The Drosophila melanogaster Genetic Reference Panel

Trudy F.C. MacKay; Stephen Richards; Eric A. Stone; Antonio Barbadilla; Julien F. Ayroles; Dianhui Zhu; Sònia Casillas; Yi Han; Michael M. Magwire; Julie M. Cridland; Mark F. Richardson; Robert R.H. Anholt; Maite Barrón; Crystal Bess; Kerstin Petra Blankenburg; Mary Anna Carbone; David Castellano; Lesley Chaboub; Laura Duncan; Zeke Harris; Mehwish Javaid; Joy Christina Jayaseelan; Shalini N. Jhangiani; Katherine W. Jordan; Fremiet Lara; Faye Lawrence; Sandra L. Lee; Pablo Librado; Raquel S. Linheiro; Richard F. Lyman; Aaron J. MacKey; Mala Munidasa; Donna Marie Muzny; Lynne Nazareth; Irene Newsham; Lora Perales; Ling Ling Pu; Carson Qu; Miquel Ràmia; Jeffrey G. Reid; Stephanie M. Rollmann; Julio Rozas; Nehad Saada; Lavanya Turlapati; Kim C. Worley; Yuan Qing Wu; Akihiko Yamamoto; Yiming Zhu; Casey M. Bergman; Kevin R. Thornton; David Mittelman; Richard A. Gibbs

doi:10.1038/nature10811

The Drosophila melanogaster Genetic Reference Panel

Trudy F.C. MacKay, Stephen Richards, Eric A. Stone, Antonio Barbadilla, Julien F. Ayroles, Dianhui Zhu, Sònia Casillas, Yi Han, Michael M. Magwire, Julie M. Cridland, Mark F. Richardson, Robert R.H. Anholt, Maite Barrón, Crystal Bess, Kerstin Petra Blankenburg, Mary Anna Carbone, David Castellano, Lesley Chaboub, Laura Duncan, Zeke HarrisMehwish Javaid, Joy Christina Jayaseelan, Shalini N. Jhangiani, Katherine W. Jordan, Fremiet Lara, Faye Lawrence, Sandra L. Lee, Pablo Librado, Raquel S. Linheiro, Richard F. Lyman, Aaron J. MacKey, Mala Munidasa, Donna Marie Muzny, Lynne Nazareth, Irene Newsham, Lora Perales, Ling Ling Pu, Carson Qu, Miquel Ràmia, Jeffrey G. Reid, Stephanie M. Rollmann, Julio Rozas, Nehad Saada, Lavanya Turlapati, Kim C. Worley, Yuan Qing Wu, Akihiko Yamamoto, Yiming Zhu, Casey M. Bergman, Kevin R. Thornton, David Mittelman, Richard A. Gibbs

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Abstract

A major challenge of biology is understanding the relationship between molecular genetic variation and variation in quantitative traits, including fitness. This relationship determines our ability to predict phenotypes from genotypes and to understand how evolutionary forces shape variation within and between species. Previous efforts to dissect the genotype-phenotype map were based on incomplete genotypic information. Here, we describe the Drosophila melanogaster Genetic Reference Panel (DGRP), a community resource for analysis of population genomics and quantitative traits. The DGRP consists of fully sequenced inbred lines derived from a natural population. Population genomic analyses reveal reduced polymorphism in centromeric autosomal regions and the X chromosome, evidence for positive and negative selection, and rapid evolution of the X chromosome. Many variants in novel genes, most at low frequency, are associated with quantitative traits and explain a large fraction of the phenotypic variance. The DGRP facilitates genotype-phenotype mapping using the power of Drosophila genetics.

Original language	English (US)
Pages (from-to)	173-178
Number of pages	6
Journal	Nature
Volume	482
Issue number	7384
DOIs	https://doi.org/10.1038/nature10811
State	Published - Feb 9 2012
Externally published	Yes

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MacKay, T. F. C., Richards, S., Stone, E. A., Barbadilla, A., Ayroles, J. F., Zhu, D., Casillas, S., Han, Y., Magwire, M. M., Cridland, J. M., Richardson, M. F., Anholt, R. R. H., Barrón, M., Bess, C., Blankenburg, K. P., Carbone, M. A., Castellano, D., Chaboub, L., Duncan, L., ... Gibbs, R. A. (2012). The Drosophila melanogaster Genetic Reference Panel. Nature, 482(7384), 173-178. https://doi.org/10.1038/nature10811

@article{45c8e7aafe274c50905781dc3c06425c,

title = "The Drosophila melanogaster Genetic Reference Panel",

abstract = "A major challenge of biology is understanding the relationship between molecular genetic variation and variation in quantitative traits, including fitness. This relationship determines our ability to predict phenotypes from genotypes and to understand how evolutionary forces shape variation within and between species. Previous efforts to dissect the genotype-phenotype map were based on incomplete genotypic information. Here, we describe the Drosophila melanogaster Genetic Reference Panel (DGRP), a community resource for analysis of population genomics and quantitative traits. The DGRP consists of fully sequenced inbred lines derived from a natural population. Population genomic analyses reveal reduced polymorphism in centromeric autosomal regions and the X chromosome, evidence for positive and negative selection, and rapid evolution of the X chromosome. Many variants in novel genes, most at low frequency, are associated with quantitative traits and explain a large fraction of the phenotypic variance. The DGRP facilitates genotype-phenotype mapping using the power of Drosophila genetics.",

author = "MacKay, {Trudy F.C.} and Stephen Richards and Stone, {Eric A.} and Antonio Barbadilla and Ayroles, {Julien F.} and Dianhui Zhu and S{\`o}nia Casillas and Yi Han and Magwire, {Michael M.} and Cridland, {Julie M.} and Richardson, {Mark F.} and Anholt, {Robert R.H.} and Maite Barr{\'o}n and Crystal Bess and Blankenburg, {Kerstin Petra} and Carbone, {Mary Anna} and David Castellano and Lesley Chaboub and Laura Duncan and Zeke Harris and Mehwish Javaid and Jayaseelan, {Joy Christina} and Jhangiani, {Shalini N.} and Jordan, {Katherine W.} and Fremiet Lara and Faye Lawrence and Lee, {Sandra L.} and Pablo Librado and Linheiro, {Raquel S.} and Lyman, {Richard F.} and MacKey, {Aaron J.} and Mala Munidasa and Muzny, {Donna Marie} and Lynne Nazareth and Irene Newsham and Lora Perales and Pu, {Ling Ling} and Carson Qu and Miquel R{\`a}mia and Reid, {Jeffrey G.} and Rollmann, {Stephanie M.} and Julio Rozas and Nehad Saada and Lavanya Turlapati and Worley, {Kim C.} and Wu, {Yuan Qing} and Akihiko Yamamoto and Yiming Zhu and Bergman, {Casey M.} and Thornton, {Kevin R.} and David Mittelman and Gibbs, {Richard A.}",

note = "Funding Information: Acknowledgements This work was supported by National Institutes of Health grant GM 45146 to T.F.C.M., E.A.S. and R.R.H.A.; R01 GM 059469 to R.R.H.A., MCI BFU 2009-09504 to A.B., R01 GM 085183 to K.R.T., NHGRI U54 HG003273 to R.A.G.; and an award through the NVIDIA Foundation{\textquoteright}s {\textquoteleft}{\textquoteleft}Compute the Cure{\textquoteright}{\textquoteright} programme to D.M.",

year = "2012",

month = feb,

day = "9",

doi = "10.1038/nature10811",

language = "English (US)",

volume = "482",

pages = "173--178",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Publishing Group",

number = "7384",

}

MacKay, TFC, Richards, S, Stone, EA, Barbadilla, A, Ayroles, JF, Zhu, D, Casillas, S, Han, Y, Magwire, MM, Cridland, JM, Richardson, MF, Anholt, RRH, Barrón, M, Bess, C, Blankenburg, KP, Carbone, MA, Castellano, D, Chaboub, L, Duncan, L, Harris, Z, Javaid, M, Jayaseelan, JC, Jhangiani, SN, Jordan, KW, Lara, F, Lawrence, F, Lee, SL, Librado, P, Linheiro, RS, Lyman, RF, MacKey, AJ, Munidasa, M, Muzny, DM, Nazareth, L, Newsham, I, Perales, L, Pu, LL, Qu, C, Ràmia, M, Reid, JG, Rollmann, SM, Rozas, J, Saada, N, Turlapati, L, Worley, KC, Wu, YQ, Yamamoto, A, Zhu, Y, Bergman, CM, Thornton, KR, Mittelman, D & Gibbs, RA 2012, 'The Drosophila melanogaster Genetic Reference Panel', Nature, vol. 482, no. 7384, pp. 173-178. https://doi.org/10.1038/nature10811

TY - JOUR

T1 - The Drosophila melanogaster Genetic Reference Panel

AU - MacKay, Trudy F.C.

AU - Richards, Stephen

AU - Stone, Eric A.

AU - Barbadilla, Antonio

AU - Ayroles, Julien F.

AU - Zhu, Dianhui

AU - Casillas, Sònia

AU - Han, Yi

AU - Magwire, Michael M.

AU - Cridland, Julie M.

AU - Richardson, Mark F.

AU - Anholt, Robert R.H.

AU - Barrón, Maite

AU - Bess, Crystal

AU - Blankenburg, Kerstin Petra

AU - Carbone, Mary Anna

AU - Castellano, David

AU - Chaboub, Lesley

AU - Duncan, Laura

AU - Harris, Zeke

AU - Javaid, Mehwish

AU - Jayaseelan, Joy Christina

AU - Jhangiani, Shalini N.

AU - Jordan, Katherine W.

AU - Lara, Fremiet

AU - Lawrence, Faye

AU - Lee, Sandra L.

AU - Librado, Pablo

AU - Linheiro, Raquel S.

AU - Lyman, Richard F.

AU - MacKey, Aaron J.

AU - Munidasa, Mala

AU - Muzny, Donna Marie

AU - Nazareth, Lynne

AU - Newsham, Irene

AU - Perales, Lora

AU - Pu, Ling Ling

AU - Qu, Carson

AU - Ràmia, Miquel

AU - Reid, Jeffrey G.

AU - Rollmann, Stephanie M.

AU - Rozas, Julio

AU - Saada, Nehad

AU - Turlapati, Lavanya

AU - Worley, Kim C.

AU - Wu, Yuan Qing

AU - Yamamoto, Akihiko

AU - Zhu, Yiming

AU - Bergman, Casey M.

AU - Thornton, Kevin R.

AU - Mittelman, David

AU - Gibbs, Richard A.

N1 - Funding Information: Acknowledgements This work was supported by National Institutes of Health grant GM 45146 to T.F.C.M., E.A.S. and R.R.H.A.; R01 GM 059469 to R.R.H.A., MCI BFU 2009-09504 to A.B., R01 GM 085183 to K.R.T., NHGRI U54 HG003273 to R.A.G.; and an award through the NVIDIA Foundation’s ‘‘Compute the Cure’’ programme to D.M.

PY - 2012/2/9

Y1 - 2012/2/9

N2 - A major challenge of biology is understanding the relationship between molecular genetic variation and variation in quantitative traits, including fitness. This relationship determines our ability to predict phenotypes from genotypes and to understand how evolutionary forces shape variation within and between species. Previous efforts to dissect the genotype-phenotype map were based on incomplete genotypic information. Here, we describe the Drosophila melanogaster Genetic Reference Panel (DGRP), a community resource for analysis of population genomics and quantitative traits. The DGRP consists of fully sequenced inbred lines derived from a natural population. Population genomic analyses reveal reduced polymorphism in centromeric autosomal regions and the X chromosome, evidence for positive and negative selection, and rapid evolution of the X chromosome. Many variants in novel genes, most at low frequency, are associated with quantitative traits and explain a large fraction of the phenotypic variance. The DGRP facilitates genotype-phenotype mapping using the power of Drosophila genetics.

AB - A major challenge of biology is understanding the relationship between molecular genetic variation and variation in quantitative traits, including fitness. This relationship determines our ability to predict phenotypes from genotypes and to understand how evolutionary forces shape variation within and between species. Previous efforts to dissect the genotype-phenotype map were based on incomplete genotypic information. Here, we describe the Drosophila melanogaster Genetic Reference Panel (DGRP), a community resource for analysis of population genomics and quantitative traits. The DGRP consists of fully sequenced inbred lines derived from a natural population. Population genomic analyses reveal reduced polymorphism in centromeric autosomal regions and the X chromosome, evidence for positive and negative selection, and rapid evolution of the X chromosome. Many variants in novel genes, most at low frequency, are associated with quantitative traits and explain a large fraction of the phenotypic variance. The DGRP facilitates genotype-phenotype mapping using the power of Drosophila genetics.

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UR - http://www.scopus.com/inward/citedby.url?scp=84863012360&partnerID=8YFLogxK

U2 - 10.1038/nature10811

DO - 10.1038/nature10811

M3 - Article

C2 - 22318601

AN - SCOPUS:84863012360

SN - 0028-0836

VL - 482

SP - 173

EP - 178

JO - Nature

JF - Nature

IS - 7384

ER -

The Drosophila melanogaster Genetic Reference Panel

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