A predictive co-expression network identifies novel genes controlling the seed-to-seedling phase transition in Arabidopsis thaliana

Abstract

Transition from a quiescent dry seed to an actively growing photoautotrophic seedling is a complex and crucial trait for plant propagation. This study provides a detailed description of global gene expression in seven successive developmental stages of seedling establishment in Arabidopsis. Using the transcriptome signature from these developmental stages we obtained a co-expression gene network which highlights interactions between known regulators of the seed-to-seedling transition and predicts the function of uncharacterized genes in seedling establishment. The co-expressed gene data sets together with transcriptional module indicates biological functions related to seedling establishment. Characterization of the homeodomain leucine zipper I transcription factor AtHB13, which is expressed during the seed-to-seedling transition, demonstrated that this gene regulates some of the network nodes and affects late seedling establishment. Knock-out mutants for athb13 showed increased primary root length as compared with wild type (Col-0) seedlings, suggesting that this transcription factor is a negative regulator of early root growth, possibly repressing cell division and/or cell elongation or the length of time cells elongate. The signal transduction pathways present during the early phases of the seed-to-seedling transition anticipate the control of important events for vigorous seedling, such as root growth. This study demonstrates that a gene co-expression network together with transcriptional modules can provide insights that are not derived from comparative transcript profiling alone.