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.
Highlights
Loss of crop productivity owing to waterlogging threatens the food security in developing countries
These reads were mapped onto the reference B73 genome and classified into two groups: reads mapped as an intact pair and reads mapped in broken pairs
The genes hexokinase, invertase, respiratory burst oxidase homolog (RBOH), plant aspartic protease A3 (PASPA3), expansins, and ubiquitin ligases were up-regulated; and lactate dehydrogenase (LDH), MT and polygalacturonases were down-regulated in stress sample
Summary
Loss of crop productivity owing to waterlogging threatens the food security in developing countries. The most impeding effect of waterlogging on plant growth is the arrested oxygen supply to the root system. PCD includes various signal transductions which involve Ca++9and protein kinases like mitogen-activated protein kinases (MAPK)[10] that trigger transcriptional regulators These functional pathways facilitate the degradation of cell wall involving proteases[11] and nucleases[12] allowing the formation of gas-filled cavities called as aerenchymous tissue. Plants maintain the ATP production through substrate-level phosphorylation[15, 16] in order to supply ATP to energy-consuming formation of aerenchyma in root cortical cells[17]. Lactate and ethanol fermentation is one of the energy-producing mechanisms that are stimulated under low oxygen conditions[18] These fermentation pathways provide NAD+ to maintain glycolysis which in turn increases the ATP generation. The ATP produced is consumed by the development of gas films to enhance the oxygen uptake in waterlogging conditions[17]
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