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CRNA hybridizations of Tsu-1 and Kas-1 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 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 – 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.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE20339 | GEO | 2010/02/17

SECONDARY ACCESSION(S): PRJNA125413

REPOSITORIES: GEO

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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)

Project description:Understanding the patterns and processes driving natural genetic variation in gene expression is of fundamental importance to biology. In this study, we examined genetic variation in gene transcription through expression QTL (eQTL) analysis in the Tsu-1 x Kas-1 recombinant inbred line (RIL) mapping population of Arabidopsis thaliana. To understand how natural variation in transcription responds to abiotic stress, we conducted eQTL in both well watered and soil drying conditions. Further, we evaluated whether elements of genome structure were associated with eQTL occurance and genes responding to treatment conditions. Overall, we identified thousands of genes that responded to soil moisture availability and hundreds of eQTLs. However, we identified very few interactions between eQTLs and environmental conditions, and both treatment conditions were enriched for similar gene ontology (GO) categories. We did find strong evidence for associations between genome structure and natural variation in transcription. In general, genes with eQTLs were positively associated with local recombination rates and levels of polymorphism while genes responding to the treatment were negatively correlated with these factors. Our study provides further insight into the origin and maintenance of natural variation in transcription and how that variation responds to environmental conditions. Expression analysis by hybridization to atSNPTILE array (Affymetrix). Seed of the 104 RILs from reciprocal crosses between A. thaliana (L.) Heynh. accessions Kas-1 (CS903) and Tsu-1 (CS1640) were sown on fritted clay (Profile Products LLC, Buffalo Grove, IL) in 2.5-inch pots. Plants were arranged in a randomized complete block design consisting of 4 blocks, and then the pots were refrigerated at 4Â°C in darkness for 6 d to cold-stratify the seeds prior to commencement of a 12 h photoperiod in Conviron ATC60 growth chambers (Controlled Environments, Winnipeg, MB), at 23Â°C and 40% humidity during the day and 20Â°C and 50% humidity during the dark period. Light intensity was approximately 330 Âµmol m-2 s-1. After four weeks of growth, half of the plants were given a drought treatment, while the others remained fully watered. The drought treatment was randomly assigned to 2 of the 4 blocks and consisted of a slow decrease in soil moisture content over the course of one week. Each day, all pots assigned to the drought treatment were weighed, and water was added to individual pots to bring them to the target gravimetric water content. The target water content decreased each day, in the following series: 100%, 90%, 80%, 70%, 60%, 45%, and 40% of field capacity. At the end of the treatment, leaf tissue was collected from both treatments for RNA extraction.

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CRNA hybridizations of Tsu-1 and Kas-1 accessions of Arabidopsis thaliana under well-watered and mild soil drying

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