Genomewide analysis of small RNA s in nonembryogenic and embryogenic tissues of citrus: micro RNA ‐and si RNA ‐mediated transcript cleavage involved in somatic embryogenesis

Summary Somatic embryogenesis ( SE ) is a process of somatic cells becoming dedifferentiated and generating embryos. SE has been widely used in biotechnology as a powerful way of regeneration and a model system for studying plant embryogenesis, but the controlling mechanisms of SE are far from clear. Here, we show the genomewide profiles of mi RNA s/si RNA s and their target genes in nonembryogenic and embryogenic tissues of ‘Valencia’ sweet orange. By high‐throughput sequencing ( HTS ) of small RNA s and RNA degradome tags, we identified 50 known and 45 novel mi RNA s, 130 miniature inverted‐repeat transposable elements ( MITE s) derived, 94 other and 235 phased small interfering RNA s (si RNA s), as well as 203 target genes. The majority of the abundantly expressed mi RNA s/si RNA s exhibit lower expression levels in embryogenic callus ( EC ) or during SE process than in nonembryogenic callus ( NEC ), which is supposed to derepress the target genes that are involved in development and stress response, thus to activate the biological processes required for cell differentiation. However, the conserved csi‐miR156a/b, miR164b and 171c directed suppression of specific transcription factors ( TF s) are supposed to inactivate the postembryonic growth thus to maintain normal SE . In this study, mi RNA ‐ and si RNA ‐mediated silencing of target genes was found under sophisticated regulation in citrus SE system; the enhancement effect of specific conserved mi RNA s on SE was discussed, providing new clues for future investigation of mechanisms that control SE .