Transcriptome analysis of microRNA156 overexpression alfalfa roots under drought stress

Citation

Arshad, M., Gruber, M.Y., Hannoufa, A. (2018). Transcriptome analysis of microRNA156 overexpression alfalfa roots under drought stress. Scientific Reports, [online] 8(1), http://dx.doi.org/10.1038/s41598-018-27088-8

Plain language summary

Drought is one of the major abiotic stresses that negatively impact alfalfa growth and productivity. The severity and frequency of drought events are expected to increase over the coming years as a results of climate change. To ensure sustainable production of forage feed and livestock, it is important to understand how plants respond to drought, and to use that knowledge to develop cultivars that can withstand drought stress.

Our research has established a role for microRNA156 and its target SPL genes in alfalfa’s drought response. In this study we investigated changes in gene expression of alfalfa genotypes overexpressing miR156OE to identify drought responsive genes that could be employed in marker assisting breeding for improved alfalfa varieties.

Our transcriptomics analysis revealed one gene WD40-2 that was silenced under drought in microRNA156 overexpression plants. Alfalfa plants overexpressing WD40-2 showed drought sensitive, whereas
those with silenced WD40-2 exhibited drought tolerant phenotypes. These findings suggest that
microRNA156 improves drought tolerance in alfalfa by silencng WD40-2. WD40-2 is thus a suitable marker for molecular-assisting breeding or gene editing to improve drought tolerance in alfalfa.

Abstract

Drought is one of the major abiotic stresses that negatively impact alfalfa growth and productivity. The role of microRNA156 (miR156) in drought has been demonstrated in plants. To date, there are no published studies investigating the role of miR156 in regulating global gene expression in alfalfa under drought. In our study, alfalfa genotypes overexpressing miR156 (miR156OE) exhibited reduced water loss, and enhanced root growth under drought. Our RNA-seq data showed that in response to drought, a total of 415 genes were upregulated and 169 genes were downregulated specifically in miR156OE genotypes. Genotypic comparison revealed that 285 genes were upregulated and 253 genes were downregulated in miR156OE genotypes relative to corresponding WT under drought. Gene Ontology enrichment analysis revealed that the number of differentially expressed genes belonging to biological process, molecular function and cell component functional groups was decreased in miR156OE genotypes under drought. Furthermore, RNA-Seq data showed downregulation of a gene encoding WD40 repeat in a miR156-specific manner. 5′ RACE experiments verified cleavage of WD40-2 transcript under drought. Moreover, alfalfa plants overexpressing WD40-2 showed drought sensitive, whereas those with silenced WD40-2 exhibited drought tolerant phenotypes. These findings suggest that miR156 improves drought tolerance in alfalfa by targeting WD40-2.

Publication date

2018-12-01