Integration of mRNA and miRNA Analysis Reveals the Post-Transcriptional Regulation of Salt Stress Response in Hemerocallis fulva

Abstract

MicroRNAs (miRNAs) belong to non-coding small RNAs which have been shown to take a regulatory function at the posttranscriptional level in plant growth development and response to abiotic stress. Hemerocallis fulva is an herbaceous perennial plant with fleshy roots, wide distribution, and strong adaptability. However, salt stress is one of the most serious abiotic stresses to limit the growth and production of Hemerocallis fulva. To identify the miRNAs and their targets involved in the salt stress resistance, the salt-tolerant H. fulva with and without NaCl treatment were used as materials, and the expression differences of miRNAs–mRNAs related to salt-tolerance were explored and the cleavage sites between miRNAs and targets were also identified by using degradome sequencing technology. In this study, twenty and three significantly differential expression miRNAs (p-value < 0.05) were identified in the roots and leaves of H. fulva separately. Additionally, 12,691 and 1538 differentially expressed genes (DEGs) were also obtained, respectively, in roots and leaves. Moreover, 222 target genes of 61 family miRNAs were validated by degradome sequencing. Among the DE miRNAs, 29 pairs of miRNA targets displayed negatively correlated expression profiles. The qRT-PCR results also showed that the trends of miRNA and DEG expression were consistent with those of RNA-seq. A gene ontology (GO) enrichment analysis of these targets revealed that the calcium ion pathway, oxidative defense response, microtubule cytoskeleton organization, and DNA binding transcription factor responded to NaCl stress. Five miRNAs, miR156, miR160, miR393, miR166, and miR396, and several hub genes, squamosa promoter-binding-like protein (SPL), auxin response factor 12 (ARF), transport inhibitor response 1-like protein (TIR1), calmodulin-like proteins (CML), and growth-regulating factor 4 (GRF4), might play central roles in the regulation of NaCl-responsive genes. These results indicate that non-coding small RNAs and their target genes that are related to phytohormone signaling, Ca2+ signaling, and oxidative defense signaling pathways are involved in H. fulva’s response to NaCl stress.

Genome-wide identification and expression analysis of the Auxin-Response factor (ARF) gene family in Medicago sativa under abiotic stress

“…Subsequently, alfalfa seedlings were treated with salt, drought, cold, and heat stress, and qRT-PCR experimentally verified their expression patterns. As reported by Zhou et al [ 55 ], ARF12 might play central roles in the regulation of NaCl-responsive genes. In addition, AcARF5 can positively regulate salt stress and drought stress in kiwifruit ( Actinidia chinensis ) [ 56 ].…”

Effects of exogenous plant regulators on growth and development of “Kyoho” grape under salt alkali stress

“…The adverse effects of salt alkali stress on Xanthium sibiricum Patr. are reduced via exogenous BR (Zhou et al, 2023). Similar research revealed that exogenous BR sprayed on cucumber leaves during salt alkali stress reduced the concentrations of ROS, MDA, and electrical conductivity in plant leaves while dramatically enhancing the activity of many antioxidant enzymes.…”

Environmental Stress and Plants 2.0

“…Salt stress is a serious abiotic stresses limiting H. fulva growth and production. In the study of Zhou et al [11], miRNA expression was significantly different in the roots and leaves of H. fulva. miRNAs are non-coding small RNAs that play a post-transcriptional regulatory role in plant growth development and response to abiotic stress.…”