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Fingerprinting Progress Report
Ross Whetten
Professor
Forestry & Environmental Resources
Overview
• Review of basic genetics terminology
• Objectives of fingerprinting project
• Strategy
• Results to date
• Work to be completed
Review of terminology
• “Genetic fingerprint” = DNA sequence markers
• Each tree has two copies of every chromosome
•
Potentially different versions of each DNA sequence
• Two copies are identical = “homozygous”
• Two copies are different = “heterozygous”
Homozygous
parent
X
Heterozygous
parent
Progeny get one copy of each DNA
(chromosome) from each parent,
recombination mixes things up
Review of terminology
• “Single nucleotide polymorphism”, or SNP,
means a change of a single base in the DNA
sequence
• “Quantitative Trait Locus”, or QTL, means a
region of DNA that affects a trait of interest
• “Gene” means a region of DNA that encodes
some product needed by the cell.
• “Regulatory sequences” control expression of
genes, but are not always near the genes they
control
Example – Blue Eyes in Humans
A small segment of human chromosome 15 (~0.5%), shown in the Variation Viewer
(http://www.ncbi.nlm.nih.gov/variation). Two genes are shown – the vertical lines are
“exons” that encode proteins; the “introns” between exons are discarded.
Alignment of two human sequences
with the same region of the mouse
genome shows a SNP between the
two human versions of the gene.
This SNP accounts for about 70%
of the blue-eye vs brown-eye color
differences in human populations,
but is completely recessive. Two C
alleles = blue eyes
Who cares about fingerprinting?
• Seedling buyers should care about family identity
•
The key predictor of seedling performance
• Fingerprinting will allow confirmation of identity
• Paper records are the best method to date;
fingerprinting will be a useful supplement
Objectives
• Screen candidate marker regions
•
Use test population with family structure as control
• Select markers that work well
• Collect samples from 4th-cycle parents
•
And ancestors, when those are known
• Extract DNA, analyze fingerprints, store in TIProot
Strategy
• Start with data from previous projects
•
PINEMAP, CTGN, ADEPT2 grants
• Select regions to screen for possible SNPs
• Amplify and sequence target regions from test
population samples
• Analyze data for SNP markers that will be useful
for fingerprinting
Results to date
• Two sets of target regions identified
•
Set 1 =144 targets; Set 2 = 151 targets
• Foliage samples collected in May 2015 from
2350 ACE progeny; DNA isolated in
September 2015
• Foliage samples collected in October 2015
from > 1000 grafts of 237 different 4th-cycle
parents at Arrowhead Breeding Center; DNA
isolated in November 2015
Results to date
• Set 1 tested on 960 samples of ACE progeny
• About 50 target regions gave acceptable data
• Set 2 tested on 24 samples; 12 haploid and 12
diploid
• About 90 target regions gave acceptable data
Work to be completed
• Finalize a set of about 140 target regions to
test on ABC DNA samples
• Work with Purchasing Department to set up
fingerprinting contract
• Submit samples; analyze data
• Organize foliage collection from remaining 4thcycle parents in cooperator orchards
• Extract DNA; complete fingerprinting
Summary
• Fingerprinting 4th-cycle breeding population is
well underway
• Fingerprints will be stored in TIProot
• Candidate SNPs and target regions identified;
data available for download from TIProot
• Limiting factor for cooperators is DNA
extraction; no reliable commercial service
provider available yet