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Genetic architecture of
developmental traits in
populations of male gypsy moths
Christopher J. Friedline, Ph.D.!
Virginia ...
Lymantria dispar
http://bugguide.net/node/view/553307Adapted from: http://www.fs.fed.us/ne/morgantown/4557/gmoth/atlas/qua...
http://green.blogs.nytimes.com/2011/09/13/the-toll-from-tree-boring-pests/?_php=true&_type=blogs&_r=0
Can we gain insight into the
genetic architecture of invasion
using L. dispar as a model?
Experimental design
• 7 populations established in
replicated common gardens
(NY, VA)
• NC (1), VA (2), NY (1),
Quebec (2)...
Parry and Grayson, EntSoc 2013
Reference Assembly
• MaSuRCA Zimin et al. (2013), Bioinformatics, 29 (21),
2669-2677
• 591,450 scaffolds (90M QC PE reads)...
ddRADseq
• 316 M reads 

(41.5 GB)
• 188 individuals
• 690 Kb/individual
[10, 1400] Kb (QC)
Peterson et al. (2012) Plos On...
SNP Calling/Filtering
• Called with Freebayes (n = 30,791)
• Kept only biallelic SNPs
• Removed > 50% missing
• Removed FI...
Phenotypes
NC NY OTIS QC32 QC93 VA1 VA2
7
8
9
10
11
12
13
Pupual Duration
NC NY OTIS QC32 QC93 VA1 VA2
0.2
0.3
0.4
0.5
0.6...
0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35
FST
0
1000
2000
3000
4000
5000
6000
7000
8000
Multilocus FIS = 0.0486, FST = 0.022...
Population Structure
Correction by PCA
• Price et al. (2006) ”Principal Components Analysis
Corrects for Stratification in ...
Population Structure
Correction by PCA
• Price et al. (2006) ”Principal Components Analysis
Corrects for Stratification in ...
Population Structure
Correction by PCA
• Price et al. (2006) ”Principal Components Analysis
Corrects for Stratification in ...
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...
468
444
44
444
73 29
9
Total Dev Time Pupual Duration
Mass
• Corrected for population structure (Price et al. 2006), binne...
Multilocus effectS27843
S5330
S13360
S23045
S23046
S14681
S14682
S27841
S30469
S25851
S10170
S23791
S12194
S25917
S7263
S7...
Blast results
Mass
reverse transcriptase*
non-LTR
retrotransposon
predicted craniofacial
development protein
sulfotransfer...
Conclusions/Future Work
• Assembly curation is likely necessary for more
robust biological conclusion
• Small effect sizes...
Acknowledgments
Johnson Lab!
Derek Johnson
Kristine Grayson
Trevor Faske
NPGI: NSF Postdoctoral Fellowship in Biology FY 2...
Genetic architecture of developmental traits in populations of male gypsy moths
Genetic architecture of developmental traits in populations of male gypsy moths
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Genetic architecture of developmental traits in populations of male gypsy moths

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Genetic architecture of developmental traits in populations of male gypsy moths

  1. 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
  2. 2. Lymantria dispar http://bugguide.net/node/view/553307Adapted from: http://www.fs.fed.us/ne/morgantown/4557/gmoth/atlas/quar1a.gif
  3. 3. http://green.blogs.nytimes.com/2011/09/13/the-toll-from-tree-boring-pests/?_php=true&_type=blogs&_r=0
  4. 4. Can we gain insight into the genetic architecture of invasion using L. dispar as a model?
  5. 5. Experimental design • 7 populations established in replicated common gardens (NY, VA) • NC (1), VA (2), NY (1), Quebec (2) + 1 lab strain (CPHST Otis Lab) • Single reference assembly (HiSeq 2500 PE) • 188 barcoded individuals • 3 phenotypes (developmental) http://www.fs.fed.us/ne/morgantown/4557/gmoth/
  6. 6. Parry and Grayson, EntSoc 2013
  7. 7. Reference Assembly • MaSuRCA Zimin et al. (2013), Bioinformatics, 29 (21), 2669-2677 • 591,450 scaffolds (90M QC PE reads) • 588,164,124 Mb (~1 Kb/contig, max=28 Kb) • 268 contigs > 10 Kb • N50 = 1.3 Kb • 35.3% GC • 32%/56% CEGMA complete/partial
  8. 8. ddRADseq • 316 M reads 
 (41.5 GB) • 188 individuals • 690 Kb/individual [10, 1400] Kb (QC) Peterson et al. (2012) Plos One 7.5 (2012): e37135-e37135
  9. 9. SNP Calling/Filtering • Called with Freebayes (n = 30,791) • Kept only biallelic SNPs • Removed > 50% missing • Removed FIS outliers (> |0.5|) • Removed MAF < 0.01 • n = 11,021
  10. 10. Phenotypes NC NY OTIS QC32 QC93 VA1 VA2 7 8 9 10 11 12 13 Pupual Duration NC NY OTIS QC32 QC93 VA1 VA2 0.2 0.3 0.4 0.5 0.6 0.7 Mass NC NY OTIS QC32 QC93 VA1 VA2 65 70 75 80 85 90 95 Total Dev Time
  11. 11. 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 FST 0 1000 2000 3000 4000 5000 6000 7000 8000 Multilocus FIS = 0.0486, FST = 0.0224, FIT = 0.0700 n=11021 [0.00, 0.34] FST MAF Bin F F F 50 0.1542 0.0234 0.174 40 0.1007 0.0303 0.128 30 0.0757 0.0295 0.103 20 0.0093 0.0169 0.0261 10 -0.0673 0.0088 -0.0579
  12. 12. 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
  13. 13. 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
  14. 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. 15. 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)
  16. 16. 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
  17. 17. Multilocus effectS27843 S5330 S13360 S23045 S23046 S14681 S14682 S27841 S30469 S25851 S10170 S23791 S12194 S25917 S7263 S7870 S1134 S14103 S8633 S13228 S14762 S2609 S26153 S17855 S9023 Top 25 (p-value) loci 0.005 0.000 0.005 0.010 mult.reg.coeff Mass regression coefficients (R2 = 0.556, R2 adj = 0.494) S10056 S20804 S30588 S21213 S11490 S23793 S29819 S18637 S14030 S21212 S12563 S24930 S26120 S23756 S23892 S12194 S14908 S15702 S12218 S15492 S30168 S29721 S28752 S19836 S10057 Top 25 (p-value) loci 1.0 0.5 0.0 0.5 1.0 mult.reg.coeff Total Dev Time regression coefficients (R2 = 0.639, R2 adj = 0.584) S16063 S6315 S10193 S18784 S21858 S5008 S2156 S18532 S18465 S12721 S12012 S28904 S2571 S20272 S6963 S30060 S3196 S3195 S16560 S17662 S10529 S20271 S18530 S6316 S16062 Top 25 (p-value) loci 1.0 0.5 0.0 0.5 1.0 1.5 mult.reg.coeff Pupual Duration regression coefficients (R2 = 0.541, R2 adj = 0.473)
  18. 18. 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+
  19. 19. 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
  20. 20. 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

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