Pig Genome Update No. 120

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.

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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/

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(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:

• Plant and Animal Genome 2015 January 10-14, 2015, San Diego

  The PAG meeting will be held in San Diego at the Town & Country Hotel. The preliminary program can be found at: https://pag.confex.com/pag/xxiii/webprogram/. The Swine Workshop will be held on Saturday January 10 (all day). As in previous years, in the morning, the Swine group will meet with the Cattle Subcommittee to hear several invited lectures. In the afternoon, the Swine group will meet separately and hear Station reports from members, Administrative Advisors and NRSP-8 Coordinators, and hold a business meeting. Important

• North American Porcine Reproductive and Respiratory Syndrome Symposium December 5-6, 2014, at Intercontinental Hotel, Magnificent Mile in Chicago (see https://ksvma.site-ym.com/?NAPRRS):

  Dates to Remember:
  - October 31st: Abstract submission deadline
  - November 3rd: Hotel reservation deadline
  - November 5th: Travel fellowship applications due
  - November 15th: Registration deadline

  Porcine reproductive and respiratory syndrome (PRRS) is the most economically significant disease of pigs in the world. A new coronavirus, porcine epidemic diarrhea virus (PEDV), is seriously impacting the industry. In addition to PRRS, this year's meeting features a special session devoted to PED. Abstract submission is invited for all three diseases: PRRS, PED and PCVAD. Travel fellowships will be available for students and post-docs. Friday evening will feature a poster session and short talks selected from the abstracts. Registration is $150 for regular attendees and $100 for students, and includes proceedings, lunch on Saturday and all refreshment breaks. A special room rate of $189/night is available from Wednesday, December 3 through Tuesday, December 9. Attendees requiring visas are encouraged to register early.

• Gordon Conference on Quantitative Genetics and Genomics February 22-27, 2015, Lucca (Italy) The Gordon Conference on Quantitative Genetics and Genomics entitled "Deciphering the Genetic Basis of Complex Phenotypes for the Benefit of Mankind" will be held at the Renaissance Tuscany Il Ciocco Resort in Lucca (Barga), Italy, February 22-27, 2015. See http://www.grc.org/GRC/programs.aspx?id=12072 for details and the preliminary program. Applications for this meeting must be submitted by January 25, 2015. GRS Speaker Abstract Deadline is November 21, 2014. There is also a Gordon Research Seminar entitled "Consequences and Evolution of Genomic Variation" associated with this Conference that will be held February 21-22; see http://www.grc.org/GRC/programs.aspx?id=15733 for details.
• Midwest ASAS/ADSA Meeting March 15-18, 2015, Des Moines, IA The 2015 Joint ADSA-ASAS Midwest Section meeting is scheduled for March 15-18 in Des Moines, IA. See https://www.asas.org/membership-services/asas-sections/midwest-section/meetings for details. In addition to the regular breeding and genetics sessions, there are preliminary plans for a Functional Genomics symposium being organized by the Breeding and Genetics and Physiology program committees; details on that Symposium will be provided at a later date. Abstract Submission Deadline: November 5, 2014, 11:59 PM (Central Standard Time).

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: cktuggle@iastate.edu     Email: ernstc@msu.edu

http://www.animalgenome.org/pig/