De novo transcriptome in roots of switchgrass (Panicum virgatum L.) reveals gene expression dynamic and act network under alkaline salt stress

Abstract

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.

Response Mechanisms of Plants Under Saline-Alkali Stress

“…Plants can respond to alkali and salt stress by regulating osmotic stress signaling pathways including mitogen-activated protein kinases (MAPKs), Ca 2+ -dependent protein kinases (CDPKs) and CBL-interacting protein kinases (CIPKs) (Shah et al, 2021;Zhang et al, 2021 (Colcombet and Hirt, 2008;Lee et al, 2015). As Ca 2+ sensors, CDPKs and CIPKs can directly convert upstream Ca 2+ signals into downstream phosphorylation signals to initiate further downstream signal transduction.…”

“…Multiple CIPK members participate in the salt stress response. In two genotypes of switchgrass cultivars (a salt-alkali tolerant genotype and a sensitive genotype), CIPK expression was upregulated mainly in the salt-tolerant cultivars, but the expression in the salt-alkali-sensitive variety was still very low (Zhang et al, 2021). In soybean, GmPKS4 improves soybean tolerance to salt and salt-alkali stresses.…”

“…Transcriptome analysis of switchgrass and alfalfa indicated that the expression levels of many transcription factors were significantly modified in response to saline-alkaline stress. They belong to major transcription factor families such as AP2/ERF, NAC, HDzip/bZIP, MYC/MYB, WRKY, and bHLH, many of whose members have been shown to be related to the salt-alkali stress response Shah et al, 2021;Zhang et al, 2021).…”

The transcription factor HcERF4 confers salt and drought tolerance in kenaf (Hibiscus cannabinus L.)

“…Soil salinization and drought can affect seed germination, crop growth and yield, which severely limits sustainable agricultural production (Zhang et al 2021a; Zhang et al 2021b). According to reports, soil salinity directly affects 20% of the world's agricultural land, and the global loss caused by drought is about 30%.…”

De novo Transcriptome Analysis in Leymus mollis to Unveil Genes Involved in Salt Stress Response

“…Transcriptome sequencing using next-generation sequencing technology is a fast and effective approach to generate genome-scale sequence resources, and provides an efficient way to investigate the mechanisms of plant response to various stresses [16][17][18][19][20]. To better understand the salt-stress response of L. mollis at transcriptional level, a comparative transcriptome analysis was performed based on the Illumina sequencing in this study.…”