Identification of Cassava MicroRNAs under Abiotic Stress

Abstract

The study of microRNAs (miRNAs) in plants has gained significant attention in recent years due to their regulatory role during development and in response to biotic and abiotic stresses. Although cassava (Manihot esculenta Crantz) is tolerant to drought and other adverse conditions, most cassava miRNAs have been predicted using bioinformatics alone or through sequencing of plants challenged by biotic stress. Here, we use high-throughput sequencing and different bioinformatics methods to identify potential cassava miRNAs expressed in different tissues subject to heat and drought conditions. We identified 60 miRNAs conserved in other plant species and 821 potential cassava-specific miRNAs. We also predicted 134 and 1002 potential target genes for these two sets of sequences. Using real time PCR, we verified the condition-specific expression of 5 cassava small RNAs relative to a non-stress control. We also found, using publicly available expression data, a significantly lower expression of the predicted target genes of conserved and nonconserved miRNAs under drought stress compared to other cassava genes. Gene Ontology enrichment analysis along with condition specific expression of predicted miRNA targets, allowed us to identify several interesting miRNAs which may play a role in stress-induced posttranscriptional regulation in cassava and other plants.

MicroRNA dynamics in a wild and cultivated species of Convolvulaceae exposed to drought stress

“…In Arabidopsis, miR160 appears to regulate auxin-ABA crosstalk, playing crucial role in seed germination (Liu et al 2007). Drought mediated downregulation of miR160 was reported in Cassava, Populus trichocarpa and Sorghum bicolor (Ballen-Taborda et al 2013;Shuai et al 2013;Hamza et al 2016). Contrary to this, miR160 was reported to accumulate in Prunus persica and Sugarcane under drought (Eldem et al 2012;Gentile et al 2015).…”

“…In another study, miR394 was shown to be downregulated in high-tolerant sugarcane cultivar but upregulated in the sensitive cultivars (Gentile et al 2013). In these cultivars, (Liu et al 2007;Ballen-Taborda et al 2013;Turner et al 2013). In Arabidopsis, miR160 appears to regulate auxin-ABA crosstalk, playing crucial role in seed germination (Liu et al 2007).…”

Identification of Drought-Responsive microRNAs from Roots and Leaves of Alfalfa by High-Throughput Sequencing

“…Studies from sequencing, microarray, qRT-PCR and northern blot have demonstrated that the expression level of miRNAs was altered by drought in lots of plant species, including Medicago truncatula [23], Vigna unguiculata [24], Manihot esculenta [25], Solanum tuberosum [26], Gossypium [27], Nicotiana tabacum [28], populous [29], Oryza sativa [6], Saccharum officinarum [30], Panicum virgatum [31], Hordeum vulgare [32], and foxtail millet [33]. Importantly, genes associated with miRNA pathway, such as DCL1 and AGO genes, were up-regulated under drought stress, implying the involvement of miRNA in plant adaptation to drought [34].…”

Recent Biotechnological Advances in the Improvement of Cassava

“…For example, Zhang et al [46] have shown that transgenic cassava expressing isopentenyltransferase (IPT) gene under the control of senescence-activated promoter (SAG12), delayed leaf senescence under both greenhouse and field conditions, leading an increase in drought resistance. Also, identification of miRNA gene targets involved in post-transcriptional abiotic stress regulation could prove useful in engineering cassava for drought resistance [48]. …”