Identification and comparative analysis of drought-associated microRNAs in two cowpea genotypes

Abstract

Background: Cowpea (Vigna unguiculata) is an important crop in arid and semi-arid regions and is a good model for studying drought tolerance. MicroRNAs (miRNAs) are known to play critical roles in plant stress responses, but drought-associated miRNAs have not been identified in cowpea. In addition, it is not understood how miRNAs might contribute to different capacities of drought tolerance in different cowpea genotypes.

Results: We generated deep sequencing small RNA reads from two cowpea genotypes (CB46, drought-sensitive, and IT93K503-1, drought-tolerant) that grew under well-watered and drought stress conditions. We mapped small RNA reads to cowpea genomic sequences and identified 157 miRNA genes that belong to 89 families. Among 44 drought-associated miRNAs, 30 were upregulated in drought condition and 14 were downregulated. Although miRNA expression was in general consistent in two genotypes, we found that nine miRNAs were predominantly or exclusively expressed in one of the two genotypes and that 11 miRNAs were drought-regulated in only one genotype, but not the other.

Conclusions: These results suggest that miRNAs may play important roles in drought tolerance in cowpea and may be a key factor in determining the level of drought tolerance in different cowpea genotypes.

Figure 1

Different drought tolerance of two cowpea genotypes. After treated with moderate drought stress (ψ_w = -1.5 MPa), IT93K503-1 plants continued to grow relatively well, but CB46 plants showed apparent symptoms of drought stress (chlorotic leaves).

Figure 2

Principal component analysis (PCA) of log2 miRNA normalized counts of two cowpea genotypes in two growth conditions.

Figure 3

Expression of selected miRNAs in two cowpea genotypes under two growth conditions. Vun_cand001 and vun_cand058 are two cowpea-specific miRNAs, and miR1515 is a conserved miRNA that is also found in other plants. A. Expression level based on normalized miRNA counts (transcripts per ten million, TPTM). B. Northern blots with mature miRNAs. U6 snRNA was used to show equal loading of total RNA in all lanes.