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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 two switchgrass genotypes 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 1,480 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 1,718 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: The 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 transcription and regulation 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.

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.

Background Low temperature is one of the main environmental factors that limits crop growth, development and production. Medicago falcata is an economically and ecologically important legume that is closely related to alfalfa and exhibits better tolerance to low temperature than alfalfa. Understanding the low-temperature-tolerance mechanism of M. falcata is important for the genetic improvement of alfalfa. Results In this study, we explored the transcriptomic changes in low-temperature-treated M. falcata roots by combining SMRT and NGS technologies. A total of 115,153 nonredundant sequences were obtained, and 8,849 AS events, 73,149 SSRs and 4,189 LncRNAs were predicted. A total of 111,587 genes from SMRT were annotated, and 11,369 DEGs were identified in this paper that are involved in plant hormone signal transduction, protein processing in endoplasmic reticulum, carbon metabolism, glycolysis/gluconeogenesis, starch and sucrose metabolism, and endocytosis pathways. We characterized 1,538 TF genes into 45 TF gene families, and the most abundant TF family was WRKY, followed by ERF, MYB, bHLH and NAC. A total of 134 genes were differentially coexpressed at all five temperature points, including 101 upregulated genes and 33 downregulated genes. PB40804, PB75011, PB110405 and PB108808 were found to play crucial roles in the tolerance of M. falcata to low temperature. The WGCNA results showed that the MEbrown module was significantly correlated with low-temperature stress in M. falcata. Electrolyte leakage was correlated with most genetic modules and corroborated that electrolyte leakage can be used as direct stress markers to reflect cell membrane damage from low-temperature stress in physiological assays. The consistency between the qRT-PCR results and RNA-Seq analyses confirm the validity of the RNA-Seq data and the analysis of the regulation of low-temperature stress in the transcriptome. Conclusions The full-length transcripts generated in this study provided a full characterization of the gene transcription of M. falcata and are useful for mining new low-temperature stress-related genes specific to M. falcata. These new findings facilitate the understanding of low-temperature-tolerance mechanisms in M. falcata.