NEW YORK (GenomeWeb) – A team of researchers from Gansu Agricultural University in China this month reported on the discovery of four microRNAs in potatoes that regulate genes involved in the plant's response to drought.
Although more work needs to be done to elucidate the relationships between the miRNAs and their targets, the findings suggest that the small, non-coding RNAs could serve as targets for enhancing the ability of potatoes to survive in dry environments.
Potatoes are one of the most economically important crops in the world, both because of their role as a food for humans and domestic animals, as well as their potential application in biofuel production. However, as with any crop plant, potato production is often hampered by drought.
When exposed to unnaturally dry conditions, plants respond with a variety of adaptations largely dependent on the regulated expression of drought-related genes, the Gansu team noted in a paper appearing in PLOS One.
"The products of these target genes play important roles not only in protecting cells from drought stress, but also in regulating genes for signal transduction in the drought stress response," they wrote. "However, the detailed regulation mechanisms of these genes are incompletely understood."
Given the numerous roles of miRNAs in post-transcriptional gene regulation in plants and animals, as well data pointing to their involvement in the drought stress responses of model plant species such as Arabidopsis thaliana, the Gansu investigators sought to uncover those that might affect drought resistance in potatoes.
To do so, they constructed small RNA libraries for control potato samples, as well as potato samples had been treated with polyethylene glycol (PEG) to induce drought stress. After high-throughput sequencing, processing, and annotation, roughly 2 million and 913,000 known miRNAs were mapped to the control and treatment groups, respectively.
In order to identify the conserved miRNAs from these collections, the data were compared with known mature plant miRNAs in miRBase. After further analysis, a total of 458 were identified in the control library and 471 known miRNAs were found in the PEG treatment library.
To find novel miRNAs in the potato, the team used the unique sRNA sequences from the two libraries to map to the potato genome and predict the secondary structures of a series of sequences surrounding mapped sites.
The resultant reads were used to identify novel miRNAs by folding the sequences of potential miRNA precursors using freely available web-based software. Free energies and the binding locations of Dicer enzymes were also used to evaluate candidate miRNAs. In total, 674 novel miRNAs were identified in the control group and 566 novel miRNAs were found in the drought treatment samples.
The researchers then sought to find which of these miRNAs were differentially expressed between their potato samples.
"Based on the deep sequencing results, the miRNAs with changes in expression levels greater than two-fold in response to drought treatment were selected," they wrote in their paper.
Of the known miRNAs that fit these criteria, 100 were downregulated and 99 were upregulated. Among novel miRNAs, 151 were downregulated and 119 were upregulated. In particular, miR-3437, miR-1076, miR-4375, miR-3695, miR-1037, miR-3637, miR-1867, miR-4235, miR-2099, and miR-2109 had "remarkable" differences in expression, they stated.
Based on target prediction, annotation, and expression analysis of the miRNAs and their putative target genes, four miRNAs were identified as regulating drought-related genes — miR-811, miR-814, miR-835, miR-4398. Their target genes include a MYB transcription factor, hydroxyproline-rich glycoprotein, quaporin, and a WRKY transcription factor, respectively.
"Relative expression trends of those miRNAs were the same as that predicted by Solexa sequencing and they showed a negative correlation with the expression of the target genes," the scientists noted.
Importantly, MYB transcription factor members have been shown to regulate plant responses to biotic and abiotic stress conditions, while WRKY transcription factors have been reported as involved in plant stress responses with overexpression of WRKY genes in Arabidopsis conferring tolerance to abiotic stress.
Meanwhile, hydroxyproline-rich glycoprotein is a functional protein involved in plant accumulation of proline, an important osmotic-adjusting material that enables plants to adapt to drought and other abiotic stresses, the scientists wrote.
Taken together, the results of the study show that differentially expressed miRNAs are involved in the "biochemical and physiological processes of plant response to drought stress," they concluded. "Further study is necessary to elucidate the functional importance of predicted miRNA-target RNA relationships."