MicroRNA expression profiling during upland cotton gland forming age by microarray and quantitative reverse-transcription polymerase chain reaction (qRT-PCR)

Plant microRNAs (miRNAs) have important impacts on growth, development, flowering, metabolism and response to stress. Studies indicate that post-transcriptional processes are important for regulating gene expression during development. However, we still have very limited knowledge on the regulatory mechanisms associated with this process. In particular, the function of miRNAs during gland morphogenesis in cotton remains unknown. In this study, we used the Affymetrix GeneChip miRNA Array (v11.0-ther Species) and quantitative reverse transcriptase-PCR (qRT-PCR) to identify additional microRNAs during gland morphogenesis of near-isogenic lines in upland cotton. The results showed that 30 miRNAs were differentially expressed: 24 up-regulated (miR156, miR157, miR166 and miR390 families) and six down-regulated (miR149, miR169, miR289, miR705, miR1224 and miR1227 families). Some microRNAs, such as ghb-miR169a_st and ghr-miR166b_st, were confirmed by qRT-PCR assays. There was no significant difference in miRNA levels between the microarray and qRT-PCR. Analysis of the transcript data for some miRNA target genes indicated that they play an important role in the pathogenesis and development of gland morphogenesis. In summary, our results showed that some known miRNAs were expressed in the gland of upland cotton, and most of them were of low abundance. This data may be useful in future studies associated with gland control involved in the terpenoid aldehyde biosynthesis pathway, genetic engineering and molecular breeding of cotton.