Transcriptomic profiling of Arabidopsis gene expression in response to varying micronutrient zinc supply

Abstract

Deficiency of the micronutrient zinc is a widespread condition in agricultural soils, causing a negative impact on crop quality and yield. Nevertheless, there is an insufficient knowledge on the regulatory and molecular mechanisms underlying the plant response to inadequate zinc nutrition [1]. This information should contribute to the development of plant-based solutions with improved nutrient-use-efficiency traits in crops. Previously, the transcription factors bZIP19 and bZIP23 were identified as essential regulators of the response to zinc deficiency in Arabidopsis thaliana [2]. A microarray experiment comparing gene expression between roots of wild-type and the mutant bzip19 bzip23, exposed to zinc deficiency, led to the identification of differentially expressed genes related with zinc homeostasis, namely its transport and plant internal translocation [2]. Here, we provide the detailed methodology, bioinformatics analysis and quality controls related to the microarray gene expression profiling published by Assunção and co-workers [2]. Most significantly, the present dataset comprises new experimental variables, including analysis of shoot tissue, and zinc sufficiency and excess supply. Thus, it expands from 8 to 42 microarrays hybridizations, which have been deposited at the Gene Expression Omnibus (GEO) under the accession number GSE77286. Overall, it provides a resource for research on the molecular basis and regulatory events of the plant response to zinc supply, emphasizing the importance of Arabidopsis bZIP19 and bZIP23 transcription factors.

Keywords: Arabidopsis; Microarray; Micronutrient; Zinc deficiency; bZIP.

Fig. 1

Microarray analysis of the transcriptomic profile of the Arabidopsis T-DNA insertion double mutant bzip19 bzip23, in relation to the wild-type Col-0 ecotype, exposed to sufficient (Zn +), deficient (Zn-) or excess (Zn ++) zinc supply, in both shoots and roots. A. Experimental design summarizing the three study variables (zinc supply, genotype and tissue type), as well as the number of replicate hybridizations performed for each experimental condition. B–E. Boxplot analysis of expression (intensity) values for all genes in each hybridization. Root tissues prior to (B) or after (C) quantile normalization of intensity values. Shoot tissues prior to (D) or after (E) quantile normalization of intensity values. Box represents all values between percentile 25 and 75 and the central line in the box indicates the median. Interval represents minimum and maximum values excluding outliers. F,G. Principal component analysis (PCA), displaying variability of each microarray hybridization in components 1 and 2 (F) or 2 and 3 (G). H. Accumulative percentage of variability (Eigen values) explained by the first 10 components of the variance analysis.