Transcriptomic analysis of salt-stress-responsive genes in lentil roots and leaves

Salt stress is a critical environmental element contributing to the growth and productivity of different crops like lentils. In this study, to better understand the mechanism of lentil response to salt stress, gene expression alterations in lentil roots and leaves were investigated using the RNA-seq technique. By performing gene expression analysis, it was shown that salt stress had greater impacts on the gene expression regulation in the root (5420 DEGs) than leaf tissue (1050 DEGs), which consequently complicates the salt stress response mechanisms highlighted in the root tissue. In addition, gene ontology (GO) and metabolic pathways analyses also showed that the root and leaf tissues had very different enriched GO terms and metabolic pathways; however, some GO terms, such as carbohydrate metabolic process, response to stress and hydrolase activity and acting on glycosyl bonds, were similar in both tissues. Additionally, as revealed by the functional analysis in both tissues, the salt stress response could be primarily obtained through sensing and signaling pathways, transcriptional reprogramming, ionic homeostasis stabilizing, increased ROS inhibition, and the transporter system and photosynthesis activation. Some candidate genes involved in hormone (such as PP2C, CKX5, ETR2, GASA1, and LOX1) and kinase signaling pathways (such as MKD1, CRK3, LECRK-IX.1, and LRK10L1.2) as well as several transcriptions (such as bHLH, AP2/ERF, MYB, and WRKY) and transporter factors (such as ABC, AAP3, PIP1B, PNC1, and NHX3) were identified to contribute to salt stress response. Considering insufficient genetic information and accurate knowledge of lentil response to salt stress, it can be said that our transcript profiling and integrated bioinformatics analyses provide some necessary information for further functional studies of candidate genes and their regulatory factors affecting response to salt stress in lentil plants.