Genome-Wide Expression of Transcriptomes and Their Co-Expression Pattern in Subtropical Maize (Zea mays L.) under Waterlogging Stress

Abstract

Waterlogging causes extensive damage to maize crops in tropical and subtropical regions. The identification of tolerance genes and their interactions at the molecular level will be helpful to engineer tolerant genotypes. A whole-genome transcriptome assay revealed the specific role of genes in response to waterlogging stress in susceptible and tolerant genotypes. Genes involved in the synthesis of ethylene and auxin, cell wall metabolism, activation of G-proteins and formation of aerenchyma and adventitious roots, were upregulated in the tolerant genotype. Many transcription factors, particularly ERFs, MYB, HSPs, MAPK, and LOB-domain protein were involved in regulation of these traits. Genes responsible for scavenging of ROS generated under stress were expressed along with those involved in carbohydrate metabolism. The physical locations of 21 genes expressed in the tolerant genotype were found to correspond with the marker intervals of known QTLs responsible for development of adaptive traits. Among the candidate genes, most showed synteny with genes of sorghum and foxtail millet. Co-expression analysis of 528 microarray samples including 16 samples from the present study generated seven functional modules each in the two genotypes, with differing characteristics. In the tolerant genotype, stress genes were co-expressed along with peroxidase and fermentation pathway genes.

Physiological and Molecular Mechanisms of Flooding Tolerance in Plants

“…Similarly, in wheat seedlings increased activity of GR and higher contents of glutathione could mitigate post hypoxia oxidative stress (Ushimaru et al 1997 ). A recent study comparing transcriptome changes in waterlogging-tolerant and -susceptible maize genotypes, showed upregulation of antioxidant defense and fermentation pathway genes as the basis of waterlogging tolerance (Thirunavukkarasu et al 2013 ). There are reports of waterlogging stressinduced increase as well as decrease in antioxidant potential in crop plants (Biemelt et al 2000 ;Kumutha et al 2009 ).…”

“…Signal transduction components that activate RopGAP4 , mitochondrial alternative oxidase (AOX), calmodulin, and CAP (calmodulin-associated peptide) were upregulated by hypoxia (Bailey-Serres and Chang 2005 ). Thirunavukkarasu et al ( 2013 ) compared the whole transcriptome of contrasting subtropical maize genotypes at three stages of waterlogging stress. Genes responsible for programmed cell death that precedes aerenchyma formation was selectively upregulated in HKI 1105 (tolerant) exposed to waterlogging.…”

DNA Marker-Assisted Selection Approach for Developing Flooding-Tolerant Maize

“…In the early stages of flooding, expression of transcription factor genes (including r2, which encodes a Myb protein that possibly binds to the GT-motif in the promoter of anaerobic response genes) markedly increased and reached a peak after 1 h of flooding, indicating that these gene products play a crucial role in regulating late-stage response genes related to the pathways for glycolysis, respiration, lipid metabolism, signal transduction, and protein metabolism (Zhang et al 2006). Thirunavukkarasu et al (2013) demonstrated the activation of these pathways with microarray data showing a large number of up-regulated genes in roots flooded for seven days, including genes associated with the synthesis of ethylene and auxin, and with the subsequent formation of aerenchyma and adventitious roots.…”

“…To this end, some expressed sequence tag (EST) clones of possible candidate genes identified by microarray analysis and/or SSH have been aligned on the maize genome, and confirmed to be located near molecular markers tightly linked to known QTLs associated with flooding tolerance (Osman et al 2013, Thirunavukkarasu et al 2013, Zou et al 2010. Similarly, miRNAs have been mapped near QTLs responsible for flooding tolerance.…”

“Omics” of Maize Stress Response for Sustainable Food Production: Opportunities and Challenges

“…The crosstalk between carbon and amino acid metabolism reveals that amino acid metabolism performs two main roles at this late stage: regulation of cytoplasmic pH, and supply of energy through breakdown of the carbon skeleton. Another study analyzed the genomewide expression of maize root transcriptomes (Thirunavukkarasu et al, 2013). This study found that related genes involved in ethylene and auxin synthesis, cell wall metabolism, G-protein activation, and aerenchyma and adventitious root formation were upregulated in the tolerant maize genotype HKI 1105 under waterlogging stress.…”