James Kijas
FOAM March 2014
Building the genomics toolbox
for a livestock genome
What makes individuals different?
+ E
Linkage
Map
Reference
Genome
Gene Expression
Array
SNP Genotyping
Array
What is the most useful component to put into the ...
Tellam
Ingham
McWilliam
Dalrymple
Jiang Yu
Kijas
Dalrymple
McWilliam
2004 2005 2006 2007 2008 2009 2010 2011 2012
Chicken ...
2004 2005 2006 2007 2008 2009 2010 2011 2012
Shotgun
Sanger based
BAC physical map
Chicken
2005 2006 2007 2008 2009 2010 2011 2012 2013
Comparative genome
Sheep DNA
Fragments
NG Sequencing
340K mutations
2014
Refe...
GWAS for
Disease
23 cases
23 controls
Test and remove
PITX3 mutants
through breeding
Selection
Sweeps
Evolution
11 K years
200 years
What is the most useful component to put into the toolbox?
Should we build a SNP chip or a Reference Genome first?
1. Do w...
Reference GenomeSNP Genotyping
ArrayTool
Required
Resources
Institutional Level
Skim Sequence / RRL / Pooling
Common analy...
Reference GenomeSNP Genotyping
ArrayTool
Applications
Genetic Diversity
Population Substructure
Gene Flow Between Groups
B...
Conservation
& Management
Food security
& Productivity
Breeding
& Adaptation
Disease
Prevention
2. What is the objective?
3. Is there a reference genome sequence for a related lineage?
yes
3. Is there a reference genome sequence for a related lineage?
If no:
- can still produce a SNP chip (all v all approach)
...
Conclusions
- tools and their applications
- criteria for planning how to populate the toolbox
Thanks
The International Sh...
Building the genomics toolbox for a livestock genome - James Kijas
Building the genomics toolbox for a livestock genome - James Kijas
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Building the genomics toolbox for a livestock genome - James Kijas

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Researchers motivated to identify genes that control differences between individuals rely on a genomics toolbox. Really useful tools include i) a reference genome assembly ii) information about where the genes and other features reside inside that genome assembly and iii) a way to collect large scale data describing the differences between genomes from different individuals. A team inside CSIRO has been developing each of these tools for the sheep genome, and putting them to work to understand what contributes to variation in production traits (eg wool growth and meat quality). The talk will focus on the approach taken over the last 5 years to build the various components of the toolkit. This has consequences for the development of genomic resources in other species which may currently have fewer available tools.

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Building the genomics toolbox for a livestock genome - James Kijas

  1. 1. James Kijas FOAM March 2014 Building the genomics toolbox for a livestock genome
  2. 2. What makes individuals different? + E
  3. 3. Linkage Map Reference Genome Gene Expression Array SNP Genotyping Array What is the most useful component to put into the toolbox? Focus on two components Genome Re-sequencing Broad Institute
  4. 4. Tellam Ingham McWilliam Dalrymple Jiang Yu Kijas Dalrymple McWilliam 2004 2005 2006 2007 2008 2009 2010 2011 2012 Chicken Sheep Cattle Pig Goat Comparative genome
  5. 5. 2004 2005 2006 2007 2008 2009 2010 2011 2012 Shotgun Sanger based BAC physical map Chicken
  6. 6. 2005 2006 2007 2008 2009 2010 2011 2012 2013 Comparative genome Sheep DNA Fragments NG Sequencing 340K mutations 2014 Reference Assembly v3.1 Under Review (Science)
  7. 7. GWAS for Disease 23 cases 23 controls Test and remove PITX3 mutants through breeding
  8. 8. Selection Sweeps
  9. 9. Evolution 11 K years 200 years
  10. 10. What is the most useful component to put into the toolbox? Should we build a SNP chip or a Reference Genome first? 1. Do we have the skills, time and cash? 2. What is the objective? 3. Is there a reference genome for a related lineage?
  11. 11. Reference GenomeSNP Genotyping ArrayTool Required Resources Institutional Level Skim Sequence / RRL / Pooling Common analytical expertise Partner with a life science co. $ Thousands – 10s K International Consortium Species Specific Physical Map - radiation hybrid map - optical map - linkage map - BAC library Deep Sequence High-end analytical expertise $ Millions 1. Do we have the skills, time and cash?
  12. 12. Reference GenomeSNP Genotyping ArrayTool Applications Genetic Diversity Population Substructure Gene Flow Between Groups Breeding Programs GWAS for Major Genes Genome Evolution Gene Regulation Proteomics Integration Platform 2. What is the objective?
  13. 13. Conservation & Management Food security & Productivity Breeding & Adaptation Disease Prevention 2. What is the objective?
  14. 14. 3. Is there a reference genome sequence for a related lineage? yes
  15. 15. 3. Is there a reference genome sequence for a related lineage? If no: - can still produce a SNP chip (all v all approach) - limited utility for some applications (eg GWAS) - increases the rationale for building a reference genome assembly
  16. 16. Conclusions - tools and their applications - criteria for planning how to populate the toolbox Thanks The International Sheep Genomics Consortium
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