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.

Transcriptomic diversity in seedling roots of European flint maize in response to cold

“…The substantial transcriptomic variation between genotypes in this study provided the opportunity to evaluate the response to cold stress in a genetically diverse germplasm. In contrast, previous transcriptome studies on abiotic stress tolerance such as waterlogging, cold stress, drought stress typically focused on only one or a few maize inbred lines or hybrids under different conditions [15,[34][35][36][37][38][39][40].…”

A Comprehensive Transcriptomics Analysis Reveals Long Non-Coding RNA to Be Involved in the Key Metabolic Pathway in Response to Waterlogging Stress in Maize

“…Investigating the mechanisms of gene regulation underlying WS conditions will contribute to a better understanding of the molecular basis for waterlogging tolerance and help maize adapt better to WS. Although the transcriptomic response involved in waterlogging conditions has been studied in previous works [10,11,45], there are few investigations focusing on early response, especially for the regulatory lncRNAs that participate in low-oxygen metabolism. The overall goal of the present study was to determine the transcriptional responses associated with the early stages of WS and characterize the role of the lncRNAs involved in key hypoxia-metabolic pathways via an RNA-Seq approach.…”

“…The cause of these changes is the dramatic reprogramming of gene expression and RNA molecules, including coding RNA (mRNA) and non-coding RNA (ncRNA) that has been quantified with the development of deep high-throughput sequencing [4,5]. Numerous investigations into Arabidopsis [6][7][8], rice [9], maize [10,11], poplar (Populus × canescens) [12], and cotton (Gossypium hirsutum) [13] have been conducted to elucidate changes in the gene transcription of mRNA in response to low oxygen or flooding stress; these studies have revealed the similarity in transcriptome responses among species [14,15]. However, knowledge of ncRNA involved in hypoxia responses is largely unknown.…”

“…Maize is an upland crop and sensitive to waterlogging stress (WS). To date, only three studies have focused on identifying the important regulators and processes involved in WS in maize through transcriptome sequencing (RNA-seq) analysis [10,11,45]. These studies focused on their central role in the adaptation process after long-term stress, but they did not provide a global view of the transcriptome at an early response stage.…”

iTRAQ-based Comparative Proteomic Analysis of Flag Leaves of Two Wheat (Triticum aestivum L.) Genotypes Differing in Waterlogging Tolerance at Anthesis

“…In the past years, great efforts have been made to investigate the mechanism of WL tolerance at the molecular level. Many genes have been demonstrated to mediate WL in cotton [8,9], rapes [10], maize [11,12], cucumber [13]. Previous studies showed that 52 and 146 proteins were differentially expressed in tomato leaves and cucumber adventitious roots in response to WL stress, respectively [14,15].…”