This document summarizes a study on the genetic architecture of developmental traits in gypsy moth populations. The study established 7 gypsy moth populations in common gardens and sequenced 188 individuals to identify 11,021 SNPs. Three phenotypes - pupal duration, mass, and total development time - were measured. Population structure was corrected using PCA. Several SNPs were significantly associated with each trait, though effect sizes were small. Multilocus models explained over 50% of trait variation. Future work could involve refining the genome assembly and studying additional populations to detect smaller genetic effects.
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Genetic architecture of developmental traits in populations of male gypsy moths
1. Genetic architecture of
developmental traits in
populations of male gypsy moths
Christopher J. Friedline, Ph.D.!
Virginia Commonwealth University
@noituloveand @cfriedline
Evolution 2014!
Raleigh, NC!
6.21.2014
14. Population Structure
Correction by PCA
• Price et al. (2006) ”Principal Components Analysis
Corrects for Stratification in Genome-wide Association
Studies." Nat Genet 38.8
• First principal component approximates FST
• Number of axes chosen using a Tracy-Widom test,
described in Eckert et al. (2010). Genetics 185:
969-982.
• Correlation of genotype vs. phenotype residuals to X2
to p-values
15. Population Structure
Correction by PCA
• Price et al. (2006) ”Principal Components Analysis
Corrects for Stratification in Genome-wide Association
Studies." Nat Genet 38.8
• First principal component approximates FST
• Number of axes chosen using a Tracy-Widom test,
described in Eckert et al. (2010). Genetics 185:
969-982.
• Correlation of genotype vs. phenotype residuals to X2
to p-values
40 20 0 20 40 60 80
PC1 (0.021%)
60
50
40
30
20
10
0
10
20
30
PC2(0.015%)
PCA of n=7 populations on 11021 loci
16. Population Structure
Correction by PCA
• Price et al. (2006) ”Principal Components Analysis
Corrects for Stratification in Genome-wide Association
Studies." Nat Genet 38.8
• First principal component approximates FST
• Number of axes chosen using a Tracy-Widom test,
described in Eckert et al. (2010). Genetics 185:
969-982.
• Correlation of genotype vs. phenotype residuals to X2
to p-values
17. Top SNP
C/C C/T T/T
Locus 14103 (ctg7180001511349/152)
0.2
0.3
0.4
0.5
0.6
0.7
Mass (p = 0.000004, FST = 0.008543)
T/T T/C C/C
Locus 14908 (ctg7180001527347/31)
65
70
75
80
85
90
95
Total Dev Time (p = 0.000111, FST = 0.016849)
A/A A/T T/T
Locus 10529 (ctg7180001452692/364)
7
8
9
10
11
12
13
Pupual Duration (p = 0.000022, FST = 0.024810)
18. 468
444
44
444
73 29
9
Total Dev Time Pupual Duration
Mass
• Corrected for population structure (Price et al. 2006), binned by MAF
• By p value (p < 0.05):
• Mass: n = 555
• Pupual duration: n = 526
• Total development time: n = 524
• By q value (Storey and Tibshirani, 2003)
• Mass: n = 3 (14103
(*,10)
, 27843
(40)
, 9023
(40)
)
• Pupual duration: n = 1 (S10529
(40)
)
• Total development time: n = 0
Significant SNPs
20. Blast results
Mass
reverse transcriptase*
non-LTR
retrotransposon
predicted craniofacial
development protein
sulfotransferase
(amine, estrogen)
Pupual duration
endonuclease-reverse
transcriptase
phosphatidylinositol 3-
kinase
Development time
reverse transcriptase
endonuclease-reverse
transcriptase
transcription initiation factor
TFIID subunit 2-like protein
chosen by p+q*!
chosen by q+
21. Conclusions/Future Work
• Assembly curation is likely necessary for more
robust biological conclusion
• Small effect sizes difficult to detect with small
sample size and populations
• High degree of multilocus effects
• Additional replicate gardens with related material
• Probabilistic genotype calling with full set
22. Acknowledgments
Johnson Lab!
Derek Johnson
Kristine Grayson
Trevor Faske
NPGI: NSF Postdoctoral Fellowship in Biology FY 2013
Rodney Dyer, VCU
Dylan Parry, SUNY-ESF
Eckert Lab!
Andrew Eckert
Brandon Lind
Erin Hobson
Ethan Harwood
VCU NARF
VCU CHiPC