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preLekára.sk / Odborné časopisy / PLOS Genetics / 2010 - 9

Gene–Environment Interactions at Nucleotide Resolution

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Interactions among genes and the environment are a common source of phenotypic variation. To characterize the interplay between genetics and the environment at single nucleotide resolution, we quantified the genetic and environmental interactions of four quantitative trait nucleotides (QTN) that govern yeast sporulation efficiency. We first constructed a panel of strains that together carry all 32 possible combinations of the 4 QTN genotypes in 2 distinct genetic backgrounds. We then measured the sporulation efficiencies of these 32 strains across 8 controlled environments. This dataset shows that variation in sporulation efficiency is shaped largely by genetic and environmental interactions. We find clear examples of QTN:environment, QTN: background, and environment:background interactions. However, we find no QTN:QTN interactions that occur consistently across the entire dataset. Instead, interactions between QTN only occur under specific combinations of environment and genetic background. Thus, what might appear to be a QTN:QTN interaction in one background and environment becomes a more complex QTN:QTN:environment:background interaction when we consider the entire dataset as a whole. As a result, the phenotypic impact of a set of QTN alleles cannot be predicted from genotype alone. Our results instead demonstrate that the effects of QTN and their interactions are inextricably linked both to genetic background and to environmental variation.

Vyšlo v časopise: Gene–Environment Interactions at Nucleotide Resolution. PLoS Genet 6(9): e32767. doi:10.1371/journal.pgen.1001144
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1001144

Souhrn

Interactions among genes and the environment are a common source of phenotypic variation. To characterize the interplay between genetics and the environment at single nucleotide resolution, we quantified the genetic and environmental interactions of four quantitative trait nucleotides (QTN) that govern yeast sporulation efficiency. We first constructed a panel of strains that together carry all 32 possible combinations of the 4 QTN genotypes in 2 distinct genetic backgrounds. We then measured the sporulation efficiencies of these 32 strains across 8 controlled environments. This dataset shows that variation in sporulation efficiency is shaped largely by genetic and environmental interactions. We find clear examples of QTN:environment, QTN: background, and environment:background interactions. However, we find no QTN:QTN interactions that occur consistently across the entire dataset. Instead, interactions between QTN only occur under specific combinations of environment and genetic background. Thus, what might appear to be a QTN:QTN interaction in one background and environment becomes a more complex QTN:QTN:environment:background interaction when we consider the entire dataset as a whole. As a result, the phenotypic impact of a set of QTN alleles cannot be predicted from genotype alone. Our results instead demonstrate that the effects of QTN and their interactions are inextricably linked both to genetic background and to environmental variation.

Zdroje

1. UngererMC

HalldorsdottirSS

PuruggananMD

MackayTFC

2003 Genotype-environment interactions at quantitative trait loci affecting inflorescence development in Arabidopsis thaliana. Genetics 165 353 365

2. SmithEN

KruglyakL

2008 Gene-environment interaction in yeast gene expression. PLoS Biol 6 e83 doi:10.1371/journal.pbio.0060083

3. GurganusMC

FryJD

NuzhdinSV

PasyukovaEG

LymanRF

1998 Genotype-environment interaction at quantitative trait loci affecting sensory bristle number in Drosophila melanogaster. Genetics 149 1883 1898

4. LillehammerM

GoddardM

NilsenH

2008 Quantitative Trait Locus-by-Environment Interaction for Milk Yield Traits on Bos taurus Autosome 6. Genetics 179 1539 1546

5. YaffeK

HaanM

ByersA

TangenC

KullerL

2000 Estrogen use, APOE, and cognitive decline: evidence of gene-environment interaction. Neurology 54 1949 1954

6. SteinerCC

WeberJN

HoekstraHE

2007 Adaptive variation in beach mice produced by two interacting pigmentation genes. PLoS Biol 5 e219 doi:10.1371/journal.pbio.0050219

7. BridghamJT

OrtlundEA

ThorntonJW

2009 An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Nature 461 515 519

8. ThreadgillDW

DlugoszAA

HansenLA

TennenbaumT

LichtiU

1995 Targeted disruption of mouse EGF receptor: effect of genetic background on mutant phenotype. Science 269 230 234

9. FlintJ

MackayTFC

2009 Genetic architecture of quantitative traits in mice, flies, and humans. Genome research 19 723 733

10. CarlborgO

HaleyCS

2004 Epistasis: too often neglected in complex trait studies? Nat Rev Genet 5 618 625

11. EshedY

ZamirD

1996 Less-than-additive epistatic interactions of quantitative trait loci in tomato. Genetics 143 1807 1817

12. CaicedoAL

StinchcombeJR

OlsenKM

SchmittJ

PuruggananMD

2004 Epistatic interaction between Arabidopsis FRI and FLC flowering time genes generates a latitudinal cline in a life history trait. Proc Natl Acad Sci U S A 101 15670 15675

13. DeutschbauerAM

DavisRW

2005 Quantitative trait loci mapped to single-nucleotide resolution in yeast. Nat Genet 37 1333 1340

14. GerkeJ

LorenzK

CohenB

2009 Genetic interactions between transcription factors cause natural variation in yeast. Science 323 498 501

15. HonigbergSM

PurnapatreK

2003 Signal pathway integration in the switch from the mitotic cell cycle to meiosis in yeast. J Cell Sci 116 2137 2147

16. LuL

RobertsG

SimonK

YuJ

HudsonAP

2003 Rsf1p, a protein required for respiratory growth of Saccharomyces cerevisiae. Curr Genet 43 263 272

17. KassirY

GranotD

SimchenG

1988 IME1, a positive regulator gene of meiosis in S. cerevisiae. Cell 52 853 862

18. MitchellAP

HerskowitzI

1986 Activation of meiosis and sporulation by repression of the RME1 product in yeast. Nature 319 738 742

19. CovitzPA

MitchellAP

1993 Repression by the yeast meiotic inhibitor RME1. Genes Dev 7 1598 1608

20. GerkeJP

ChenCTL

CohenBA

2006 Natural isolates of Saccharomyces cerevisiae display complex genetic variation in sporulation efficiency. Genetics 174 985 997

21. JohnstonM

1999 Feasting, fasting and fermenting. Glucose sensing in yeast and other cells. Trends Genet 15 29 33

22. JohnstonM

FlickJS

PextonT

1994 Multiple mechanisms provide rapid and stringent glucose repression of GAL gene expression in Saccharomyces cerevisiae. Mol Cell Biol 14 3834 3841

23. DunnB

LevineRP

SherlockG

2005 Microarray karyotyping of commercial wine yeast strains reveals shared, as well as unique, genomic signatures. BMC Genomics 6 53

24. CarretoL

EirizMF

GomesAC

PereiraPM

SchullerD

2008 Comparative genomics of wild type yeast strains unveils important genome diversity. BMC Genomics 9 524

25. CharronMJ

DubinRA

MichelsCA

1986 Structural and functional analysis of the MAL1 locus of Saccharomyces cerevisiae. Mol Cell Biol 6 3891 3899

26. ManolioTA

CollinsFS

CoxNJ

GoldsteinDB

HindorffLA

2009 Finding the missing heritability of complex diseases. Nature 461 747 753

27. WilsonPW

D'AgostinoRB

LevyD

BelangerAM

SilbershatzH

1998 Prediction of coronary heart disease using risk factor categories. Circulation 97 1837 1847

28. KacserH

BurnsJA

1981 The molecular basis of dominance. Genetics 97 639 666

29. GibsonG

1996 Epistasis and pleiotropy as natural properties of transcriptional regulation. Theoretical population biology 49 58 89

30. GertzJ

GerkeJP

CohenBA

2010 Epistasis in a quantitative trait captured by a molecular model of transcription factor interactions. Theoretical population biology 77 1 5

31. GertzJ

CohenBA

2009 Environment-specific combinatorial cis-regulation in synthetic promoters. Mol Syst Biol 5 244

32. CheverudJM

RoutmanEJ

1995 Epistasis and its contribution to genetic variance components. Genetics 139 1455 1461

33. MurphyHA

KuehneHA

FrancisCA

SniegowskiPD

2006 Mate choice assays and mating propensity differences in natural yeast populations. Biol Lett 2 553 556

34. StoriciF

LewisLK

ResnickMA

2001 In vivo site-directed mutagenesis using oligonucleotides. Nat Biotechnol 19 773 776

35. WillJL

KimHS

ClarkeJ

PainterJC

FayJC

2010 Incipient balancing selection through adaptive loss of aquaporins in natural Saccharomyces cerevisiae populations. PLoS Genet 6 e1000893 doi:10.1371/journal.pgen.1000893

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2010 Číslo 9
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