Genome-wide identification of eggplant (Solanum melongena L.) miRNAs and their targets reveals differential regulation of heterostyly [Array]

MicroRNAs (miRNAs), a class of endogenous, non-coding, ~21 nucleotide RNAs, regulate the expression of their target genes by mRNA cleavage or translation inhibition. In plants, miRNAs have been demonstrated to play crucial roles in regulating diverse cellular, physiological, and developmental processes. The identification of all the miRNAs is not yet complete; there are no studies on their possible links with the difference in heterostyly observed in eggplant (Solanum melongena L.). In the present study, small RNAs and their targets were identified in S-morph and L-morph styles during the development of eggplant pistil, using high-throughput small RNA microarray and degradome sequencing. Most of the miRNAs were found to be highly conserved in comparison to other plants. Among the 686 miRNAs on the microarray chip, 10 were demonstrated to be differentially expressed, among which ten were identified as pistil development-related miRNAs. The expression profiles of the eggplant miRNAs obtained through the microarray assays were validated by quantitative real-time polymerase chain reaction (qRT-PCR) for randomly selected miRNAs. We also annotated the target genes for differentially expressed miRNAs taking advantage of GO annotations and KEGG pathway analysis. And the pathway Cysteine and methionine metabolism, with a minimal P value, involved the largest number of miRNA target genes. The profiling of the miRNAs and their target genes described in the present study provides new information on the miRNA network during the development of eggplant pistil.