Differential quantitative regulation of specific gene groups and pathways under drought stress in rice

• Published in: Genomics (San Diego, Calif.) Vol. 111; no. 6; pp. 1699 - 1712
• Main Authors: Sharma, Eshan, Jain, Mukesh, Khurana, Jitendra P.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.12.2019
• Subjects: Dehydration - genetics; Dehydration - metabolism; DNA, Plant - genetics; DNA, Plant - metabolism; Drought; Gene Expression Regulation, Plant; Gene Ontology; Microarray; Nucleotide Motifs; Oryza - genetics; Oryza - metabolism; Pathway analysis; Plant Proteins - biosynthesis; Plant Proteins - genetics; Response Elements; Rice (Oryza sativa indica); RNA-seq; Stress, Physiological; Pathway analysis; RNA-seq; Rice (Oryza sativa indica); Drought; Microarray; Gene Ontology
• ISSN: 0888-7543; 1089-8646
• DOI: 10.1016/j.ygeno.2018.11.024

Abiotic stresses like drought are detrimental for growth and development and lead to loss in crop production. To be able to adapt and survive under such adverse conditions, synchronous regulation of a rather large number of genes is required. Here, we have used a bioinformatics approach to identify gene groups and associated pathways from microarray and RNA-seq experiments that are restricted in their gene expression amplitude within fold change intervals (FCI) under drought stress conditions. We find that the expression of genes as functional groups is coordinated quantitatively, in a fold change specific manner, and differs among three rice cultivars distinct in their drought stress response. By networking these groups and further categorization into components like ubiquitin proteasome system, we identify relatively less studied E2 ubiquitin conjugating enzyme coding genes as an important constituent of differential drought stress response in rice. By extending this approach to find hexamer DNA motifs in the upstream promoter regions of genes within the FCIs under stress, we find that genes with strong to very strong or a moderate expression under stress are coordinated through cis-regulatory motifs. Few of these, such as TSO1, L-Box, PE1, GT binding site, ABRE/G-box or AP2/ERF binding site can be candidate cis-regulatory motifs to coordinate fold change limited gene expression under drought stress. This work thus provides an insight into a quantitative regulation of gene expression under drought stress in rice and a useful resource for designing approaches towards coordinating the expression of identified candidate genes under stress in order to achieve drought tolerance in rice. •Genome-wide identification of functional groups with quantitatively coordinated gene expression.•A bioinformatics method for gene set enrichment within fold change intervals(FCI).•Ubiquitin proteasome system component E2 genes express differentially during drought stress in rice.•Candidate cis-regulatory elements as a resource to coordinate fold change limited gene expression under stress.