title: A combination of gene expression ranking and co-expression network analysis increases discovery rate in large-scale mutant screens for novel Arabidopsis thaliana abiotic stress genes.
abstract: As challenges to food security increase, the demand for lead genes for improving crop production is growing. However, genetic screens of plant mutants typically yield very low frequencies of desired phenotypes. Here, we present a powerful computational approach for selecting candidate genes for screening insertion mutants. We combined ranking of Arabidopsis thaliana regulatory genes according to their expression in response to multiple abiotic stresses (Multiple Stress [MST] score), with stress-responsive RNA co-expression network analysis to select candidate multiple stress regulatory (MSTR) genes. Screening of 62 T-DNA insertion mutants defective in candidate MSTR genes, for abiotic stress germination phenotypes yielded a remarkable hit rate of up to 62%; this gene discovery rate is 48-fold greater than that of other large-scale insertional mutant screens. Moreover, the MST score of these genes could be used to prioritize them for screening. To evaluate the contribution of the co-expression analysis, we screened 64 additional mutant lines of MST-scored genes that did not appear in the RNA co-expression network. The screening of these MST-scored genes yielded a gene discovery rate of 36%, which is much higher than that of classic mutant screens but not as high as when picking candidate genes from the co-expression network. The MSTR co-expression network that we created, AraSTressRegNet is publicly available at http://netbio.bgu.ac.il/arnet. This systems biology-based screening approach combining gene ranking and network analysis could be generally applicable to enhancing identification of genes regulating additional processes in plants and other organisms provided that suitable transcriptome data are available.
authors.affiliation: French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel.
authors.forename: Vanessa
authors.initials: V
authors.lastname: Ransbotyn
authors.forename: Esti
authors.initials: E
authors.lastname: Yeger-Lotem
authors.forename: Omer
authors.initials: O
authors.lastname: Basha
authors.forename: Tania
authors.initials: T
authors.lastname: Acuna
authors.forename: Christoph
authors.initials: C
authors.lastname: Verduyn
authors.forename: Michal
authors.initials: M
authors.lastname: Gordon
authors.forename: Vered
authors.initials: V
authors.lastname: Chalifa-Caspi
authors.forename: Matthew A
authors.initials: MA
authors.lastname: Hannah
authors.forename: Simon
authors.initials: S
authors.lastname: Barak
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D015870:Gene Expression; D053263:Gene Regulatory Networks; D017343:Genes, Plant; D016254:Mutagenesis, Insertional; D020411:Oligonucleotide Array Sequence Analysis; D013312:Stress, Physiological / Q000235:genetics*
keywords: Arabidopsis thaliana; abiotic stress; co-expression network; mutant screen; systems biology; transcriptome