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

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.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.Drought is one of the main abiotic factors that cause reduction or total loss of crop production. Because water is becoming limited for agriculture in many areas of the world, the investigation of natural mechanisms of drought tolerance is an important strategy for understanding the biological basis of response to drought stress and for selection of plants with improved drought tolerance [1,2]. Cowpea [Vigna unguiculata (L.) Walp.] is an economically important crop in semi-arid and arid tropical regions in Africa, Asia, and Central and South America, where cowpea is consumed as human food and nutritious fodder to livestock [3,4]. As a leguminous species, cowpea belongs to the same tribe (Phaseoleae) as common bean and soybean. Compared to these close relatives and most other crops, cowpea is well adapted to these regions because of its ability to fix nitrogen in poor soil and greater drought tolerance [4,5]. Therefore, cowpea is an excellent system for investigating the genetic basis of drought tolerance.Efforts have been made to identify genetic elements that are involved in drought stress response in cowpea. For example, over a doze