UC Riverside

Abiotics stresses such as drought, cold, and salt are very pervasive in modern agriculture, which cause tremendous yield loss each year worldwide. MicroRNAs (miRNAs) play important regulatory roles in abiotic stress responses. To understand the roles of miRNAs in crop responses to abiotic stresses, we used next-generation sequencing techniques to profile the small RNA population in crops with and without stress treatments. We identified many novel as well as stress-regulated miRNAs in: cowpea, rice, maize and sorghum. Specifically, we identified 157 candidate miRNAs in cowpea, 227 in rice, 298 in maize and 407 in sorghum, many of which are novel. We identified 44, 28, 31 and 42 stress-regulated miRNAs in cowpea, rice, maize and sorghum, respectively. Interestingly, majority (81%) of stress-regulated miRNAs in maize were cold stress-regulated, while the majority (79%) in sorghum are drought stress-regulated. We further show that the gain of species-specific miRNA families, rather than family expansion, is responsible for different stress tolerance in maize and sorghum. We provided solid evidence to show that 80 of rice candidate miRNAs originated from MITEs and transposons. Additionally, homology search and structural analysis in collinear regions of maize, sorghum and rice recovered another 26, 10 and 3 miRNAs in maize, sorghum and rice, respectively. We provided clear evidence for orthologous and paralogous miRNA gene expression diversification by northern blot and/or digital expression analysis. Finally, we estimated that the birth rate of miRNAs in cereal genome was 23.55 genes per million years and the death rate was 0.63 and 17.01 genes per million years for orthologous and paralogous miRNA genes, respectively.