Integrated analysis of long non-coding RNAs and mRNAs reveals the regulatory network of maize seedling root responding to salt stress

Background Long non-coding RNAs (lncRNAs) play important roles in response to abiotic stresses in plants, by acting as cis- or trans-acting regulators of protein-coding genes. As a widely cultivated crop worldwide, maize is sensitive to salt stress particularly at the seedling stage. However, it is unclear how the expressions of protein-coding genes are affected by non-coding RNAs in maize responding to salt tolerance. Results The whole transcriptome sequencing was employed to investigate the differential lncRNAs and target transcripts responding to salt stress between two maize inbred lines with contrasting salt tolerance. We developed a flexible, user-friendly, and modular RNA analysis workflow, which facilitated the identification of lncRNAs and novel mRNAs from whole transcriptome data. Using the workflow, 12,817 lncRNAs and 8,320 novel mRNAs in maize seedling roots were identified and characterized. A total of 742 lncRNAs and 7,835 mRNAs were identified as salt stress-responsive transcripts. Moreover, we obtained 41 cis- and 81 trans-target mRNA for 88 of the lncRNAs. Among these target transcripts, 11 belonged to 7 transcription factor (TF) families including bHLH, C2H2, Hap3/NF-YB, HAS, MYB, WD40, and WRKY. The above 8,577 salt stress-responsive transcripts were further classified into 28 modules by weighted gene co-expression network analysis. In the salt-tolerant module, we constructed an interaction network containing 79 nodes and 3081 edges, which included 5 lncRNAs, 18 TFs and 56 functional transcripts (FTs). As a trans-acting regulator, the lncRNA MSTRG.8888.1 affected the expressions of some salt tolerance-relative FTs, including protein-serine/threonine phosphatase 2C and galactinol synthase 1, by regulating the expression of the bHLH TF. Conclusions The contrasting genetic backgrounds of the two inbred lines generated considerable variations in the expression abundance of lncRNAs and protein-coding transcripts. In the co-expression networks responding to salt stress, some TFs were targeted by the lncRNAs, which further regulated the salt tolerance-related functional transcripts. We constructed a regulatory pathway of maize seedlings to salt stress, which was mediated by the hub lncRNA MSTRG.8888.1 and participated by the bHLH TF and its downstream target transcripts. Future work will be focused on the functional revelation of the regulatory pathway.

Comparative transcriptome and metabolome analysis reveal glutathione metabolic network and functional genes underlying blue and red-light mediation in maize seedling leaf

Background Light quality severely affects biosynthesis and metabolism-associated process of glutathione. However, the role of specific light is still unclear on the glutathione metabolism. In this article, comparatively transcriptome and metabolome methods are used to fully understand the blue and red-light conditions working on the glutathione metabolism in maize seedling leaf. Results There are 20 differently expressed genes and 4 differently expressed metabolites in KEGG pathway of glutathione metabolism. Among them, 12 genes belong to the glutathione S-transferase family, 3 genes belong to the ascorbate peroxidase gene family and 2 genes belong to the ribonucleoside-diphosphate reductase gene family. Three genes, G6PD, SPDS1, and GPX1 belong to the gene family of glucose 6-phosphate dehydrogenase, spermidine synthase, and glutathione peroxidase, respectively. Four differently expressed metabolites are identified. Three of them, Glutathione disulfide, Glutathione, and l-γ-Glutamyl-L-amino acid are decreased while L-Glutamate is increased. In addition, Through PPI analysis, two annotated genes gst16 and DAAT, and 3 unidentified genes 100381533, pco105094 and umc2770, identified as RPP13-like3, BCAT-like1and GMPS, were obtained. By the analysis of protein sequence and PPI network, we predict that pco105094 and umc2770 were involved in the GSSG-GSH and AsA-GSH cycle in the network of glutathione metabolism. Conclusions Compared to red light, blue light remarkably changed the transcription signal transduction and metabolism of glutathione metabolism. Differently expressed genes and metabolic mapped to the glutathione metabolism signaling pathways. In total, we obtained three unidentified genes, and two of them were predicted in current glutathione metabolism network. This result will contribute to the research of glutathione metabolism of maize.

Transcriptomic Characterization of the Effects of Selenium on Maize Seedling Growth

Selenium (Se) is a trace mineral element in soils that can be beneficial to plants in small amounts. Although maize is among the most economically important crops, there are few reports on the effects of Se on maize seedling growth at the molecular level. In this study, the growth of maize seedlings treated with different concentrations of Na2SeO3 was investigated, and the physiological characteristics were measured. Compared with the control, a low Se concentration promoted seedling growth, whereas a high Se concentration inhibited it. To illustrate the transcriptional effects of Se on maize seedling growth, samples from control plants and those treated with low or high concentrations of Se were subjected to RNA sequencing. The differentially expressed gene (DEG) analysis revealed that there were 239 upregulated and 106 downregulated genes in the low Se treatment groups, while there were 845 upregulated and 1,686 downregulated DEGs in the high Se treatment groups. Both the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation analyses showed a low concentration of the Se-stimulated expression of “DNA replication” and “glutathione (GSH) metabolism”-related genes. A high concentration of Se repressed the expression of auxin signal transduction and lignin biosynthesis-related genes. The real-time quantitative reverse transcription PCR (qRT-PCR) results showed that in the low Se treatment, “auxin signal transduction,” “DNA replication,” and lignin biosynthesis-related genes were upregulated 1.4- to 57.68-fold compared to the control, while, in the high Se concentration treatment, auxin signal transduction and lignin biosynthesis-related genes were downregulated 1.6- to 16.23-fold compared to the control. Based on these transcriptional differences and qRT-PCR validation, it was found that a low dosage of Se may promote maize seedling growth but becomes inhibitory to growth at higher concentrations. This study lays a foundation for the mechanisms underlying the effects of Se on maize seedling growth.

Mycorrhizal fungi Glomus spp. propagation in zeolite enriched with mycorrhiza helper bacteria for controlling nematode in coffee

Arbuscular mycorrhizal fungi (AMF) play a role in suppressing the nematode Pratylenchus coffeae. Mycorrhizal helper bacteria (MHB) can increase the effectiveness of AMF to control the diseases. The experimental purpose was to increase the spore population of AMF Glomus spp. in zeolite-based formulation inoculated with liquid consortia of Pseudomonas diminuta and Bacillus subtilis as MHB. The experimental design was a completely random design with six treatments consisted of 106, 107, 108, and 109 CFU/mL MHB liquid inoculants. The control treatments were water and 2% molasses. All treatments were replicated four times. A total of 300 mL/pot Liquid inoculant of MHB have been inoculated a three day before transplanting the maize seedling to the Zeolite inoculated with Glomus spp. in the pot. One month after MHB inoculation, Glomus formulation in Zeolite with different levels of MHB increased the degree of infection. Three months after MHB inoculation, spore content in Zeolite increased. The density of P. diminuta and B. subtilis in zeolite-based mycorrhizal inoculant increased at the end of the experiment. Liquid inoculant MHB contained 108 CFU/mL enhanced spora number fourth times compared to the control. This experiment suggests that P. diminuta and B. subtilis were effective to increase the spore density of AMF inoculant.

Ameliorative effect of melatonin improves drought tolerance by regulating growth, photosynthetic traits and leaf ultrastructure of maize seedlings

Background Melatonin is considered a potential plant growth regulator to enhance the growth of plants and increase tolerance to various abiotic stresses. Nevertheless, melatonin’s role in mediating stress response in different plant species and growth cycles still needs to be explored. This study was conducted to understand the impact of different melatonin concentrations (0, 50, 100, and 150 μM) applied as a soil drench to maize seedling under drought stress conditions. A decreased irrigation approach based on watering was exposed to maize seedling after drought stress was applied at 40–45% of field capacity. Results The results showed that drought stress negatively affected the growth behavior of maize seedlings, such as reduced biomass accumulation, decreased photosynthetic pigments, and enhanced the malondialdehyde and reactive oxygen species (ROS). However, melatonin application enhanced plant growth; alleviated ROS-induced oxidative damages by increasing the photosynthetic pigments, antioxidant enzyme activities, relative water content, and osmo-protectants of maize seedlings. Conclusions Melatonin treatment also enhanced the stomatal traits, such as stomatal length, width, area, and the number of pores under drought stress conditions. Our data suggested that 100 μM melatonin application as soil drenching could provide a valuable foundation for improving plant tolerance to drought stress conditions.

Maize seedling emergence in response to climatic variability in a tropical rainforest area

<p>Environmental factors causing low seedling emergence often observed in tropical maize (Zea mays L.) are poorly documented. This study was conducted to investigate the effects of weather factors on maize seedling emergence at the Obafemi Awolowo University Teaching and Research Farm (OAU TRF). Five maize varieties sown weekly, in 3-replicate RCBD experiments throughout the 2016 and 2017 cropping seasons, were used to monitor emergence percentage (E %), emergence index (EI) and emergence rate index (ERI). Climatic data were obtained from the automatic weather station located on the farm. Analysis of variance revealed highly significant (P ≤ 0.01) environmental effect for all traits. Soil moisture (Sm), relative humidity, air temperature, heat unit and soil heat flux (SHF) showed significant (P ≤ 0.05) correlation coefficients with all traits, but there was no relationship between the emergence traits and grain yield. Stepwise multiple regression and sequential path coefficient analyses indicated that increased Sm, rather than rainfall per se, increased the speed of emergence. Minimum air temperature and SHF with direct effects, and heat unit with indirect effect, negatively affected emergence the most. Relatively low Tmin and SHF, along with just enough Sm maximized seedling emergence in the rainforest agro-ecology of southwestern Nigeria.</p>

Horizontal ridging with mulching as the best tillage practice to reduce surface runoff and erosion in a Mollisol hillslope at the maize seedling stage

Soil erosion features and ideal tillage practices are not very clear at the crop seedling stage in Chinese Mollisols. Simulated rainfall experiments were conducted at the rainfall intensities of 50 and 100 mm h-1 to investigate the differences in soil erosion of a 5° hillslope during the maize seedling stage between conservation and conventional tillage measures, including cornstalk mulching (Cm), horizontal ridging (Hr), horizontal ridging + mulching (Hr+Cm), vertical ridging + mulching (Vr+Cm), flat-tillage (CK), and vertical ridging (Vr). The results demonstrated that crops could remit soil erosion at the seedling stage by reducing the kinetic energy and changing the distribution of raindrops. The conservation tillage measures significantly alleviated total runoff (11.7%–100%) and sediment yield (71.1%–100%), postponed runoff-yielding time (85 s–26.1 min), decreased runoff velocity (71.5%–96.7%), and reduced runoff and soil loss rate, compared to the conventional tillage measures. Practices with mulching showed better performance than Hr. Mulching reduced sediment concentration by decreasing runoff velocity and soil particle filtration in a manner similar to buffer strips. The contour ridge ruptured earlier at 100 mm h-1 than at 50 mm h-1 and changed the characteristics of the soil erosion by providing a larger sediment source to the surface flow. Runoff strength, rather than soil erodibility, was the key factor affecting soil erosion. Decreasing runoff velocity was more important than controlling runoff amount. The Hr + Cm treatment exhibited the lowest soil erosion and is, thus, recommended at the corn seedling stage.

Efficacy of Root Zone Temperature Increase in Root and Shoot Development and Hormone Changes in Different Maize Genotypes

In the context of global warming, the effects of warming in the root zone of crops on maize seedling characteristics deserve research attention. Previous studies on the adaptive traits of dryland maize have mainly focused on soil moisture and nutrients, rather than analyzing potential factors for the adaptive traits of root zone warming. This study was conducted to investigate the effects of different root zone warming ranges on the agronomic traits, hormones, and microstructures of maize seedling roots and leaves. The results showed that minor increases in the root zone temperature significantly enhanced maize seedling growth. However, when the temperature in the root zone was excessive, the stem diameter, root surface area, root volume, total root length, dry matter accumulation, and root/shoot biomass of maize seedlings sharply decreased. Under high temperature stress in the root zone, the root conduit area; root stele diameter; root content of trans-zeatin (ZT), gibberellin A3 (GA3), and indoleacetic acid (IAA); leaf thickness; upper and lower epidermis thickness; and leaf content of ZT and GA3 were significantly decreased. The hormone content and microstructure changes might be an important reason for root growth maldevelopment and nutrient absorption blockage, and they also affected the leaf growth of maize seedlings. Compared with the ‘senescent’ maize type Shaandan 902 (SD902), the plant microstructure of the ‘stay-green’ maize type Shaandan 609 (SD609) was less affected by increased temperatures, and the ability of the root system to absorb and transport water was stronger, which might explain its tolerance of high temperature stress in the root zone.