Open Access Open Badges Research article

Transcriptomic complexity in young maize primary roots in response to low water potentials

Nina Opitz1, Anja Paschold1, Caroline Marcon1, Waqas Ahmed Malik2, Christa Lanz3, Hans-Peter Piepho2 and Frank Hochholdinger1*

Author Affiliations

1 Institute of Crop Science and Resource Conservation (INRES), Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany

2 Institute for Crop Science, Bioinformatics Unit, University of Hohenheim, 70599 Stuttgart, Germany

3 Department of Molecular Biology, Max-Planck-Institute for Developmental Biology, 72076 Tübingen, Germany

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BMC Genomics 2014, 15:741  doi:10.1186/1471-2164-15-741

Published: 29 August 2014



Widespread and more frequently occurring drought conditions are a consequence of global warming and increase the demand for tolerant crop varieties to feed the growing world population. A better understanding of the molecular mechanisms underlying the water deficit response of crops will enable targeted breeding strategies to develop robust cultivars.


In the present study, the transcriptional response of maize (Zea mays L.) primary roots to low water potentials was monitored by RNA sequencing (RNA-Seq) experiments. After 6 h and 24 h of mild (-0.2 MPa) and severe (-0.8 MPa) water deficit conditions, the primary root transcriptomes of seedlings grown under water deficit and control conditions were compared. The number of responsive genes was dependent on and increased with intensification of water deficit treatment. After short-term mild and severe water deficit 249 and 3,000 genes were differentially expressed, respectively. After a 24 h treatment the number of affected genes increased to 7,267 and 12,838 for mild and severe water deficit, respectively, including more than 80% of the short-term responsive genes. About half of the differentially expressed genes were up-regulated and maximal fold-changes increased with treatment intensity to more than 300-fold. A consensus set of 53 genes was differentially regulated independently of the nature of deficit treatment. Characterization revealed an overrepresentation of the Gene Ontology (GO) categories “oxidoreductase activity” and “heme binding” among regulated genes connecting the water deficit response to ROS metabolism.


This study gives a comprehensive insight in water deficit responsive genes in young maize primary roots and provides a set of candidate genes that merit further genetic analyses in the future.

Drought; Low water potential; Maize; RNA-Seq; Root; Transcriptome; Water deficit