Structural and Functional Characteristics of miRNAs in Five Strategic Millet Species and Their Utility in Drought Tolerance

Abstract

Millets are the strategic food crops in arid and drought-prone ecologies. Millets, by virtue of nature, are very well-adapted to drought conditions and able to produce sustainable yield. Millets have important nutrients that can help prevent micro-nutrient malnutrition. As a result of the adverse effect of climate change and widespread malnutrition, millets have attained a strategic position to sustain food and nutritional security. Although millets can adapt well to the drought ecologies where other cereals fail completely, the yield level is very low under stress. There is a tremendous opportunity to increase the genetic potential of millet crops in dry lands when the genetics of the drought-tolerance mechanism is fully explained. MicroRNAs (miRNAs) are the class of small RNAs that control trait expression. They are part of the gene regulation but little studied in millets. In the present study, novel miRNAs and gene targets were identified from the genomic resources of pearl millet, sorghum, foxtail millet, finger millet, and proso millet through in silico approaches. A total of 1,002 miRNAs from 280 families regulating 23,158 targets were identified using different filtration criteria in five millet species. The unique as well as conserved structural features and functional characteristics of miRNA across millets were explained. About 84 miRNAs were conserved across millets in different species combinations, which explained the evolutionary relationship of the millets. Further, 215 miRNAs controlling 155 unique major drought-responsive genes, transcription factors, and protein families revealed the genetics of drought tolerance that are accumulated in the millet genomes. The miRNAs regulating the drought stress through specific targets or multiple targets showed through a network analysis. The identified genes regulated by miRNA genes could be useful in developing functional markers and used for yield improvement under drought in millets as well as in other crops.

Genome-Wide Identification and Transcriptional Analysis of AP2/ERF Gene Family in Pearl Millet (Pennisetum glaucum)

“…Lately, multiple novel drought stress-responsive microRNAs (miRNA) have beenidentified from the genomic resources of pearl millet, sorghum, foxtail millet, finger millet, and proso millet through in silico approaches [ 54 ]. By searching their database, 23 pearl millet miRNAs are predicted to target 67 different PgERF genes ( Table S9 ), suggesting they might be involved in drought-inducible post-transcriptional regulation.…”

Unveiling the biosynthesis, mechanisms, and impacts of miRNAs in drought stress resilience in plants

“…A drought-inducible bHLH102bHLH/HLH transcription factor is a member of the BR signaling cascade and is involved in cell elongation in cotton plants (Lu et al, 2018). Recent evidence shows that miRNA399 and miRNA396 target the bHLH transcription factor which potentially reduces the stomatal density and thus lowers the loss of water to induce drought stress tolerance in sorghum (Chakraborty et al, 2020). The up-regulation of miRNA (vun_cand015) in drought-tolerant cowpea plants, which target the bHLH transcription factor during exposure to drought stress, was also reported, indicating its role in abiotic stress tolerance (Barrera-Figueroa et al, 2011).…”

Non-Coding RNAs in Response to Drought Stress

“…Genome-wide transcriptome studies have identified several drought-responsive lncR-NAs in different plant species [96,97,115,[255][256][257][258]. For example, studies on the identification of drought-responsive lncRNAs in grass families detected 664 potential candidates in maize [102], 98 in rice [119], 19 in foxtail millet [259] and 1597 in switchgrass [117].…”