly. However, these new technologies present new challenges with respect to data handling and mining. Some so called "junk DNA" may be just that. Surprisingly, when 2 megabases DNA that is highly conserved across species, but lacks known genes, was deleted from the mouse no phenotype was observed. This raises the question were the wrong phenotypes measured or is this conserved DNA actually an artifact? Next years meeting will be held in early May. (kindly provided by J. Reecy)


The Symposium on Epistasis: Predicting Phenotypes and Evolutionary Trajectories was held, May 31 to June 3, 2007, at Iowa State University, Ames, IA. The meeting was extremely interesting in that it brought together two groups, evolutionists, and plant and animal breeders to discuss epistasis. While no consensus was reached on the best way to estimate and use such effects the discussions were lively and useful.


The final meeting of the CSREES-USDA multistate project NC-1004 on Genetic and Functional Genomic Approaches to Improve Production and Quality of Pork was held June 22 and 23 at North Carolina State University. Research stations in attendance presented results on ongoing research and discussed plans and opportunities to collaborate under the new 5-year multistate project NC-1037, which was recently approved. The NC-1037 project carries the same title as NC-1004 and will have a substantial focus on genetic aspects of health. Details can be found at http://nimss.umd.edu/homepages/home.cfm?trackID=8917 . The meeting was followed in the afternoon of June 23 by a symposium in honor of Dr. O.W. Robinson, with presentations by several of his former students. Dr. Robinson recently retired and has made many contributions to swine genetics during his career (kindly provided by J. Dekkers).


The Swine Genome Sequencing Workshop was recently held in St. Croix. The meeting was well attended and included specific issues of the sequencing project, identifying approaches to ensure broad and rapid utilization of the sequence information, developing educational programs, and examining ways to find additional financial support. A full report of the recent meeting will be posted soon at(http://www.piggenome.org/newsletter.php) .


SNP chip under discussion. One of the issues being discussed is the need for a SNP chip in pigs. There has been some development in this area and a "private" chip of about 7.5K SNPs is under manufacture by Illumina for a group of European scientists. Gary Rohrer has agreed to head a committee of interested researchers to work on developing a 10K chip and a group of scientists led by the University of Illinois put in a proposal for a 50K chip to be funded in part by USDA. Look for developments to be reported in the future.


Improvements to the Animal QTLdb have recently been made by the Bioinformatics Coordinator and his team. New data including mapping of Affy array elements to QTL maps for pigs and cattle and SNPs stored in Genbank to the respective chicken, pigs and cattle QTL maps have been added to the QTLdb (http://www.animalgenome.org/QTLdb.) If they is any additional information that you would like added, please contact James Reecy at jreecy@iastate.edu.


The new pig oligo arrays are here and can be ordered. New swine oligo arrays can now be ordered (http://www.pigoligoarray.org/). Validation of arrays is taking place. Thanks to efforts of a number of the swine genome community members, a validation experiment, funded in part by the participants and the USDA Pig Genome Coordinator, will take place over the next few months. The plan is to report the information to the community at the earliest possible date.


Upcoming meetings (see: (http://www.animalgenome.org/pigs/community/meetings.html)

Items for Pig Genome Update 86 can be sent to me by no later than August 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

cc: Muquarrab Qureshi, CSREES and Caird Rexroad II, ARS

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USDA/CSREES sponsored
Pig Genome Coordination Program
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