Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource

Genome Research

Volumn 22, Issue 8, 2012, Pages 1558-1566

  King, Elizabeth G ^a   Merkes, Chris M ^b   McNeil, Casey L ^b   Hoofer, Steven R ^b   Sen, Saunak ^c   Broman, Karl W ^d   Long, Anthony D ^a   Macdonald, Stuart J ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF KANSAS   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d UNIVERSITY OF WISCONSIN SCHOOL OF MEDICINE AND PUBLIC HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALCOHOL DEHYDROGENASE;

ANIMAL EXPERIMENT; ARTICLE; CONTROLLED STUDY; DROSOPHILA MELANOGASTER; ENZYME ACTIVITY; FEMALE; GENE LOCUS; GENE MAPPING; GENE STRUCTURE; GENETIC ANALYSIS; GENETIC LINKAGE; GENETIC TRAIT; GENETIC VARIABILITY; GENOMICS; MALE; NONHUMAN; PRIORITY JOURNAL; RECOMBINANT INBRED STRAIN; RECOMBINATION REPAIR; SINGLE NUCLEOTIDE POLYMORPHISM;

ALCOHOL DEHYDROGENASE; ALLELES; ANIMALS; CHROMOSOME MAPPING; CROSSES, GENETIC; DROSOPHILA MELANOGASTER; DROSOPHILA PROTEINS; ENZYME ACTIVATION; FEMALE; GENE FREQUENCY; GENETIC VARIATION; GENOTYPING TECHNIQUES; INBREEDING; MALE; MODELS, ANIMAL; PHENOTYPE; QUANTITATIVE TRAIT, HERITABLE;

EID: 84863868317     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.134031.111     Document Type: Article

References (49)

1. Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, et al. 2000. The genome sequence of Drosophila melanogaster. Science 287: 2185-2195.
2. Andolfatto P, Wall JD, Kreitman M. 1999. Unusual haplotype structure at the proximal breakpoint of In(2L)t in a natural population of Drosophila melanogaster. Genetics 153: 1297-1311.
3. Aylor DL, Valdar W, Foulds-Mathes W, Buus RJ, Verdugo RA, Baric RS, Ferris MT, Frelinger JA, Heise M, Frieman MB, et al. 2011. Genetic analysis of complex traits in the emerging Collaborative Cross. Genome Res 21: 1213-1222.
4. Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA. 2008. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3: e3376. doi: 10.1371/journal.pone.0003376.
5. Broman KW. 2005. The genomes of recombinant inbred lines. Genetics 169: 1133-1146.
6. Broman KW, Sen S. 2009. A guide to QTL mapping with R/qtl. Springer, New York.
7. Buckler ES, Holland JB, Bradbury PJ, Acharya CB, Brown PJ, Browne C, Ersoz E, Flint-Garcia S, Garcia A, Glaubitz JC, et al. 2009. The genetic architecture of maize flowering time. Science 325: 714-718.
8. Choudhary M, Laurie CC. 1991. Use of in vitro mutagenesis to analyze the molecular basis of the difference in Adh expression associated with the allozyme polymorphism in Drosophila melanogaster. Genetics 129: 481-488.
9. Churchill GA, Doerge RW. 1994. Empirical threshold values for quantitative trait mapping. Genetics 138: 963-971.
10. Churchill GA, Airey DC, Allayee H, Angel JM, Attie AD, Beatty J, Beavis WD, Belknap JK, Bennett B, Berrettini W, et al. 2004. The Collaborative Cross, a community resource for the genetic analysis of complex traits. Nat Genet 36: 1133-1137.
11. Clark AG, Wang L. 1994. Comparative evolutionary analysis of metabolism in 9 Drosophila species. Evolution 48: 1230-1243.
12. Dzitoyeva S, Dimitrijevic N, Manev H. 2003. γ-Aminobutyric acid B receptor 1 mediates behavior-impairing actions of alcohol in Drosophila: Adult RNA interference and pharmacological evidence. Proc Natl Acad Sci 100: 5485-5490.
13. Hirschhorn JN, Gajdos ZK. 2011. Genome-wide association studies: Results from the first few years and potential implications for clinical medicine. Annu Rev Med 62: 11-24.
14. Huang X, Paulo MJ, Boer M, Effgen S, Keizer P, Koornneef M, van Eeuwijk FA. 2011. Analysis of natural allelic variation in Arabidopsis using a multiparent recombinant inbred line population. Proc Natl Acad Sci 108: 4488-4493.
15. Keane TM, Goodstadt L, Danecek P, White MA, Wong K, Yalcin B, Heger A, Agam A, Slater G, Goodson M, et al. 2011. Mouse genomic variation and its effect on phenotypes and gene regulation. Nature 477: 289-294.
16. King JJ, McDonald JF. 1987. Post-translational control of alcohol dehydrogenase levels in Drosophila melanogaster. Genetics 115: 693-699.
17. King EG, Macdonald SJ, Long AD. 2012. Properties and power of the Drosophila Synthetic Population Resource for the routine dissection of complex traits. Genetics 191. doi: 10.1534/genetics.112.138537.
18. Kover PX, Valdar W, Trakalo J, Scarcelli N, Ehrenreich IM, Purugganan MD, Durrant C, Mott R. 2009. A Multiparent Advanced Generation Inter-Cross to fine-map quantitative traits in Arabidopsis thaliana. PLoS Genet 5: e1000551. doi: 10.1371/journal.pgen.1000551.
19. Lander ES, Botstein D. 1989. Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121: 185-199.
20. Laurie CC, Stam LF. 1988. Quantitative analysis of RNA produced by slow and fast alleles of Adh in Drosophila melanogaster. Proc Natl Acad Sci 85: 5161-5165.
21. Laurie CC, Stam LF. 1994. The effect of an intronic polymorphism on alcohol dehydrogenase expression in Drosophila melanogaster. Genetics 138: 379-385.
22. Laurie CC, Bridgham JT, Choudhary M. 1991. Associations between DNA sequence variation and variation in expression of the Adh gene in natural populations of Drosophila melanogaster. Genetics 129: 489-499.
23. Laurie-Ahlberg CC, Maroni G, Bewley GC, Lucchesi JC, Weir BS. 1980. Quantitative genetic variation of enzyme activities in natural populations of Drosophila melanogaster. Proc Natl Acad Sci 77: 1073-1077.
24. Laurie-Ahlberg CC, Stam LF. 1987. Use of P-element-mediated transformation to identify the molecular basis of naturally occurring variants affecting Adh expression in Drosophila melanogaster. Genetics 115: 129-140.
25. Macdonald SJ, Long AD. 2007. Joint estimates of quantitative trait locus effect and frequency using synthetic recombinant populations of Drosophila melanogaster. Genetics 176: 1261-1281.
26. Mackay TF. 2001. The genetic architecture of quantitative traits. Annu Rev Genet 35: 303-339.
27. Mackay TF. 2010. Mutations and quantitative genetic variation: Lessons from Drosophila. Philos Trans R Soc Lond B Biol Sci 365: 1229-1239.
28. Mackay TF, Richards S, Stone EA, Barbadilla A, Ayroles JF, Zhu D, Casillas S, Han Y, Magwire MM, Cridland JM, et al. 2012. The Drosophila melanogaster Genetic Reference Panel. Nature 482: 173-178.
29. Mann TP. 2006. Numerically stable hidden Markov model implementation. http://bozeman.genome.washington.edu/compbio/mbt599-2006/hmm-scaling-revised. pdf.
30. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A, et al. 2009. Finding the missing heritability of complex diseases. Nature 461: 747-753.
31. Matzkin LM, Merritt TJ, Zhu CT, Eanes WF. 2005. The structure and population genetics of the breakpoints associated with the cosmopolitan chromosomal inversion In(3R)Payne in Drosophila melanogaster. Genetics 170: 1143-1152.
32. McCarthy MI, Abecasis GR, Cardon LR, Goldstein DB, Little J, Ioannidis JP, Hirschhorn JN. 2008. Genome-wide association studies for complex traits: Consensus, uncertainty and challenges. Nat Rev Genet 9: 356-369.
33. McMullen MD, Kresovich S, Villeda HS, Bradbury P, Li H, Sun Q, Flint-Garcia S, Thornsberry J, Acharya C, Bottoms C, et al. 2009. Genetic properties of themaize nested associationmapping population. Science 325: 737-740.
34. Mott R, Talbot CJ, Turri MG, Collins AC, Flint J. 2000. A method for fine mapping quantitative trait loci in outbred animal stocks. Proc Natl Acad Sci 97: 12649-12654.
35. Nuzhdin SV, Pasyukova EG, Dilda CL, Zeng ZB, Mackay TF. 1997. Sex-specific quantitative trait loci affecting longevity in Drosophila melanogaster. Proc Natl Acad Sci 94: 9734-9739.
36. Philip VM, Sokoloff G, Ackert-Bicknell CL, Striz M, Branstetter L, Beckmann MA, Spence JS, Jackson BL, Galloway LD, Barker P, et al. 2011. Genetic analysis in the Collaborative Cross breeding population. Genome Res 21: 1223-1238.
37. Pinheiro J, Bates D, DebRoy S, Sarkar D, R Development Core Team. 2011. nlme: Linear and Nonlinear Mixed Effects Models. R package version 3.1-101.
38. Pritchard JK. 2001. Are rare variants responsible for susceptibility to complex diseases? Am J Hum Genet 69: 124-137.
39. Pritchard JK, Cox NJ. 2002. The allelic architecture of human disease genes: Common disease-common variant. . .or not? Hum Mol Genet 11: 2417-2423.
40. R Development Core Team. 2011. R: A language and environment for statistical computing. R Foundation for Statistical Computing. http://www.R-project.org/.
41. Rabiner LR. 1989. A tutorial on hidden Markov models and selected applications in speech recognition. Proc IEEE 77: 257-286.
42. Reich DE, Lander ES. 2001. On the allelic spectrum of human disease. Trends Genet 17: 502-510.
43. Rockman MV, Kruglyak L. 2008. Breeding designs for recombinant inbred advanced intercross lines. Genetics 179: 1069-1078.
44. Stam LF, Laurie CC. 1996. Molecular dissection of a major gene effect on a quantitative trait: The level of alcohol dehydrogenase expression in Drosophila melanogaster. Genetics 144: 1559-1564.
45. Teuscher F, Broman KW. 2007. Haplotype probabilities for multiple-strain recombinant inbred lines. Genetics 175: 1267-1274.
46. Weiss KM, Terwilliger JD. 2000. How many diseases does it take to map a gene with SNPs? Nat Genet 26: 151-157.
47. Yalcin B, Flint J, Mott R. 2005. Using progenitor strain information to identify quantitative trait nucleotides in outbred mice. Genetics 171: 673-681.
48. Yang J, Benyamin B, McEvoy BP, Gordon S, Henders AK, Nyholt DR, Madden PA, Heath AC, Martin NG, Montgomery GW, et al. 2010. Common SNPs explain a large proportion of the heritability for human height. Nat Genet 42: 565-569.
49. Zhu Q, Ge D, Maia JM, Zhu M, Petrovski S, Dickson SP, Heinzen EL, Shianna KV, Goldstein DB. 2011. A genome-wide comparison of the functional properties of rare and common genetic variants in humans. Am J Hum Genet 88: 458-468.