1. Meetings Issue
Quick reference for upcoming deadlines (see details below).
- Plant and Animal Genome XXIII (San Diego), January 10-14, 2015.
- North American PRRS Symposium (Chicago), December 5 - 6, 2014.
- Gordon Conference (Italy) February 22 - 27, 2015.
- Midwest ASAS/ADSA meeting (Iowa) March 15-18 2015.
Summary of ISAG meeting July 2014
The 34th meeting of the International Society of Animal Genetics convened in historic Xi'An China on July 27 to Aug 1, 2014. Attendance was over 1,100 scientists from 44 countries. The facilities were spacious and the scientific sessions were well-organized. The social events were excellent, including a trip to see the 2,000+ year old Terra Cotta warriors, part of the burial site of Qin Shi Huang, the first emperor of China.
Many plenary talks and Workshops were of direct interest to pig genome scientists, including workshops on Pig Genetics and Genomics, Comparative and Functional Genomics, Genetics of Immune Response and Disease Resistance Workshop, Domestic Animal Sequencing, and Domestic Animal Epigenetics. Reports of many of these Workshops (current and previous Workshops) and other Workshops can be found at the ISAG website: http://www.isag.us/committees.asp. For the plenary talks, several stood out and were highly relevant to pig genetics and animal agriculture. Dr. Martien Groenen (Wageningen University, The Netherlands) presented his research on introgression mapping, describing his whole genome re-sequencing analysis of gene flow from Chinese to European breeds. Dr. Lusheng Huang (Jiangxi Agricultural University, China) described substantial resources and data documenting extensive phenotypic and genotypic diversity in Chines pig breeds. Dr. Larry Schook (University of Illinois, USA) described the work being done with pigs to use and further develop them as biomedical models. Dr. Joan Lunney (USDA-ARS, USA) provided a detailed description of the highly productive PRRSV Host Genetics Consortium, emphasizing the need for such large collaborative projects to combat diseases such as PRRS, but acknowledged the large effort and time needed to create and sustain such research projects. Dr. Zhiying Zhang (Northwest Agriculture and Forestry University, China) described his research on miRNA and miRNA binding site variation and its role in pig and other livestock breeding, as well as his work toward CRISPR/CAS9 gene editing of miRNA binding sites to test functionality of such variants.
One important decision that affects future ISAG conferences was made at the 2014 ISAG business meeting. To "frameshift" the ISAG meeting so that it does not occur in the same year as the World Congress on Genetics Applied to Livestock Production (see next report), the following schedule was adopted. The next meeting of ISAG will be held in Salt Lake City, Utah on July 23-27, 2016, and the meeting after Salt Lake City will be just one year later, in 2017, in Dublin, Ireland. From then on, ISAG meetings will be held in odd years.
Summary of WCGALP meeting August 2014.
The 10th World Congress on Genetics Applied to Livestock Production was.held at the Westin Bayshore Conference Center located on the bay in beautiful Vancouver, British Columbia, Canada, August 17-22, 2014. A total of over 1,450 delegates representing 58 countries enjoyed a week of excellent science and fabulous sights. Plenary lectures opened each morning including presentations by Jerry Taylor ("Animal Breeding in the Next-Generation Sequencing Era"), Michael Lohuis ("Bridging the Gap Between Scientific Facts and Societal Perceptions about Agriculture"), Joseph Felsenstein ("Phylogenies Meet Quantitative Genetics: Some Attempts to Extrapolate"), Peter Visscher ("Quantitative Genetics of Complex Traits in Human Populations"), and Carlos Bustamante ("Population Genetics in the Personal Genome Era"). Oral and Poster sessions kept delegates engaged throughout the day. Proceedings papers and the virtual meeting including recordings of many of the presentations are available at the congress website http://www.wcgalp.com . The joint US-Canada organizing committee is to be commended for hosting such a successful conference. Everyone is looking forward as plans are underway for the 11th WCGALP in Auckland, New Zealand in February 2018.
2. Information on NAGRP Bioinformatic tools - new and updated.
The NAGRP Bioinformatics Team has been working on new and updated tools and resources that impact pig genome scientists. See their recent updates at http://www.animalgenome.org/community/mail/view.php?f=db/6492. Of direct interest:
- Animal QTLdb updates: Announcing Release 24 of the Animal QTLdb: A sum of 3,876 new QTL have been added to the database since last release. This brings the current total number of QTL in the database to 28,624, including 11,610 in Pig.
- Data repository: The pig 70K SNP chip annotations are now available from the NAGRP data repository. Thanks to Jeremy Walker (JWalker neogen.com) for this resource.
- Announcement since the September Update #3: The state of art online alignment tool - Jbrowse - has been setup for QTL/association data alignment with annotated genes among other genome features. The advantage of Jbrowse is that it allows easy user quantitative data - XYPlot, Density, in BAM or VCF format - to be loaded for comparisons directly to user's browser in a local environment. See: http://i.animalgenome.org/jbrowse/
3. Upcoming meetings - Highlighting meetings with close deadlines
(For meetings of relevance to the genomics community over the next 6-12 months, see: http://www.animalgenome.org/pig/community/meetings.html Highlighted meetings:
4. We want to hear from you!
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 planned for Feb 15, June 15 and October 15 each year. Any contribution should be sent to the Coordinators one week prior to these dates.
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: email@example.com Email: firstname.lastname@example.org http://www.animalgenome.org/pig/
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