Development of Microsatellite Markers in Bioenergy Crops, Switchgrass

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Development of Microsatellite Markers in
Bioenergy Crops, Switchgrass Hybrid Poplar
Shreni Keniya Knox College, IL Lee
Gunter Environmental Sciences Division ORNL
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A Few Predictions.

• Oil and natural gas reserves will deplete in a
  few decades
• Fossil fuels will last just another 200 years

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The Solution

• BIOENERGY Fuel Sources
• SWITCHGRASS
• (Panicum virgatum L.)
• HYBRID POPLAR
• (Populus spp. Salix spp.)

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Bioenergy Feedstock Development Program (BFDP)

• Sponsored by U.S. DOE
• To improve biomass feedstock quality quantity
  by traditional breeding methods

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But Recently

• DNA and Protein Markers have become popular
• Alloenzymes/Isoenzymes
• RAPDs
• RFLPs
• SSRs

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Microsatellites or SSRs

• Short tandem repeats of simple or complex di-,
  tri-, tetra nucleotides
• Usually found in unique DNA sequences
• Used for linkage analysis in locating genes
• Useful in determining quantitative trait loci
  (QTL)

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The Objective Is

• To test novel primers in
• 3 parental populations in switchgrass
• 3 Populus spp. 4 Salix spp.

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Species
DNA Extraction
Sequencing and primer design
atggctatcgtatcgattttgctatgcgagcggttaaaatctatgttggg
atatggtatttgaatctcgtatcgctgtatcgctgatgcgcgcgcgcgcg
cgcgcgcgcgcttatctgctatcgttsagctatcgttcgggttaggttta
tatgtagtctcgtcgctcatagttagctggttatcttatcgtctcgatct
Clone
Genotype analysis of fluorescent PCR
PCR
Gel Electrophoresis
Analysis of marker polymorphism
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Gel Electrophoresis
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Switchgrass genome
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SSR Analysis In Switchgrass
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SSR Analysis In Populus
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SSR Analysis in Willow
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The Bigger Picture

• A genetic map can help estimate
• how many genes control a trait,
• where the genes are located
• how much affect does each gene have on a trait
• if individual genes have any effect on more than
  one trait
• if they function similarly in different
  environments and
• if the effect of one gene influence the effect(s)
  of others

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Acknowledgements

• Research was funded by the Department of Energy's
  Office of Fuels Development (OFD) through the
  Bioenergy Feedstock Development Program at ORNL.
  Research participation sponsored by the HERE/GLCA
  program at ORISE.
• We would like to thank
• Zamin Yang of ESD for cloning and sequencing
  work, and for her help with fluorescent
  genotyping
• Ken Vogel, USDA-ARS, Lincoln, NE for providing
  plant material for 'Kanlow' parent VK15 and
  'Summer' parent VS16 and
• Ali Missaoui, Department of Crop and Soil
  Science at the University of Georgia for
  providing genomic DNA from 'Alamo' P13 and P19.