Microarray data of phytohormone related genes in potato exposed to French marigold essential oil

Subject: Flower strips of French marigold are commonly used pest repellents in potato fields. However, the effect of French marigold volatiles on potato metabolism is unknown. Phytohormones have important roles in integrating signals and regulating vital processes in plants. Since it is shown that different volatiles affect phytohormone signaling pathways, it is assumed that phytohormones have an important role in response to essential oil (EO) as well. Thus, a microarray transcriptome analysis and annotation of differentialy expresed transcripts into different phytohormone metabolic pathways was performed to study the effects of French marigold EO on laboratory-grown potato phytohormone homeostasis. 

Material and methods:

Analysis: cDNA microarray cross-referenced with the KEGG Pathways Database (Kyoto Encyclopedia of Genes and Genomes) 

Sample type: mRNA isolated from potato samples exposed for 8 h to EO and untreated control plants				

Platform: SurePrint G3 Custom Gene Expression (Agilent, Inc., Santa Clara, CA)

Label protocol: labeled (Cy3 or Cy5) cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit				

Hybridization protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer	

Scan protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263

Data processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1				

Software: R 3.6 (R Core Team, 2019)

Statistics: Moderated t-statistics, moderated F-statistic, and log-odds of differential expression were estimated by robust empirical Bayes moderation using the limma-trend method.

Data presentation: Data shown correspond to log2 of fold change (log2FC) values (with FC >= 2 cut off and) of differentially expressed transcripts (p <= 0.05, n=4). Classification into different phytohormonal metabolic pathways has been achived by using KEGG genes database. Obtained research data are presented in 4 csv files. Names of the files are abbreviated names of corresponding phytohormone groups.

Highlight: Results revealed jasmonic acid biosynthetic pathway as the most affected one, with the highest number of altered transcripts and with one of the genes from this pathway (12-oxophytodienoate reductase 1-like) having highest expression rate.

Abbreviations:
ABA = abscisic acid				
ACC = 1-aminocyclopropane-1-carboxylic acid		
JA = jasmonic acid				
SA = salicylic acid