Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

CRNA hybridizations of 18 accessions of Arabidopsis thaliana under well-watered and mild soil drying

ABSTRACT: These data provide a basis for exploration of gene expression differences between physiologically diverse 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 M-bM-^@M-^S 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 18 physiologically diverse accessions. 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. The basic experimental design involves 18 accessions crossed with two environmental levels (well-watered soil and mild soil drying) and 3 biological replicates per accession/treatment combination.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: David Des Marais

PROVIDER: E-GEOD-27550 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Physiological genomics of response to soil drying in diverse Arabidopsis accessions.

Des Marais David L DL McKay John K JK Richards James H JH Sen Saunak S Wayne Tierney T Juenger Thomas E TE

The Plant cell 20120309 3

Arabidopsis thaliana, like many species, is characterized by abundant genetic variation. This variation is rapidly being cataloged at the sequence level, but careful dissection of genetic variation in whole-organism responses to stresses encountered in the natural environment are lacking; this functional variation can be exploited as a natural mutant screen to determine gene function. Here, we document physiological and transcriptomic response to soil drying in 17 natural accessions of Arabidops ...[more]

PMID: 22408074

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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)

Dataset Information

CRNA hybridizations of 18 accessions of Arabidopsis thaliana under well-watered and mild soil drying

Publications

Physiological genomics of response to soil drying in diverse Arabidopsis accessions.

Similar Datasets

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