Transcriptional variation in response to salt stress in commonly used Arabidopsis thaliana accessions

Plant Physiology and Biochemistry

Volumn 73, Issue , 2013, Pages 189-201

  Chan, Zhulong ^a   Loescher, Wayne ^a   Grumet, Rebecca ^a  

^a MICHIGAN STATE UNIVERSITY   (United States)

Author keywords

Abiotic stress; Expression level polymorphism; Glabrous; Phenotypic buffering; Salinity stress

Indexed keywords

ARABIDOPSIS THALIANA;

ARABIDOPSIS PROTEIN; INORGANIC SALT; SODIUM CHLORIDE; THALLIUM; TRANSCRIPTOME; WS;

ABIOTIC STRESS; ARABIDOPSIS; ARTICLE; COL; COL(GL); COLUMBIA-0; DAS; DAYS AFTER SOWING; EXPRESSION LEVEL POLYMORPHISM; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; GENETICS; GLABROUS; GLABROUS MUTANT OF COL; METABOLISM; MUTATION; PHENOTYPE; PHENOTYPIC BUFFERING; PHYSIOLOGICAL STRESS; PLANT GENE; SALINITY; SALT STRESS; SALT TOLERANCE; SPECIES DIFFERENCE; TRUE LEAVES; WASSILEWSKIJA-2;

ABIOTIC STRESS; COL; COL(GL); COLUMBIA-0; DAS; DAYS AFTER SOWING; EXPRESSION LEVEL POLYMORPHISM; GLABROUS; GLABROUS MUTANT OF COL; PHENOTYPIC BUFFERING; SALINITY STRESS; TL; TRUE LEAVES; WASSILEWSKIJA-2; WS;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; GENETIC VARIATION; MUTATION; PHENOTYPE; SALINITY; SALT-TOLERANCE; SALTS; SODIUM CHLORIDE; SPECIES SPECIFICITY; STRESS, PHYSIOLOGICAL; TRANSCRIPTION, GENETIC; TRANSCRIPTOME;

EID: 84892651358     PISSN: 09819428     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.plaphy.2013.09.013     Document Type: Article

References (41)

1. Chen W.J., Chang S.H., Hudson M.E., Kwan W.K., Li J., Estes B., Knoll D., Shi L., Zhu T. Contribution of transcriptional regulation to natural variations in Arabidopsis. Genome Biol. 2005, 6:R32.
2. Kliebenstein D.J. Systems biology uncovers the foundation of natural genetic diversity. Plant Physiol. 2010, 152:480-486.
3. Kliebenstein D.J., West M.A.L., van Leeuwen H., Kim K., Doerge R.W., Michelmore R., St Clair D. Genomic survey of gene expression diversity in Arabidopsis thaliana. Genetics 2006, 172:1179-1189.
4. Van Poecke R.M.P., Sato M., Lenarz-Wyatt L., Weisberg S., Katagiri F. Natural variation in RPS2-mediated resistance among Arabidopsis accessions: correlation between gene expression profiles and phenotypic responses. Plant Cell. 2007, 19:4046-4060.
5. Des Marais D.L., McKay J.K., Richards J.H., Sen S., Wayne T., Juenger T.E. Physiological genomics of response to soil drying in diverse Arabidopsis accessions. Plant Cell 2012, 24:893-914.
6. Munns R., Tester M. Mechanisms of salinity tolerance. Annu. Rev. Plant Biol. 2008, 59:651-681.
7. Galpaz N., Reymond M. Natural variation in Arabidopsis thaliana revealed a genetic network controlling germination under salt stress. PLoS ONE 2010, 5:e15198.
8. Jha D., Shirley N., Tester M., Roy S.J. Variation in salinity tolerance and shoot sodium accumulation in Arabidopsis ecotypes linked to differences in natural expression levels of transporters involved in sodium transport. Plant Cell Environ. 2010, 33:793-804.
9. Katori T., Ikeda A., Iuchi S., Kobayashi M., Shinozaki K., Maehashi K., Sakaa Y., Tanaka S., Taji T. Dissecting the genetic control of natural genetic variation in salt tolerance of Arabidopsis thaliana accessions. J.Exp. Bot. 2010, 61:1125-1138.
10. De-Rose-Wilson L., Gaut B.S. Mapping salinity tolerance during Arabidopsis thaliana germination and seedling growth. PLoS ONE 2011, 6:e22832.
11. Labidi N., Lachaal M., Chibani F., Grignon C., Hajji M. Variability in the response to sodium chloride of eight ecotypes of Arabidopsis thaliana. J. Plant Nutr. 2002, 25:2627-2638.
12. Quesada V., Garcia-Martinez S., Piqueras P., Ponce M.R., Micol J.L. Genetic architecture of NaCl tolerance in Arabidopsis. Plant Physiol. 2002, 130:951-963.
13. Baumbusch L.O., Sundal I.K., Hughes D.W., Galau G.A., Jakobsen S. Efficient protocols for CAPS-based mapping in Arabidopsis. Plant Mol. Biol. Rep. 2001, 19:137-149.
14. Park K.M., Choi Y.H., Park W.M., Na H.J., Na N.J., Chung W.I., Kim D.S. Proteomic pattern-based identification of molecular phenotypes from Arabidopsis thaliana ecotypes. Plant Sci. 2009, 177:7-18.
15. Passardi F., Dobias J., Valério L., Guimil S., Penel C., Dunand C. Morphological and physiological traits of three major Arabidopsis thaliana accessions. J. Plant Physiol. 2009, 164:980-992.
16. Hauser M.T., Harr B., Schlotterer C. Trichome distribution in Arabidopsis thaliana and its close relative Arabidopsis lyrata: molecular analysis of the candidate gene GLABROUS1. Mol. Biol. Evol. 2001, 18:1754-1763.
17. Borevitz J.O., Hazen A.P., Michael T.P., Morris G.P., Baxter I.R., Hu T.T., Chen H., Werner J.D., Nordborg M., Salt D.E., Kay S.A., Chory J., Weigel D., Jones J.D., Ecker J.R. Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana. Proc. Natl. Acad. Sci. U. S. A. 2007, 104:12057-12062.
18. Morohashi K., Grotewold E. Asystems approach reveals regulatory circuitry for Arabidopsis trichome initiation by the GL3 and GL1 selectors. PLoS Genet. 2009, 5:e1000396. 10.1371/journal.pgen.1000396.
19. Aukerman M.J., Hirschfeld M., Webster L., Weaver M., Clark T., Amasino R.M., Sharrock R.A. Adeletion in the PHYD gene of the Arabidopsis Wassilewskija ecotype defines a role for phytochrome D in red/far-red light sensing. Plant Cell. 1997, 8:1317-1326.
20. Schreuder M.D.J., Brewer C.A., Heine C. Modeled influences of non-exchanging trichomes on leaf boundary layers and gas exchange. J.Theor. Biol. 2001, 210:23-32.
21. van Buskirk H.A., Thomashow M.F. Arabidopsis transcription factors regulating cold acclimation. Physiol. Plant 2006, 126:72-80.
22. Vogel J.T., Zarka D.G., Van Buskirk H.A., Fowler S.G., Thomashow M.F. Roles of the CBF2 and ZAT12 transcription factors in configuring the low temperature transcriptome of Arabidopsis. Plant J. 2005, 41:195-211.
23. Schramm F., Larkindale J., Kiehlmann E., Ganguli A., Englich G., Vierling E., von Koskull-Döring P. Acascade of transcription factor DREB2A and heat stress transcription factor HsfA3 regulates the heat stress response of Arabidopsis. Plant J. 2008, 53:264-274.
24. Jiang Y., Deyholos M.K. Comprehensive transcriptional profiling of NaCl-stressed Arabidopsis roots reveals novel classes of responsive genes. BMC Plant Biol. 2006, 6:25.
25. Kamei A., Seki M., Umezawa T., Ishida J., Satou M., Akiyama K., Zhu J.-K., Shinozaki K. Analysis of gene expression profiles in Arabidopsis salt overly sensitive mutants sos2-1 and sos3-1. Plant Cell Environ. 2005, 28:1267-1275.
26. Walia H., Wilson C., Condamine P., Liu X., Ismail A.M., Zeng L., Wanamaker S.I., Mandal J., Xu J., Cui X., Close T.J. Comparative transcriptional profiling of two contrasting rice genotypes under salinity stress during the vegetative growth stage. Plant Physiol. 2005, 139:822-835.
27. Potters G., Pasternak T.P., Guisez Y., Palme K.J., Jansen M.A.K. Stress-induced morphogenic responses: growing out of trouble?. Trends Plant Sci. 2007, 12:98-105.
28. Chao B., Dilkes H., Luo A., Douglas E., Yakubova B., Lahner D., Salt D. Polyploids exhibit higher potassium uptake and salinity tolerance in Arabidopsis. Science 2013, 341:658-659.
29. Sharma S., Lin W., Villamor J.G., Verslues P.E. Divergent low water potential response in Arabidopsis thaliana accessions Landsberg erecta and Shahdara. Plant Cell Env 2013, 36:994-1008.
30. Batista R., Saibo N., Lurenco T., Oliveira M.M. Microarray analyses reveal that plant mutagenesis may induce more transcriptomic changes than transgene insertion. Proc. Natl. Acad. Sci. U. S. A. 2008, 105:3640-3645.
31. Clark R.M., Schweikert G., Toomajain C., Ossowski S., Zeller G., Shinn P., Wathmann W., Hu T.T., Fu G., Hinds D.A., Chen H., Frazer K.A., Huson D.H., Scholkopf B., Nordborg M., Ratsch G., Ecker J.R., Weigel D. Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science 2007, 317:338-342.
32. Tan X.P., Meyers B.C., Kozik A.A., West M., Morgante M., St Clair D.A., Bent A.F., Michelmore R.W. Global expression analysis of nucleotide binding site-leucine rich repeat-encoding and related genes in Arabidopsis. BMC Plant Biol. 2007, 7:56.
33. Bauer Z., Gomez-Gomez L., Boller T., Felix G. Sensitivity of different ecotypes and mutants of Arabidopsis thaliana toward the bacterial elicitor flagellin correlates with the presence of receptor binding sites. J.Biol. Chem. 2001, 276:45669-45676.
34. Boerjan W., Vuylsteke M. Integrative genetical genomics in Arabidopsis. Nat. Genet. 2009, 41:144-145.
35. Fu H., Keurentjes J.J.B., Bouwmeester H., America T., Verstappen F.W.A., Ward J.L., Beale M.H., de Vos R.C.H., Dijkstra M., Scheltema R.A., Johannes F., Kornneef M., Vreugdenhil D., Breitling R., Jansen R.C. System-wide molecular evidence for phenotypic buffering in Arabidopsis. Nat. Genet. 2009, 41:166-167.
36. Gentleman R.C., Carey V.J., Bates D.J., Bolstad B.M., Dettling M., Dudoit S., Ellis B., Gautier L., Ge Y., Gentry J., Hornik K., Hothorn T., Huber W., Iacus S., Irizarry R., Leisch F., Li C., Maechler M., Rossini A., Sawitzki G., Smith C., Smyth G., Tierney L., Yang Y., Zhang J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004, 5:R80.
37. Bolstad B.M., Irizarry R.A., Astrand M., Speed T.P. Acomparison of normalization methods for high density oligonucleotide array data based on bias and variance. Bioinformatics 2003, 19:185-193.
38. Wettenhall J.M., Simpson K.M., Satterley K., Smyth G.K. affylmGUI: a graphical user interface for linear modeling of single channel microarray data. Bioinformatics 2006, 22:897-899.
39. Provart N., Zhu T. Abrowser-based functional classification SuperViewer for Arabidopsis genomics. Curr. Comput. Mol. Biol. 2003, 271-272.
40. de Hoon M.J.L., Imoto S., Nolan J., Miyano S. Open source clustering software. Bioinformatics 2004, 20:1453-1454. http://bioinformatics.oupjournals.org.
41. Thimm O., Blasing O., Gibon Y., Nagel A., Meyer S., Kruger P., Selbig J., Muller L.A., Rhee S.Y., Stitt M. MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J. 2004, 37:914-939.