Genomic DNA hybridizations of Col-0, Tsu-1, and Kas-1 accessions of Arabidopsis thaliana

ABSTRACT: These data provide a basis for the detection of sequence based polymorphisms between the Col-1, Tsu-1, and Kas-1 accessions of Arabidopsis thaliana. The experimental data provides an initial characterization of differences among the accessions, as well as a means for improving gene expression studies with the filtering of SFP from arrays studies. 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 – 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. Each accession has 6 replicates, single channel on the ATH1 array. Samples were processed in two balanced batches (bioprime random labeling, hybridization,scanning). A total of 18 arrays

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Thomas Juenger 

PROVIDER: E-GEOD-20340 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress