Deep Sequencing Identifies Cotton miRNA Roles in Response to Stress of Drought and Salinity

Soil salinity (salinity) and water deficit (drought) are two common environmental factors that adversely affect plant growth and productivity. microRNAs (miRNAs) are known as important gene regulators, playing roles in various biological processes including development and stress response, such as stress of salinity and drought. Unfortunately, what miRNAs and how miRNAs participate in response to stress of salinity and drought is still poorly understood in cotton. In this study, we first employed small RNA high-throughput sequencing to identify microRNAs from three cotton libraries treated by control, drought, and salinity. A total of 342 cotton miRNAs with precursor were identified, including 267 known miRNAs and 75 novel miRNAs. 283 of 342 miRNAs expressed differentially amongst the three treatments. Moreover, target prediction, GO-based functional classification, and KEGG-based functional enrichment also showed these identified miRNAs might play roles in response to stress of salinity and drought through targeting a series of stress-related genes and regulatory pathways. CitationRank-based literature mining was employed to sort out the importance of genes that were reported to be related to stress of salinity and drought, respectively. It turned out NAC family, MYB family and MAPK family were ranked top under the context of salinity and drought, indicating their critical roles for plant to combat stress of salinity and drought. According to our target prediction, we could associate a series of cotton miRNAs with these top-ranked genes, including miR164, miR172, miR396, miR1520, miR6158, ghr-n24, ghr-n56, and ghr-n59. Interestingly, in addition to stress response, at least 164 cotton miRNAs were also identified to target 210 genes that are known to take part in fiber development. Together, our result identified many miRNAs that play roles in response to stress of drought and salinity, as well as fiber development. It would contribute to stress-resistant breeding of cotton and understanding fiber development.