Background: Soil salinization is a major limiting factor for crop cultivation. Switchgrass is a perennial rhizomatous bunchgrass that is considered an ideal plant for marginal lands, including sites with saline soil. Here we investigated the physiological responses and transcriptome changes in the roots of Alamo (alkaline-tolerant genotype) and AM-314/MS-155 (alkaline-sensitive genotype) under alkaline salt stress. Results: Alkaline salt stress significantly affected the membrane, osmotic adjustment and antioxidant systems in switchgrass roots, and the ASTTI values between Alamo and AM-314/MS-155 were divergent at different time points. A total of 108,319 unigenes were obtained after reassembly, including 73,636 unigenes in AM-314/MS-155 and 65,492 unigenes in Alamo. A total of 10,219 DEGs were identified, and the number of upregulated genes in Alamo was much greater than that in AM-314/MS-155 in both the early and late stages of alkaline salt stress. The DEGs in AM-314/MS-155 were mainly concentrated in the early stage, while Alamo showed greater advantages in the late stage. These DEGs were mainly enriched in plant-pathogen interactions, ubiquitin-mediated proteolysis and glycolysis/gluconeogenesis pathways. We characterized 1480 TF genes into 64 TF families, and the most abundant TF family was the C2H2 family, followed by the bZIP and bHLH families. A total of 1718 PKs were predicted, including CaMK, CDPK, MAPK and RLK. WGCNA revealed that the DEGs in the blue, brown, dark magenta and light steel blue 1 modules were associated with the physiological changes in roots of switchgrass under alkaline salt stress. The consistency between the qRT-PCR and RNA-Seq results confirmed the reliability of the RNA-seq sequencing data. A molecular regulatory network of the switchgrass response to alkaline salt stress was preliminarily constructed on the basis of transcriptional regulation and functional genes. Conclusions: Alkaline salt tolerance of switchgrass may be achieved by the regulation of ion homeostasis, transport proteins, detoxification, heat shock proteins, dehydration and sugar metabolism. These findings provide a comprehensive analysis of gene expression dynamic and act network induced by alkaline salt stress in two switchgrass genotypes and contribute to the understanding of the alkaline salt tolerance mechanism of switchgrass and the improvement of switchgrass germplasm.

Leymus chinensis is a perennial forage grass that has good palatability, high yield and high feed value, but seed dormancy is a major problem limiting the widespread cultivation of L. chinensis. Here, we performed transcriptomic and metabolomic analysis of hulled and de-hulled seeds of L. chinensis treated with or without GA₃ to investigate the changes in gene and metabolites associated with dormancy release induced by GA₃. The germination test revealed that the optimum concentration of GA₃ for disruption of L. chinensis seed dormancy was 577 μM. A total of 4327 and 11,919 differentially expressed genes (DEGs) and 871 and 650 differentially abundant metabolites were identified in de-hulled and hulled seeds treated with GA₃, respectively, compared with seeds soaked in sterile water. Most of the DEGs were associated with starch and sucrose metabolism, protein processing in the endoplasmic reticulum, endocytosis and ribosomes. Furthermore, isoquinoline alkaloid biosynthesis, tyrosine metabolism, starch and sucrose metabolism, arginine and proline metabolism, and amino sugar and nucleotide sugar metabolism were significantly enriched pathways. Integrative analysis of the transcriptomic and metabolomic data revealed that starch and sucrose metabolism is one of the most important pathways that may play a key role in providing carbon skeletons and energy supply for the transition of L. chinensis seeds from a dormant state to germination by suppressing the expression of Cel61a, egID, cel1, tpsA, SPAC2E11.16c and TPP2, enhancing the expression of AMY1.1, AMY1.2, AMY1.6 and GLIP5, and inhibiting the synthesis of cellobiose, cellodextrin, and trehalose while promoting the hydrolysis of sucrose, starch, cellobiose, cellodextrin, and trehalose to glucose. This study identified several key genes and provided new insights into the molecular mechanism of seed dormancy release induced by GA₃ in L. chinensis. These putative genes will be valuable resources for improving the seed germination rate in future breeding studies.

Thioredoxin (TRX) is a small molecule protein that participates in the redox process and plays a decisive role in various functions of plants. However, the role of TRX in Medicago sativa (alfalfa), a widely cultivated perennial herb of legume, is still poorly understood. Here, we isolated MsTRX from alfalfa and determined the characteristics in improving salt tolerance by assaying the phenotype and physiological changes and the expression of stress-response genes in transgenic tobacco. The expression of MsTRX was similar in alfalfa roots, leaves, and inflorescences, and was downregulated in response to cold, drought, and salt treatment. The overexpression of MsTRX in tobacco promoted the accumulation of soluble sugar (SS) and proline; enhanced the activity of peroxidase (POD); and induced the upregulation of beta-amylase 1 (BAM1), lipid-transfer protein 1 (LTP1), candidate signal molecules/sensor relay proteins (CBSX3), superoxide dismutase [Cu-Zn] (Cu/Zn-SOD), superoxide dismutase [Mn] (Mn-SOD), protein gamma response 1 (GR1), dehydrin DHN1-like (ERD10B), and serine/threonine-protein kinase (SnRK2), as well as the downregulation of phyB activation-tagged suppressor1 (BAS1) and serine/threonine-protein kinase that phosphorylates LHCII protein 7 (STN7) under salt stress. These results indicated that MsTRX improves salt tolerance via maintaining osmotic homeostasis, scavenging reactive oxygen species (ROS), and regulating the transcription of stress-response genes in plants. In our study, we provided a new understanding of how MsTRX improves salt stress in plants and how MsTRX can be included in future breeding programs to improve salt tolerance in alfalfa.

Identification and Analysis of PGM and SUS Gene Families in Leymus Chinensis Seed Transcriptome

Background: Leymus chinensis is a perennial forage grass that has good palatability, high yield and high feed value, but seed dormancy is a major problem limiting the widespread cultivation of L. chinensis. The aim of this study was to investigate the underlying molecular mechanism and identify candidate genes associated with dormancy disruption by gibberellic acid (GA₃) through transcriptomic and metabolomic analysis.Results: The germination test revealed that the optimum concentration of GA₃ for disruption of L. chinensis seed dormancy was 200 μg/L. Compared with seeds soaked in sterile water, a total of 4,327 and 11,919 differentially expressed genes (DEGs) and 871 and 650 differentially abundant metabolites were identified in de-hulled and hulled seeds treated with GA₃, respectively. Most of the DEGs were associated with starch and sucrose metabolism, protein processing in the endoplasmic reticulum, endocytosis and ribosomes. Furthermore, isoquinoline alkaloid biosynthesis, tyrosine metabolism, starch and sucrose metabolism, arginine and proline metabolism, and amino sugar and nucleotide sugar metabolism were significantly enriched pathways. Integrative analysis of the transcriptomic and metabolomic data revealed that starch and sucrose metabolism is one of the most important pathways that may play a key role in the energy supply for the transition of L. chinensis seeds from a dormant state to germination by suppressing the expression of Cel61a, egID, cel1, tpsA, SPAC2E11.16c and TPP2, along with enhancing the expression of AMY1.1, AMY1.2, AMY1.6 and GLIP5, and finally inhibiting the synthesis of cellobiose, cellodextrin, and trehalose while promoting the hydrolysis of sucrose, starch, cellobiose, cellodextrin, and trehalose to glucose.Conclusions: This study identified several key genes and provided new insights into the molecular mechanism of seed dormancy release by GA₃ in L. chinensis. These putative genes will be valuable resources for improving the seed germination rate in future breeding studies.