Comparative Genomics of Hardwood Tree Species http://www.hardwoodgenomics.org Comparative Genomics of Hardwood Tree Species http://www.hardwoodgenomics.org The Hardwood Genomics Project: Outcomes and Future Directions after Four Years of Resource Development Meg Staton
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The Hardwood Genomics Project: Outcomes and Future Directions after Four Years of Resource Development
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Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
The Hardwood Genomics Project: Outcomes and Future Directions after Four Years of
Resource DevelopmentMeg Staton
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Comparative Genomics of Environmental Stress Responses in North American Hardwoods
• February 1, 2011 – January 31, 2015
• Creating genomic resources for hardwood trees
• Current and increasingly devastating forest threats: invasive pests and pathogens, climate change
• Enable population, evolutionary and conservation genetics
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
The TeamPenn State University
John Carlson, PI
Teodora Best, Research Associate
Nicole Zembower, Technician
Di Wu, PhD Student
Nick Wheeler, Manager
University of Notre Dame
Jeanne Romero-Severson, Co-PI
Dan Borkowski, PhD Student
Arpita Konar, PhD Student
Andrea Noakes, PhD Student
Lauren Fiedler, Technician
Olivia Choudhary
Michigan Tech University
Oliver Gailing, Co-PI
Sandra Owusu, PhD Student
Sudhir Khodwekar, PhD Student
University Tennessee
Scott Schlarbaum, Co-PI
Ami Sharp, Research AssociateJason Hogan, Research AssociateJames Simons, Research Associate
Margaret Staton, Bioinformatics,
Jack Davitt, Research Associate
Nathan Henry, Research Associate
Thomas Lane, Research Associate
University of Missouri
Mark Coggeshall, Co-PI
Christopher Heim, MS student
Clemson University
Haiying Liang, Co-PI
Chis Saski, Director of CUGI
Tatyana Zhebentyayev, Research Associate
Ketia Shumaker, PI
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Tulip Poplar
Sweetgum
Honeylocust
Northern Red Oak
Black Walnut
Sugar Maple
Blackgum
Green Ash
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Deliverables
1. Develop Deep EST Sequence Resources
2. BAC Libraries and BAC Sequencing
3. Mapping Populations
4. Genetic Map Construction
5. Phenotyping and QTL Map Construction
6. Website
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Deliverables
1. Develop Deep EST Sequence Resources
2. BAC Libraries and BAC Sequencing
3. Mapping Populations
4. Genetic Map Construction
5. Phenotyping and QTL Map Construction
6. Website
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Transcriptome Libraries
Stress treatments on full or half sib seedlings• Ozone treatments
– all species except HL– 4 levels of ozone across 4
Full Sibling Mapping PopulationsHost Species DNA Collected No. Seedlings
Honeylocust Yes 226+ half sibs (149 full sibs so far)
Northern Red Oak Yes 339 full sibs (PE confirmed)
Black Walnut Yes 323 full sibs (PE confirmed)
Tulip Poplar Yes 212 full sibs (controlled cross)
Green Ash* Yes 328 full sibs (controlled cross)
*Produced by Jennifer Koch, FS Northern Research Station
Herbarium samples are being obtained for all parent trees• vouchers will be deposited at the Dunn-Palmer Herbarium at MU • imaged and uploaded to the TROPICOS website
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Deliverables
1. Develop Deep EST Sequence Resources
2. BAC Libraries and BAC Sequencing
3. Mapping Populations
4. Genetic Map Construction
5. Phenotyping and QTL Map Construction
6. Website
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Genetic Map Construction
• Northern Red Oak– 509 full sibs
• 37 genomic SSRs• 71 EST-SSRs
– 250 full sibs• GBS: double digest RAD
tag strategy• Up to 7,994 SNPs
useable
– Map currently has SSRs + 500 RAD tag SNPs
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Genetic Map Construction
• Black walnut– 300 full sibs submitted for GBS
• Honeylocust– 96 full sibs submitted for GBS
• Tulip poplar– 196 EST-SSRs – 365 full sibs
• Green ash– 370 full sibs– DNA extraction complete– SSR optimization underway
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Deliverables
1. Develop Deep EST Sequence Resources
2. BAC Libraries and BAC Sequencing
3. Mapping Populations
4. Genetic Map Construction
5. Phenotyping and QTL Map Construction
6. Website
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Phenotyping
• Follow on to the current funded study• Northern Red Oak
– Full sib population established at UT– Replicated clonal orchard: 339 sibs plus parents were grafted and established
at Missouri, with each tree represented 2-4 times
• Phenotyping in 2013, 2014– leafing date– bud burst– leaf morphology– leaf N content