title: Expression quantitative trait locus mapping across water availability environments reveals contrasting associations with genomic features in Arabidopsis.
abstract: The regulation of gene expression is crucial for an organism's development and response to stress, and an understanding of the evolution of gene expression is of fundamental importance to basic and applied biology. To improve this understanding, we conducted expression quantitative trait locus (eQTL) mapping in the Tsu-1 (Tsushima, Japan) × Kas-1 (Kashmir, India) recombinant inbred line population of Arabidopsis thaliana across soil drying treatments. We then used genome resequencing data to evaluate whether genomic features (promoter polymorphism, recombination rate, gene length, and gene density) are associated with genes responding to the environment (E) or with genes with genetic variation (G) in gene expression in the form of eQTLs. We identified thousands of genes that responded to soil drying and hundreds of main-effect eQTLs. However, we identified very few statistically significant eQTLs that interacted with the soil drying treatment (GxE eQTL). Analysis of genome resequencing data revealed associations of several genomic features with G and E genes. In general, E genes had lower promoter diversity and local recombination rates. By contrast, genes with eQTLs (G) had significantly greater promoter diversity and were located in genomic regions with higher recombination. These results suggest that genomic architecture may play an important a role in the evolution of gene expression.
authors.affiliation: Department of Integrative Biology and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712.
authors.forename: David B
authors.initials: DB
authors.lastname: Lowry
authors.forename: Tierney L
authors.initials: TL
authors.lastname: Logan
authors.forename: Luca
authors.initials: L
authors.lastname: Santuari
authors.forename: Christian S
authors.initials: CS
authors.lastname: Hardtke
authors.forename: James H
authors.initials: JH
authors.lastname: Richards
authors.forename: Leah J
authors.initials: LJ
authors.lastname: DeRose-Wilson
authors.forename: John K
authors.initials: JK
authors.lastname: McKay
authors.forename: Saunak
authors.initials: S
authors.lastname: Sen
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Juenger
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000502:physiology; D002874:Chromosome Mapping; D055864:Droughts; D004777:Environment; D015870:Gene Expression; D018506:Gene Expression Regulation, Plant / Q000235:genetics*; D056726:Genetic Association Studies; D014644:Genetic Variation / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics; D010641:Phenotype; D011401:Promoter Regions, Genetic / Q000235:genetics; D040641:Quantitative Trait Loci / Q000235:genetics*; D013312:Stress, Physiological; D014867:Water / Q000502:physiology
chemical_list: D014867:Water
references.citation: Plant J. 2002 Aug;31(3):279-92
references.pmid: 12164808
references.citation: Genetics. 2007 Mar;175(3):1441-50
references.pmid: 17179097
references.citation: PLoS Biol. 2012;10(11):e1001422
references.pmid: 23152720
references.citation: Nat Genet. 2012 Jan 08;44(2):212-6
references.pmid: 22231484
references.citation: Curr Opin Plant Biol. 2007 Apr;10(2):142-8
references.pmid: 17300985
references.citation: Genet Res. 1974 Feb;23(1):23-35
references.pmid: 4407212
references.citation: Genome Res. 2003 Oct;13(10):2260-4
references.pmid: 12975314
references.citation: Genome Res. 2010 Aug;20(8):1103-11
references.pmid: 20508143
references.citation: Theor Popul Biol. 1975 Apr;7(2):256-76
references.pmid: 1145509
references.citation: Nat Rev Genet. 2011 Dec 06;13(1):59-69
references.pmid: 22143240
references.citation: Mol Biol Evol. 2009 Sep;26(9):2047-59
references.pmid: 19506001
references.citation: BMC Genomics. 2011 Jun 30;12:336
references.pmid: 21718468
references.citation: Evolution. 2007 May;61(5):995-1016
references.pmid: 17492956
references.citation: Annu Rev Plant Biol. 2010;61:651-79
references.pmid: 20192755
references.citation: Plant Physiol. 2010 May;153(1):185-97
references.pmid: 20335401
references.citation: Science. 2002 Apr 26;296(5568):752-5
references.pmid: 11923494
references.citation: Plant J. 2010 Sep;63(5):715-27
references.pmid: 20553421
references.citation: J Exp Bot. 2007;58(2):221-7
references.pmid: 17075077
references.citation: PLoS Biol. 2010 Sep 28;8(9):
references.pmid: 20927412
references.citation: Nat Rev Genet. 2007 Mar;8(3):206-16
references.pmid: 17304246
references.citation: Front Genet. 2013 Jan 10;3:317
references.pmid: 23335938
references.citation: Nat Rev Genet. 2007 May;8(5):382-93
references.pmid: 17404584
references.citation: Mol Biol Evol. 2003 Sep;20(9):1377-419
references.pmid: 12777501
references.citation: Proc Natl Acad Sci U S A. 2007 Jan 30;104(5):1708-13
references.pmid: 17237218
references.citation: Bioinformatics. 2003 May 1;19(7):889-90
references.pmid: 12724300
references.citation: Nucleic Acids Res. 2005 Nov 10;33(20):e175
references.pmid: 16284200
references.citation: Nat Genet. 2009 Feb;41(2):166-7
references.pmid: 19169256
references.citation: Nature. 2005 Feb 3;433(7025):481-7
references.pmid: 15690032
references.citation: Development. 2012 Nov;139(22):4095-8
references.pmid: 23093420
references.citation: PLoS Biol. 2008 Apr 15;6(4):e83
references.pmid: 18416601
references.citation: J Exp Bot. 2012 Jun;63(10):3741-8
references.pmid: 22412184
references.citation: Curr Opin Plant Biol. 2012 Apr;15(2):192-8
references.pmid: 22265229
references.citation: Proc Biol Sci. 2013 May 22;280(1763):20131043
references.pmid: 23698015
references.citation: Science. 2010 Oct 15;330(6002):372-6
references.pmid: 20947766
references.citation: Annu Rev Plant Biol. 2009;60:93-114
references.pmid: 19012536
references.citation: Science. 2010 Oct 15;330(6002):326-7
references.pmid: 20947750
references.citation: Proc Natl Acad Sci U S A. 2012 Jan 24;109(4):1204-9
references.pmid: 22233810
references.citation: Plant J. 2007 Apr;50(2):347-63
references.pmid: 17376166
references.citation: Ann N Y Acad Sci. 2010 Sep;1206:56-79
references.pmid: 20860683
references.citation: Nature. 1992 Apr 9;356(6369):519-20
references.pmid: 1560824
references.citation: Plant Cell. 2012 Mar;24(3):893-914
references.pmid: 22408074
references.citation: Genetics. 2006 Feb;172(2):1155-64
references.pmid: 15956669
references.citation: Plant Physiol. 2002 Dec;130(4):2129-41
references.pmid: 12481097
references.citation: PLoS Genet. 2008 Oct;4(10):e1000232
references.pmid: 18949031
references.citation: Genome Res. 2008 Dec;18(12):2024-33
references.pmid: 18818371
references.citation: Nature. 2012 Sep 13;489(7415):208
references.pmid: 22972285
references.citation: Mol Biol Evol. 2011 Aug;28(8):2359-69
references.pmid: 21389272
references.citation: Evolution. 2008 Sep;62(9):2155-77
references.pmid: 18616572
references.citation: Evolution. 2008 Dec;62(12):3014-26
references.pmid: 18691264
references.citation: Trends Genet. 2001 Sep;17(9):481-5
references.pmid: 11525814
references.citation: Front Genet. 2011 Oct 17;2:70
references.pmid: 22303365
references.citation: PLoS Genet. 2011 Jan 20;7(1):e1001279
references.pmid: 21283786
references.citation: Theor Appl Genet. 1968 Jun;38(6):226-31
references.pmid: 24442307
references.citation: Plant Cell. 1995 Jul;7(7):1099-1111
references.pmid: 12242400
references.citation: Science. 2009 Feb 13;323(5916):930-4
references.pmid: 19150810
references.citation: Trends Ecol Evol. 2008 Jul;23(7):377-85
references.pmid: 18501470
references.citation: BMC Genomics. 2012 Mar 27;13:117
references.pmid: 22453064
references.citation: Genet Res. 1997 Oct;70(2):155-74
references.pmid: 9449192
references.citation: J Exp Bot. 2008;59(11):2991-3007
references.pmid: 18552355
references.citation: Annu Rev Ecol Evol Syst. 2008 Dec 1;39:21-42
references.pmid: 20419035
references.citation: Trends Plant Sci. 2006 Aug;11(8):375-81
references.pmid: 16843035
references.citation: PLoS Biol. 2005 Jul;3(7):e196
references.pmid: 15907155
references.citation: Plant Cell Environ. 2010 Aug 1;33(8):1268-84
references.pmid: 20302603
references.citation: Curr Opin Plant Biol. 2011 Jun;14(3):240-5
references.pmid: 21561798
references.citation: Mol Ecol. 2003 May;12(5):1137-51
references.pmid: 12694278
references.citation: PLoS Genet. 2005 Aug;1(2):e13
references.pmid: 16110339
references.citation: Science. 2007 Jul 20;317(5836):338-42
references.pmid: 17641193
references.citation: Genome. 2011 Jan;54(1):10-8
references.pmid: 21217801
references.citation: PLoS Genet. 2006 Dec 29;2(12):e222
references.pmid: 17196041
references.citation: Am J Hum Genet. 2003 Jun;72(6):1527-35
references.pmid: 12740762
references.citation: Development. 2010 Oct;137(19):3153-65
references.pmid: 20823061
references.citation: PLoS Biol. 2007 Sep;5(9):e236
references.pmid: 17803357
references.citation: Proc Natl Acad Sci U S A. 2003 Aug 5;100(16):9440-5
references.pmid: 12883005
references.citation: Genetics. 1993 Aug;134(4):1289-303
references.pmid: 8375663
references.citation: Mol Ecol. 2013 Jun;22(11):3014-27
references.pmid: 23601112
references.citation: Proc Natl Acad Sci U S A. 2007 May 15;104 Suppl 1:8597-604
references.pmid: 17494740
references.citation: PLoS Genet. 2011 Jul;7(7):e1002162
references.pmid: 21750684
references.citation: Nat Commun. 2013;4:1827
references.pmid: 23652015
references.citation: Nature. 2012 Apr 04;484(7392):55-61
references.pmid: 22481358
references.citation: Genome Res. 2011 May;21(5):725-33
references.pmid: 21467266
references.citation: Plant Cell. 2009 Jul;21(7):1877-96
references.pmid: 19574434
references.citation: Nucleic Acids Res. 2010 Jul;38(Web Server issue):W64-70
references.pmid: 20435677
references.citation: Ecol Lett. 2005 Sep;8(9):1010-1020
references.pmid: 34517682
references.citation: Nat Genet. 2011 Aug 28;43(10):956-63
references.pmid: 21874002