Candidate Genes Detected in Transcriptome Studies Are Strongly Dependent on Genetic Background

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2011 Feb 2

PMID 21283582

Citations 18

Authors

Pernille Sarup

Jesper G Sorensen

Torsten N Kristensen

Ary A Hoffmann

Volker Loeschcke

Ken N Paige

Peter Sorensen

Affiliations

Soon will be listed here.

Abstract

Whole genome transcriptomic studies can point to potential candidate genes for organismal traits. However, the importance of potential candidates is rarely followed up through functional studies and/or by comparing results across independent studies. We have analysed the overlap of candidate genes identified from studies of gene expression in Drosophila melanogaster using similar technical platforms. We found little overlap across studies between putative candidate genes for the same traits in the same sex. Instead there was a high degree of overlap between different traits and sexes within the same genetic backgrounds. Putative candidates found using transcriptomics therefore appear very sensitive to genetic background and this can mask or override effects of treatments. The functional importance of putative candidate genes emerging from transcriptome studies needs to be validated through additional experiments and in future studies we suggest a focus on the genes, networks and pathways affecting traits in a consistent manner across backgrounds.

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References

Ayroles J, Carbone M, Stone E, Jordan K, Lyman R, Magwire M . Systems genetics of complex traits in Drosophila melanogaster. Nat Genet. 2009; 41(3):299-307. PMC: 2752214. DOI: 10.1038/ng.332. View

Kristensen T, Pedersen K, Vermeulen C, Loeschcke V . Research on inbreeding in the 'omic' era. Trends Ecol Evol. 2009; 25(1):44-52. DOI: 10.1016/j.tree.2009.06.014. View

Ayroles J, Hughes K, Rowe K, Reedy M, Rodriguez-Zas S, M Drnevich J . A genomewide assessment of inbreeding depression: gene number, function, and mode of action. Conserv Biol. 2009; 23(4):920-30. DOI: 10.1111/j.1523-1739.2009.01186.x. View

Feder M, Walser J . The biological limitations of transcriptomics in elucidating stress and stress responses. J Evol Biol. 2005; 18(4):901-10. DOI: 10.1111/j.1420-9101.2005.00921.x. View

Crnokrak P, Roff D . Inbreeding depression in the wild. Heredity (Edinb). 1999; 83 ( Pt 3):260-70. DOI: 10.1038/sj.hdy.6885530. View

Williams L, Oleksiak M . Signatures of selection in natural populations adapted to chronic pollution. BMC Evol Biol. 2008; 8:282. PMC: 2570689. DOI: 10.1186/1471-2148-8-282. View

Sarup P, Sorensen P, Loeschcke V . Flies selected for longevity retain a young gene expression profile. Age (Dordr). 2010; 33(1):69-80. PMC: 3063640. DOI: 10.1007/s11357-010-9162-8. View

Sorensen J, Nielsen M, Loeschcke V . Gene expression profile analysis of Drosophila melanogaster selected for resistance to environmental stressors. J Evol Biol. 2007; 20(4):1624-36. DOI: 10.1111/j.1420-9101.2007.01326.x. View

Jumbo-Lucioni P, Ayroles J, Chambers M, Jordan K, Leips J, Mackay T . Systems genetics analysis of body weight and energy metabolism traits in Drosophila melanogaster. BMC Genomics. 2010; 11:297. PMC: 2880307. DOI: 10.1186/1471-2164-11-297. View

10.

Kristensen T, Sorensen P, Pedersen K, Kruhoffer M, Loeschcke V . Inbreeding by environmental interactions affect gene expression in Drosophila melanogaster. Genetics. 2006; 173(3):1329-36. PMC: 1526705. DOI: 10.1534/genetics.105.054486. View

11.

Wu Z, Irizarry R . Preprocessing of oligonucleotide array data. Nat Biotechnol. 2004; 22(6):656-8. DOI: 10.1038/nbt0604-656b. View

12.

Clark M, Thorne M, Vieira F, Cardoso J, Power D, Peck L . Insights into shell deposition in the Antarctic bivalve Laternula elliptica: gene discovery in the mantle transcriptome using 454 pyrosequencing. BMC Genomics. 2010; 11:362. PMC: 2896379. DOI: 10.1186/1471-2164-11-362. View

13.

Kristensen T, Sorensen P, Kruhoffer M, Pedersen K, Loeschcke V . Genome-wide analysis on inbreeding effects on gene expression in Drosophila melanogaster. Genetics. 2005; 171(1):157-67. PMC: 1456508. DOI: 10.1534/genetics.104.039610. View

14.

Schweiger W, Boddu J, Shin S, Poppenberger B, Berthiller F, Lemmens M . Validation of a candidate deoxynivalenol-inactivating UDP-glucosyltransferase from barley by heterologous expression in yeast. Mol Plant Microbe Interact. 2010; 23(7):977-86. DOI: 10.1094/MPMI-23-7-0977. View

15.

Morozova T, Ayroles J, Jordan K, Duncan L, Carbone M, Lyman R . Alcohol sensitivity in Drosophila: translational potential of systems genetics. Genetics. 2009; 183(2):733-45, 1SI-12SI. PMC: 2766331. DOI: 10.1534/genetics.109.107490. View

16.

Edwards A, Ayroles J, Stone E, Carbone M, Lyman R, Mackay T . A transcriptional network associated with natural variation in Drosophila aggressive behavior. Genome Biol. 2009; 10(7):R76. PMC: 2728530. DOI: 10.1186/gb-2009-10-7-r76. View

17.

Telonis-Scott M, Hallas R, McKechnie S, Wee C, Hoffmann A . Selection for cold resistance alters gene transcript levels in Drosophila melanogaster. J Insect Physiol. 2009; 55(6):549-55. DOI: 10.1016/j.jinsphys.2009.01.010. View

18.

Hughes K, Ayroles J, Reedy M, M Drnevich J, Rowe K, Ruedi E . Segregating variation in the transcriptome: cis regulation and additivity of effects. Genetics. 2006; 173(3):1347-55. PMC: 1526654. DOI: 10.1534/genetics.105.051474. View

19.

Williams N, Gaynor R, Scoggin S, Verma U, Gokaslan T, Simmang C . Identification and validation of genes involved in the pathogenesis of colorectal cancer using cDNA microarrays and RNA interference. Clin Cancer Res. 2003; 9(3):931-46. View

20.

Renaut S, Nolte A, Bernatchez L . Mining transcriptome sequences towards identifying adaptive single nucleotide polymorphisms in lake whitefish species pairs (Coregonus spp. Salmonidae). Mol Ecol. 2010; 19 Suppl 1:115-31. DOI: 10.1111/j.1365-294X.2009.04477.x. View