Project name: Glycine max Alternatively Spliced Transcript Detecting Microarray (GmASDM).

Description: Plants remember what they have experienced and are thereby able to confront repeated stresses more promptly and strongly. A subset of genes showed increased transcript levels under drought stress conditions, followed by a return to basal levels during recovery (watered) states, and then displayed elevated levels again under subsequent drought conditions. To screen for a set of drought stress memory genes in soybean (Glycine max L. cv. Daepoong), we designed a 180K DNA chip comprising 60-bp probes synthesized in situ to examine 55,588 loci. Through microarray analysis using the DNA chip, we identified 2,165 and 2,385 genes with more than 4-fold increases or decreases in transcript levels, respectively, under initial (first) drought stress conditions, when compared with the non-treated control. The transcript levels of the genes returned to basal levels during recovery (watered) states, then 677 and 987 genes displayed more than 16-fold elevated or reduced levels, respectively, under subsequent (second) drought conditions, when compared to the non-treated control. Gene Ontology analysis classified the drought stress memory genes into several functional categories, including those involved in trehalose biosynthesis and drought tolerance responses. We selected a number of drought stress memory genes encoding various transcription factors, protein phosphatase 2Cs, and late embryogenesis abundant proteins, and confirmed the microarray data by quantitative reverse-transcription real-time PCR. Upon repeated watering and subsequent (third) drought treatment, the elevated levels of the drought stress memory gene transcripts were propagated into newly developed second leaves, although at reduced levels when compared to the second drought treatment on the first leaves.Overall design: Based on the whole soybean (G. max var. Williams 82) genome database available from Phytozome (http://www.phytozome.net) (Goodstein et al. 2011), three 60-nt-long feature probes were designed from a representative transcript of each gene, beginning 60 bp upstream from the end of the stop codon and shifting downstream at 30-bp intervals; the three resulting probes covered 120 bp: 60 bp of coding sequence (CDS) and 60 bp in the 3' untranslated region (3'-UTR). Additional probes for alternatively spliced transcripts, chloroplast genes, mitochondrial genes, and selection markers such as gfp, gus, hyg, bar, and kan were included. A total of 175,391 probes were designed and synthesized in situ on the 180K DNA chip, which was manufactured by Agilent Co. (Santa Clara, CA, USA).

Data type: Transcriptome or Gene expression

Sample scope: Multiisolate

Relevance: Agricultural

Last updated: 2020-07-01