Genome-Wide Profiling of MiRNAs and Their Target Genes Reveal Complex miRNA Regulation during Somatic Embryogenesis in Cotton

MicroRNAs (miRNAs) are endogenous non-coding ~21 nucleotide (nt) small versatile regulatory RNAs in plants and animals, which play diverse roles in development and stress responses. miRNAs and their targets have been widely studied in model plants, but limited knowledge is available on the miRNA population of cotton (Gossypium hirsutum) and global identification of related targets through degradome sequencing has not been developed previously. In this study, we identified small RNAs and their targets by high throughput small RNA and degradome sequencing, comparing hypocotyls (CK) and embryogenic callus (EC) of G. hirsutum YZ1, both are typical developmental stages during cotton somatic embryogenesis (SE). Totally 36 differentially expressed known miRNA families were identified, as well as 25 novel miRNAs. 234 transcripts in EC and 322 transcripts in CK were found to be the targets of 23 and 30 known miRNA families respectively, as well as 16 transcripts targeted by 8 novel miRNAs. Interestingly, four trans-acting small interfering RNAs (tas3-siRNAs) were also found in small RNA libraries, which perfectly matched their precursors. series of targets were further validated via RNA ligase-mediated 5′ rapid amplification of cDNA ends (RLM 5′-RACE). Expression patterns of several miRNAs and their targets were also validated by qRT-PCR during SE process. The profiling of miRNAs and their targets provides new information on the miRNAs network during cotton SE.