Transcriptome-IPMS analysis reveals a tissue-dependent miR156/SPL13 regulatory mechanism in alfalfa drought tolerance

Abstract

Background We previously reported on the interplay between miR156/SPL13 and WD40–1/DFR to improve response to drought stress in alfalfa (Medicago sativa L.). Here we aimed to investigate whether the role of miR156/SPL13 module in drought response is tissue-specific, and to identify SPL13-interacting proteins. We analyzed the global transcript profiles of leaf, stem, and root tissues of one-month old RNAi-silenced SPL13 (SPL13RNAi) alfalfa plants exposed to drought stress and conducted protein-protein interaction analysis to identify SPL13 interacting partners. Result Transcript analysis combined with weighted gene co-expression network analysis showed tissue and genotype-specific gene expression patterns. Moreover, pathway analysis of stem-derived differentially expressed genes (DEG) revealed upregulation of genes associated with stress mitigating primary and specialized metabolites, whereas genes associated with photosynthesis light reactions were silenced in SPL13RNAi plants. Leaf-derived DEG were attributed to enhanced light reactions, largely photosystem I, II, and electron transport chains, while roots of SPL13RNAi plants upregulated transcripts associated with metal ion transport, carbohydrate, and primary metabolism. Using immunoprecipitation combined with mass spectrometry (IPMS) we showed that SPL13 interacts with proteins involved in photosynthesis, specialized metabolite biosynthesis, and stress tolerance. Conclusions We conclude that the miR156/SPL13 module mitigates drought stress in alfalfa by regulating molecular and physiological processes in a tissue-dependent manner.

Research on lncRNA related to drought resistance of Shanlan upland rice

“…Among them, we found that miR156 was significantly up-regulated in plants under drought stress. Overexpression of miR156 can increase the levels of abscisic acid and antioxidants in plants [ 38 ] and affect photosynthesis and photorespiration by silencing SPL13, thereby alleviating the damage caused by drought stress [ 39 ]. GO enrichment analysis of its target genes indicated that the terms hormone operation (GO:0,009,914) and transport (GO:0,006,810) were enriched, indicating that our results are consistent with results of previous studies.…”

Molecular Characterization of the miR156/MsSPL Model in Regulating the Compound Leaf Development and Abiotic Stress Response in Alfalfa

“…These observations show that the miR156/SPL module may contribute to genetic variability through the regulation of plant development and abiotic stress responses. The phenotypic changes and stress response were similar to those of the miR156-overexpressing alfalfa genotypes, including delayed flowering, reduced stem length, and increased shoot branching, and played a positive role in abiotic stress tolerance [ 14 , 47 , 48 , 49 ]. This observation suggests that the miR156/SPL module is integrated with the plant developmental and stress response.…”

Combining QTL mapping and RNA-Seq Unravels candidate genes for Alfalfa (Medicago sativa L.) leaf development

“…Identification of these genes can help us better understanding of tissue-gene relationship. In alfalfa, RNA-seq analysis uncovered molecular mechanisms underlying abiotic stress, including salt [ 52 , 53 ], drought [ 54 , 55 ], and cold tolerance [ 56 ]. Meanwhile, pathways involved in early flowering [ 57 ] and differentially expressed genes related to defoliation traits [ 58 ] had also been identified in alfalfa by transcriptome analysis.…”