Transcription profiling by tiling array of Arabidopsis thaliana leaf growth and development
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
SUBMITTER: Lars Hennig
PROVIDER: E-MTAB-1056 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
Systems-based analysis of Arabidopsis leaf growth reveals adaptation to water deficit.
Baerenfaller Katja K Massonnet Catherine C Walsh Sean S Baginsky Sacha S Bühlmann Peter P Hennig Lars L Hirsch-Hoffmann Matthias M Howell Katharine A KA Kahlau Sabine S Radziejwoski Amandine A Russenberger Doris D Rutishauser Dorothea D Small Ian I Stekhoven Daniel D Sulpice Ronan R Svozil Julia J Wuyts Nathalie N Stitt Mark M Hilson Pierre P Granier Christine C Gruissem Wilhelm W
Molecular systems biology 20120101
Leaves have a central role in plant energy capture and carbon conversion and therefore must continuously adapt their development to prevailing environmental conditions. To reveal the dynamic systems behaviour of leaf development, we profiled Arabidopsis leaf number six in depth at four different growth stages, at both the end-of-day and end-of-night, in plants growing in two controlled experimental conditions: short-day conditions with optimal soil water content and constant reduced soil water c ...[more]
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Project description:These data provide a basis for exploration of gene expression differences between physiologically extreme accessions of Arabidopsis thaliana. Recent studies have documented remarkable genetic variation among Arabidopsis thaliana accessions collected from diverse habitats and across its geographical range. Of particular interest are accessions with putatively locally adapted phenotypes â i.e., accessions with attributes that are likely adaptive under the climatic or habitat conditions of their sites of origin. These genotypes are especially valuable as they may provide insight into the genetic basis of adaptive evolution as well as allow the discovery of genes of ecological importance. Therefore we studied the physiology, genome content and gene expression of two physiologically extreme accessions (Tsu-1 from a wet environment in Tsushima, Japan and Kas-1 from a dry environment in Kashmir, India). The gene expression studies were conducted under two levels of soil moisture and accompanied by physiological measurements to characterize early responses to soil moisture deficit. Genomic hybridization experiments identified 42,503 single feature polymorphisms (SFP) between accessions, providing an initial screen for putative SNPs, indels, or changes in gene content. Microarray transcript profiling of leaf RNA identified a large number (5,996) of genes exhibiting robust constitutive differences in expression including many genes involved in general growth and development as well as abiotic stress pathways. Interestingly, mild soil drying resulted in only subtle physiological responses but resulted in gene expression changes in hundreds of transcripts, including 352 genes exhibiting differential responses between accessions. Our results highlight the value of genomic studies of natural accessions as well as identify a number of candidate genes for the observed constitutive and induced physiological differences between Tsu-1 and Kas-1. The basic experimental design involves two accessions (Tsu-1 and Kas-1) crossed with two environmental levels (well-watered soil and mild soil drying) and 3 biological replicates per accession/treatment combination (2 x 2 x 6 =24 arrays total)
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