RNAseq revealed the important gene pathways controlling adaptive mechanisms under waterlogged stress in maize

Abstract

Waterlogging causes yield penalty in maize-growing countries of subtropical regions. Transcriptome analysis of the roots of a tolerant inbred HKI1105 using RNA sequencing revealed 21,364 differentially expressed genes (DEGs) under waterlogged stress condition. These 21,364 DEGs are known to regulate important pathways including energy-production, programmed cell death (PCD), aerenchyma formation, and ethylene responsiveness. High up-regulation of invertase (49-fold) and hexokinase (36-fold) in roots explained the ATP requirement in waterlogging condition. Also, high up-regulation of expansins (42-fold), plant aspartic protease A3 (19-fold), polygalacturonases (16-fold), respiratory burst oxidase homolog (12-fold), and hydrolases (11-fold) explained the PCD of root cortical cells followed by the formation of aerenchyma tissue during waterlogging stress. We hypothesized that the oxygen transfer in waterlogged roots is promoted by a cross-talk of fermentative, metabolic, and glycolytic pathways that generate ATPs for PCD and aerenchyma formation in root cortical cells. SNPs were mapped to the DEGs regulating aerenchyma formation (12), ethylene-responsive factors (11), and glycolysis (4) under stress. RNAseq derived SNPs can be used in selection approaches to breed tolerant hybrids. Overall, this investigation provided significant evidence of genes operating in the adaptive traits such as ethylene production and aerenchyma formation to cope-up the waterlogging stress.

Figure 1

Representation of differentially expressed genes during waterlogging stress in selected Gene ontology (GO) categories in maize. Differentially expressed genes were annotated according to GO categories cellular component, molecular function, and biological process. Number of genes represent the differentially expressed genes in waterlogging tolerant genotype HKI 1105.

Figure 2

Frequency of SNPs mapped in genomic regions in waterlogging tolerant genotype (HKI 1105) of maize. SNPs were mapped differentially in various genomic regions of non-stress and stress samples. X-axis represents the genomic regions in which SNPs were mapped and y-axis represents SNP frequency.

Figure 3

Energy-production pathways regulated in waterlogging tolerant genotype under stressed condition. (a) Energy-production pathways regulated during waterlogging stress. Here arrows denote the expression level of waterlogging responsive genes in maize roots. Expression level marked here includes greater than 2 fold change. Refer the paper for abbreviations. (b) Heatmap of energy-production pathway regulating genes. X-axis denotes non-stress and stress conditions. Y-axis denotes the gene models of energy-production pathway genes. Refer Table S4 for details of energy-production pathway genes.

Figure 4

Programmed cell death (PCD) of root cells leading to aerenchyma formation regulated in waterlogging tolerant genotype under stressed conditions. (a) PCD pathway and aerenchyma formation during waterlogging stress. Here arrows denote the expression level of waterlogging responsive genes in maize roots. Expression level marked here includes greater than 2 fold change. Refer the paper for abbreviations. (b) Heatmap of PCD and (c) aerenchyma formation genes. X-axis denotes non-stress and stress conditions. Y-axis denotes the gene models. Refer Table S5 and Table S6 for details of PCD and aerenhcyma formation genes.

Figure 5

Ethylene-responsive pathways regulated in waterlogging tolerant genotype under stressed conditions. (a) Ethylene-responsive pathways regulated during waterlogging stress. Here arrows denote the expression level of waterlogging responsive genes in maize roots. Expression level marked here includes greater than 2 fold change. Refer the paper for abbreviations. (b) Heatmap of ethylene-responsive pathway regulating genes. X-axis denotes non-stress and stress conditions. Y-axis denotes the gene models of ethylene-responsive pathway genes. Refer Table S7 for details of ethylene-responsive pathway genes.

Figure 6

Crosstalk of different pathways regulated in waterlogging tolerant genotype under stressed condition to sustain the biological activities. Water-logging tolerance governed by interactions among several metabolic events viz., glycolysis, programmed cell death, aerenchyma formation.