Integration of mRNA and microRNA analysis reveals the molecular mechanisms underlying drought stress tolerance in maize (Zea mays L.)

Abstract

Drought is among the most serious environmental issue globally, and seriously affects the development, growth, and yield of crops. Maize (Zea mays L.), an important crop and industrial raw material, is planted on a large scale worldwide and drought can lead to large-scale reductions in maize corn production; however, few studies have focused on the maize root system mechanisms underlying drought resistance. In this study, miRNA–mRNA analysis was performed to deeply analyze the molecular mechanisms involved in drought response in the maize root system under drought stress. Furthermore, preliminary investigation of the biological function of miR408a in the maize root system was also conducted. The morphological, physiological, and transcriptomic changes in the maize variety “M8186” at the seedling stage under 12% PEG 6000 drought treatment (0, 7, and 24 h) were analyzed. With prolonged drought stress, seedlings gradually withered, the root system grew significantly, and abscisic acid, brassinolide, lignin, glutathione, and trehalose content in the root system gradually increased. Furthermore, peroxidase activity increased, while gibberellic acid and jasmonic acid gradually decreased. Moreover, 32 differentially expressed miRNAs (DEMIRs), namely, 25 known miRNAs and 7 new miRNAs, and 3,765 differentially expressed mRNAs (DEMRs), were identified in maize root under drought stress by miRNA-seq and mRNA-seq analysis, respectively. Through combined miRNA–mRNA analysis, 16 miRNA–target gene pairs, comprising 9 DEMIRs and 15 DEMRs, were obtained. In addition, four metabolic pathways, namely, “plant hormone signal transduction”, “phenylpropane biosynthesis”, “glutathione metabolism”, and “starch and sucrose metabolism”, were predicted to have important roles in the response of the maize root system to drought. MiRNA and mRNA expression results were verified by real-time quantitative PCR. Finally, miR408a was selected for functional analysis and demonstrated to be a negative regulator of drought response, mainly through regulation of reactive oxygen species accumulation in the maize root system. This study helps to elaborate the regulatory response mechanisms of the maize root system under drought stress and predicts the biological functions of candidate miRNAs and mRNAs, providing strategies for subsequent mining for, and biological breeding to select for, drought-responsive genes in the maize root system.

Identification and analysis of differentially expressed trihelix genes in maize (Zea mays) under abiotic stresses

“…For drought stress treatments, three-leaf-old seedlings of the inbred line B73 were immersed in 20% (w/v) polyethylene glycol 6000 (PEG-6000) solution, and were treated for 4 and 24 h, respectively. The roots of the seedlings were collected for analysis ( Jiao et al, 2022 ; Zeng et al, 2019 ). Six seedlings were treated per sample, and three biological replicates were conducted for each sample.…”

The Emerging Role of Non-Coding RNAs (ncRNAs) in Plant Growth, Development, and Stress Response Signaling

“…A list of several drought-responsive ncRNAs has been summarized by Gelaw et al [160], which are listed in Table 1 [161][162][163][164][165][166][167][168][169][170][171][172][173]. Most of them target genes involved in ethylene and ABA synthesis or signaling, calcium signaling, starch and sucrose synthesis, and a variety of other metabolic processes.…”

“…Root development miR165/166-RLD1/2 Gautam et al [85] miR156-SPL10 Barrera-Rojas et al [86] miR165-SHR Carlsbecker et al [87] Leaf development miR319-TCP Bresso et al [106] miR390-TAS3 Husbands et al [108] miR396-GRF Omidbakhshfard et al [124] Seed, endosperm, nutrient development miR156, miR166, miR172, miR319, miR396 Khemka et al [132] miR156-SPL14/SPL16 Miao et al [133] Drought stress miR169-NFYA5 Li et al [128] miR408a-Laccase Jiao et al [163] miRNA-mediated drought-responsive regulatory network Balyan et al [165] miR169-NFYA3 Ni et al [167] Salt stress osa-miR12477-LAO Parmar et al [180] Flooding/hypoxia miR156/SPL Feyissa et al [199] Heat stress miR164-NAC Tsai et al [218] Cold stress miR319-TCP Thiebaut et al [225] miR319-OsPCF6 and OsTCP21…”

A Novel Senescence-Specific Gene (ZmSAG39) Negatively Regulates Darkness and Drought Responses in Maize

“…Plants are vulnerable to environmental stress in all aspects of growth and develop ment, which can cause serious damage to plant survival and production. Among these environmental factors, drought stress is one of the most important challenges limiting crop growth and grain yield [2,30]. On the one hand, drought stress causes dehydration which leads to ion stress and osmotic stress, thus destroying the dynamic balance of cells On the other hand, drought stress induces oxidative stress, which produces a large number of reactive oxygen species (ROS) that cause membrane lipid oxidation, protein and DNA damage, leading to plant wilting and even death [31].…”

“…Plants are vulnerable to environmental stress in all aspects of growth and development, which can cause serious damage to plant survival and production. Among these environmental factors, drought stress is one of the most important challenges limiting crop growth and grain yield [2,30]. On the one hand, drought stress causes dehydration, which leads to ion stress and osmotic stress, thus destroying the dynamic balance of cells.…”