Outline Programme


4th ISAFG Day 1: Afternoon, Monday 10th October 2011
11:00 – Registration opens
15:30 – 16:00 Welcome and Opening Session
15:40 – 16:00 Patrick Cunningham (Chief Scientific Advisor to the Irish Government)
16:00 – 16:40 Plenary Session 1
16:00 – 16:40 Elaine Mardis (The Genome Institute at Washington University School of Medicine)
Title: The impact of next-generation sequencing technology on genomics.
16:40 – 17:10 Coffee Break
17:10 – 18:30 Plenary Session 2
17:10 – 17:50 David Hume (The Roslin Institute and the University of Edinburgh)
Title: Macrophage systems biology
17:50 – 18:30 Eckhard Wolf (Ludwig-Maximilians-Universität München)
Title: Molecular profiles as sensors and drivers of embryo developmental potential and uterine
receptivity in livestock

Session Chairs:
David MacHugh (University College Dublin), Paul Coussens (Michigan State University) and Patrick Cunningham (Chief Scientific Advisor to the Irish Government and Trinity College Dublin).
18:30 – 20.00 Wine Reception and Poster Session
 
4th ISAFG Day 2: Morning, Tuesday 11th October 2011
09:00 – 10:30 Session 1: Epigenomics
Presentations representing the burgeoning area of epigenetic phenomena such as genomic imprinting, chromatin remodelling, non-coding RNAs and their effects on phenotypes of economic or veterinary importance in domestic animals.

Invited speaker
09:00 – 09:30 Rebecca Oakey (King’s College London)
Title: Investigating the role of DNA methylation in human growth disorders.

Selected abstract speakers
09:30 – 09:45 Chris Ashwell (North Carolina State University)
Title: Genome-wide methylation analysis of chicken primordial germ cells.
09:45 – 10:00 James Reecy (Iowa State University)
Title: QTL mapping study on muscle and adipose related traits in mice reveals significant imprinting
and interaction effects.
10:00 – 10:15 Hasan Khatib (University of Wisconsin)
Title: DNA methylation status of the PHLDA2 gene is associated with early embryonic development in cattle.

Commercial presentation from the Title Sponsor
10:15 – 10:35 André Eggen (Illumina® Inc.)
Title: Applying new genomic technologies in research and breeding.

Session Chairs:
Charles Spillane (NUI Galway) and Hasan Khatib (University of Wisconsin)
10:35 – 11:00 Coffee Break
11:00 – 13:00 Session 2: Physiological Genomics
This session is focused on how genomics and functional genomics methods can be used to enhance studies of reproduction, metabolism, neurobiology and other complex physiological functions in domestic animal species.

Invited speakers
11:00 – 11:30 James MacLeod (University of Kentucky)
Title: Complexity of the equine mRNA transcriptome.
11:30 – 12:00 Alex Evans (University College Dublin)
Title: Physiology and genomics of reproductive tissues in cattle.

Selected abstract speakers
12:00 – 12:15 Beatrice McGivney (University College Dublin)
Title: Investigation of myostatin pathway gene expression in untrained and trained Thoroughbred
horse skeletal muscle.
12:15 – 12:30 Anthony Doran (Teagasc and NUI Maynooth)
Title: Genome-wide associations for carcass traits in Irish Holstein-Friesian cattle.
12:30 – 12:45 Anu Sironen (Agrifood Research Finland)
Title: An exonic insertion within the Tex14 gene causes infertility in Yorkshire boars.
12:45 – 13:00 Paul McGettigan (University College Dublin)
Title: An atlas of gene expression in the bovine reproductive tissues.

Session Chairs:
Patrick Lonergan (University College Dublin) and David MacHugh (University College Dublin)
13:00 – 14:00 Lunch
 
4th ISAFG 2011 Day 2: Afternoon, Tuesday 11th October 2011
14:00 – 15:30 Session 3: Systems Biology
The application of systems biology approaches to investigating and understanding the genetic and biochemical regulatory networks and pathways underlying health, welfare and production traits in domestic animal species will be featured.

Invited speakers
14:00 – 14:30 Haja Kadarmideen (University of Copenhagen)
Title: Unravelling and exploiting the missing links in the genome - phenome axis by systems genetics.
14:30 – 15:00 Tom Freeman (The Roslin Institute and the University of Edinburgh)
Title: A gene expression atlas of the pig.

Selected abstract speakers
15:00 – 15:15 Pierre Blavy (INRA)
Title: A new method for modeling reactions and regulations to analyze high-throughput data.
15:15 – 15:30 Antonio Reverter (CSIRO Livestock Industries)
Title: Using regulatory and epistatic networks to extend the findings of a genome scan:
A case example with pigmentation in Merino sheep.

Session Chairs:
David Lynn (Teagasc) and Tom Freeman (The Roslin Institute and the University of Edinburgh)
15:30 – 16:00 Coffee Break
16:00 – 18:00 Session 4: Genomics and Animal Health
This session focuses on the application of genomics and ancillary technologies to understanding problems in animal health and immunobiology and on development of new tools for the prevention and control of infectious animal diseases.

Invited speakers
16:00 – 16:30 Paul Coussens (Michigan State University)
Title: New concepts in the study of M. avium subsp. paratuberculosis (MAP)
immuno-pathogenesis suggested by data from a series of functional genomics studies.
16:30 – 17:00 Christopher Tuggle (Iowa State University)
Title: Blood transcriptomic analysis of the early porcine immune response to identify biomarkers
associated with superior disease control.

Selected abstract speakers
17:00 – 17:15 Nicholas Sanderson (Institute for Animal Health)
Title: Assembly and characterisation of the first cattle KIR haplotype.
17:15 – 17:30 Mark Fife (Institute for Animal Health)
Title: Refining the SAL1 locus for disease resistance in chickens.
17:30 – 17:45 Mairead Bermingham (The Roslin Institute and the University of Edinburgh)
Title: A genome-wide association study identifies resistance loci for bovine tuberculosis in the
Northern Ireland Holstein Friesian dairy cattle population.
17:45 – 18:00 Nuria Mach (INRA)
Title: Blood transcriptome as an emerging molecular phenotype to refine immune traits in pig.

Session Chairs:
Cliona O’Farrelly (Trinity College Dublin) and Elizabeth Glass (The Roslin Institute and the University of Edinburgh)
19:30 – Symposium Gala Dinner
 
4th ISAFG Day 3: Morning, Wednesday 12th October 2011
09:00 – 10:30 Session 5: Genomics and Animal Industries
Presentations in this session highlight the practical impact of genomics, functional genomics and proteomics on animal production, processing and consumption.

Invited speakers
09:00 – 09:30 Emmeline Hill (University College Dublin and Equinome Ltd.)
Title: Horses for courses - genetic variation at the myostatin gene (MSTN) locus and the prediction of
Thoroughbred horse racing performance.
09:30 – 10:00 Mario Calus (Wageningen University)
Title: Practical applications of genomics in livestock.

Selected abstract speakers
10:00 – 10:15 Marie Damon (INRA)
Title: Transcriptomic analysis of Longissimus muscle to identify genes associated with pig meat quality.
10:15 – 10:30 Adriana do Carmo (UNESP – São Paulo State University)
Title: From parentage testing to traceability: A multipurpose low density SNP panel suitable for breed
identification and parentage discovery across taurine and indicine cattle.

Session Chairs:
Donagh Berry (Teagasc) and John Williams (Parco Tecnologico Padano)
10:30 – 11:00 Coffee Break
11:00 – 13:00 Session 6: Computational Biology and Bioinformatics
Development and application of computational methods and software for analysis, data mining and interpretation of high-dimensional genomics, functional genomics and proteomics data.

Invited speakers
11:00 – 11:30 John Quackenbush (Dana-Farber Cancer Institute and the Harvard School of Public Health)
Title: Network and state space models: science and science fiction approaches to cell fate predictions.
11:30 – 12:00 Carl-Johan Rubin (Uppsala University)
Title: Whole genome resequencing of chicken populations reveals loci under selection
during chicken domestication.

Selected abstract speakers
12:00 – 12:15 Mehmet Cinar (University of Bonn)
Title: Weighted gene co-expression network analysis applied to meat quality and carcass composition traits.
12:15 – 12:30 Amir Foroushani (Teagasc and Simon Fraser University)
Title: A novel pathway analysis approach based on significantly enriched pathway signatures.
12:30 – 12:45 Frances Turner (ARK Genomics)
Title: Use of biological replicates in a large RNA-seq dataset.
12:45 – 13:00 Marie-Laure Endale (INRA)
Title: In silico prediction of microRNAs targeting alleles of the Swine Leukocyte Antigen complex.

Session Chairs:
Daniel Bradley (Trinity College Dublin) and Antonio Reverter (CSIRO Livestock Industries)
13:00 – 14:00 Lunch
 
4th ISAFG Day 3: Afternoon, Wednesday 12th October 2011
14:00 – 15:30 Session 7: Application of New Genomics Technologies
How next-generation sequencing, RNA-seq transcriptomics, genomic sequence enrichment, proteomics and other high-throughput, massively parallel technologies can be applied in domestic animal research.

Invited speaker
14:00 – 14:30 Tad Sonstegard (USDA-ARS)
Title: Applied genomics for genetic improvement: paving the way for biological discovery.

Selected abstract speakers
14:30 – 14:45 Barbara Harlizius (Institute for Pig Genetics)
Title: RNA sequencing of liver and testis from boars with divergent haplotypes affecting androstenone levels.
14:45 – 15:00 Ingrid Balcells (Universitat Autònoma de Barcelona)
Title: Differential microRNA expression in ovary of high and low prolificacy pregnant sows from an
Iberian x Meishan F2 intercross.
15:00 – 15:15 Michael Mullen (Teagasc)
Title: Polymorphism discovery and allele frequency estimation using high-throughput DNA
sequencing of target-enriched pooled DNA samples.
15:15 – 15:30 Stephen Park (University College Dublin)
Title: A complete nuclear genome sequence from the extinct Eurasian wild aurochs (Bos primigenius).

Session Chairs:
Torres Sweeney (University College Dublin) and José Fernando Garcia (UNESP – São Paulo State University)
15.30 – 16:00 Coffee Break
16:00 – 17:00 Session 8: Discussion, Final Remarks and Close of Meeting