Transcriptome analysis reveals salt-stress-regulated biological processes and key pathways in roots of peanut (Arachis hypogaea L.)

Transcriptome Analysis Reveals Molecular Mechanisms under Salt Stress in Leaves of Foxtail Millet (Setaria italica L.)

Foxtail millet (Setaria italica L.) is an important cereal for managing future water scarcity and ensuring food security, due to its strong drought and salt stress resistance owing to its developed root system. However, the molecular responses of foxtail millet leaves to salt stress are largely unknown. In this study, seeds of 104 foxtail millet accessions were subjected to 0.17 mol·L^-1 NaCl stress during germination, and various germination-related parameters were analyzed to derive 5 salt-sensitive accessions and 13 salt-tolerant accessions. Hong Gu 2000 and Pu Huang Yu were the most salt-tolerant and salt-sensitive accessions, respectively. To determine the mechanism of the salt stress response, transcriptomic differences between the control and salt-treated groups were investigated. We obtained 2019 and 736 differentially expressed genes under salt stress in the salt-sensitive and salt-tolerant accessions, respectively. The transcription factor families bHLH, WRKY, AP2/ERF, and MYB-MYC were found to play critical roles in foxtail millet's response to salt stress. Additionally, the down-regulation of ribosomal protein-related genes causes stunted growth in the salt-sensitive accessions. The salt-tolerant accession alleviates salt stress by increasing energy production. Our findings provide novel insights into the molecular mechanism of foxtail millet's response to salt stress.

Transcriptomic and Metabolomic Analyses Reveal the Differential Regulatory Mechanisms of Compound Material on the Responses of Brassica campestris to Saline and Alkaline Stresses

Oilseed rape not only has the function of improve saline and alkaline soils, but also alleviate the local feed shortage. However, medium- and high-degree soil salinization and alkalinization always inhibit the growth of oilseed rape. Studies have shown that compound material can improve the tolerance to saline and alkaline stress of crops, but the difference in the regulation mechanism of compound material on oilseed rape in saline and alkaline soils is not clear. This study explored the difference through determining the leaf ion contents, physiological indexes, transcriptomics, and metabolomics of oilseed rape in salinized soil (NaCl 8 g kg^-1) and alkalinized soil (Na₂CO₃ 8 g kg^-1) at full flowering stage, respectively after the application of compound material. The results showed that in salinized and alkalinized soil, the compound material upregulated the genes related to the regulation of potassium ion transport, and changed the amino acid metabolic pathway, which reduced the contents of Na⁺, malondialdehyde (MDA), and relative conductivity (REC) in leaves, and increased the contents of K⁺ and Mg²⁺ and the activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT). However, there were differences in the regulation mechanism of compound material in salinized and alkalinized soil. In salinized soil, the compound material improved the tolerance of oilseed rape to saline stress by upregulating transcription factors mannose-1-phosphate guanylyltransferase (GPMM) and Glutamine--fructose-6-phosphate transaminase (GFPT) and downregulating phosphomannomutase (PMM) to change nucleotide metabolism pathway and lipid metabolism pathway. In alkalized soil, the compound material improved the tolerance of oilseed rape to alkaline stress by upregulating transcription factors Phenylalanine ammonia lyase (PAL) to change the biosynthesis pathway of other secondary metabolites. Therefore, the compound material can improve the tolerance of oilseed rape to saline and alkaline stress by regulating the genetic adaptability and apparent plasticity, but the mechanisms were different. This study provides a practical method for the ecological environment restoration and the development of animal husbandry.

Elucidating the Molecular Mechanisms by which Seed-Borne Endophytic Fungi, Epichloë gansuensis, Increases the Tolerance of Achnatherum inebrians to NaCl Stress

Seed-borne endophyte Epichloë gansuensis enhance NaCl tolerance in Achnatherum inebrians and increase its biomass. However, the molecular mechanism by which E. gansuensis increases the tolerance of host grasses to NaCl stress is unclear. Hence, we firstly explored the full-length transcriptome information of A. inebrians by PacBio RS II. In this work, we obtained 738,588 full-length non-chimeric reads, 36,105 transcript sequences and 27,202 complete CDSs from A. inebrians. We identified 3558 transcription factors (TFs), 15,945 simple sequence repeats and 963 long non-coding RNAs of A. inebrians. The present results show that 2464 and 1817 genes were differentially expressed by E. gansuensis in the leaves of E+ and E− plants at 0 mM and 200 mM NaCl concentrations, respectively. In addition, NaCl stress significantly regulated 4919 DEGs and 502 DEGs in the leaves of E+ and E− plants, respectively. Transcripts associated with photosynthesis, plant hormone signal transduction, amino acids metabolism, flavonoid biosynthetic process and WRKY TFs were differentially expressed by E. gansuensis; importantly, E. gansuensis up-regulated biology processes (brassinosteroid biosynthesis, oxidation–reduction, cellular calcium ion homeostasis, carotene biosynthesis, positive regulation of proteasomal ubiquitin-dependent protein catabolism and proanthocyanidin biosynthesis) of host grass under NaCl stress, which indicated an increase in the ability of host grasses’ adaptation to NaCl stress. In conclusion, our study demonstrates the molecular mechanism for E. gansuensis to increase the tolerance to salt stress in the host, which provides a theoretical basis for the molecular breed to create salt-tolerant forage with endophytes.

Comparative Transcriptome Analysis of Halophyte Zoysia macrostachya in Response to Salinity Stress

As one of the most severe environmental stresses, salt stress can cause a series of changes in plants. In salt tolerant plant Zoysia macrostachya, germination, physiology, and genetic variation under salinity have been studied previously, and the morphology and distribution of salt glands have been clarified. However, no study has investigated the transcriptome of such species under salt stress. In the present study, we compared transcriptome of Z. macrostachya under normal conditions and salt stress (300 mmol/L NaCl, 24 h) aimed to identify transcriptome responses and molecular mechanisms under salt stress in Z. macrostachya. A total of 8703 differently expressed genes (DEGs) were identified, including 4903 up-regulated and 3800 down-regulated ones. Moreover, a series of molecular processes were identified by Gene Ontology (GO) analysis, and these processes were suggested to be closely related to salt tolerance in Z. macrostachya. The identified DEGs concentrated on regulating plant growth via plant hormone signal transduction, maintaining ion homeostasis via salt secretion and osmoregulatory substance accumulation and preventing oxidative damage via increasing the activity of ROS (reactive oxygen species) scavenging system. These changes may be the most important responses of Z. macrostachya under salt stress. Some key genes related to salt stress were identified meanwhile. Collectively, our findings provided valuable insights into the molecular mechanisms and genetic underpinnings of salt tolerance in Z. macrostachya.

Comparative Transcriptome Analysis Reveals Molecular Defensive Mechanism of Arachis hypogaea in Response to Salt Stress

Abiotic stresses comprise all nonliving factors, such as soil salinity, drought, extreme temperatures, and metal toxicity, posing a serious threat to agriculture and affecting the plant production around the world. Peanut (Arachis hypogaea L.) is one of the most important crops for vegetable oil, proteins, minerals, and vitamins in the world. Therefore, it is of importance to understand the molecular mechanism of peanut against salt stress. Six transcriptome sequencing libraries including 24-hour salt treatments and control samples were constructed from the young leaves of peanut. A comprehensive analysis between two groups detected 3,425 differentially expressed genes (DEGs) including 2,013 upregulated genes and 1,412 downregulated genes. Of these DEGs, 141 transcription factors (TFs) mainly consisting of MYB, AP2/ERF, WRKY, bHLH, and HSF were identified in response to salinity stress. Further, GO categories of the DEGs highly related to regulation of cell growth, cell periphery, sustained external encapsulating structure, cell wall organization or biogenesis, antioxidant activity, and peroxidase activity were significantly enriched for upregulated DEGs. The function of downregulated DEGs was mainly enriched in regulation of metabolic processes, oxidoreductase activity, and catalytic activity. Fourteen DEGs with response to salt tolerance were validated by real-time PCR. Taken together, the identification of DEGs' response to salt tolerance of cultivated peanut will provide a solid foundation for improving salt-tolerant peanut genetic manipulation in the future.

Nitric oxide modulating ion balance in Hylotelephium erythrostictum roots subjected to NaCl stress based on the analysis of transcriptome, fluorescence, and ion fluxes

Soil salinization is one of the main stress factors that affect both growth and development of plants. Hylotelephium erythrostictum exhibits strong resistance to salt, but the underlying genetic mechanisms remain unclear. In this study, hydroponically cultured seedlings of H. erythrostictum were exposed to 200 mM NaCl. RNA-Seq was used to determine root transcriptomes at 0, 5, and 10 days, and potential candidate genes with differential expression were analyzed. Transcriptome sequencing generated 89.413 Gb of raw data, which were assembled into 111,341 unigenes, 82,081 of which were annotated. Differentially expressed genes associated to Na+ and K+ transport, Ca2+ channel, calcium binding protein, and nitric oxide (NO) biosynthesis had high expression levels in response to salt stress. An increased fluorescence intensity of NO indicated that it played an important role in the regulation of the cytosolic K+/Na+ balance in response to salt stress. Exogenous NO donor and NO biosynthesis inhibitors significantly increased and decreased the Na+ efflux, respectively, thus causing the opposite effect for K+ efflux. Moreover, under salt stress, exogenous NO donors and NO biosynthesis inhibitors enhanced and reduced Ca2+ influx, respectively. Combined with Ca2+ reagent regulation of Na+ and K+ fluxes, this study identifies how NaCl-induced NO may function as a signaling messenger that modulates the K+/Na+ balance in the cytoplasm via the Ca2+ signaling pathway. This enhances the salt resistance in H. erythrostictum roots.

Peanut (Arachis hypogaea L.): A Prospective Legume Crop to Offer Multiple Health Benefits Under Changing Climate

Peanut is a multipurpose oil-seed legume, which offer benefits in many ways. Apart from the peanut plant's beneficial effects on soil quality, peanut seeds are nutritious and medicinally and economically important. In this review, insights into peanut origin and its domestication are provided. Peanut is rich in bioactive components, including phenolics, flavonoids, polyphenols, and resveratrol. In addition, the involvement of peanut in biological nitrogen fixation is highly significant. Recent reports regarding peanut responses and N₂ fixation ability in response to abiotic stresses, including drought, salinity, heat stress, and iron deficiency on calcareous soils, have been incorporated. As a biotechnological note, recent advances in the development of transgenic peanut plants are also highlighted. In this context, regulation of transcriptional factors and gene transfer for the development of stress-tolerant peanut genotypes are of prime importance. Above all, this review signifies the importance of peanut cultivation and human consumption in view of the scenario of changing world climate in order to maintain food security.