Transcriptome analysis of miRNAs expression reveals novel insights into adventitious root formation in lotus (Nelumbo nucifera Gaertn.).

MicroRNA (miRNA)-regulated gene expression plays an important role in various plant metabolic processes. Although adventitious roots are critical to plant growth in lotus, the role of miRNA in AR formation remains unclear. Expression profiling of miRNAs was carried out during three different developmental stages of ARs in lotus: no induction of AR stage, initial stage of ARs, and maximum number of ARs. These data are referenced with the whole lotus genome as already identified through high-throughput tag-sequencing. 1.3 × 10⁷ tags were achieved, of which 11,035,798, 11,436,062, and 12,542,392 clean tags were obtained from each stage, respectively. miRNA analysis revealed that miRNAs were less than 10% among all small RNAs. In total, 310 miRNAs (240 up-regulated and 70 down-regulated miRNAs) exhibited expression changes from the no induction stage to the initial stage. Moreover, expression of 140 miRNAs was increased and that of 123 miRNAs was decreased between the initial and maximum AR stages, mostly by ~ - 4-4-fold. miRNAs involved in metabolic pathways differed between the initial stage/no induction stage and the maximum number stage/initial stage. Several miRNAs in the initial stage/no induction stage were related to plant hormone metabolism and pyruvate and MAPK pathways, while major miRNAs in the maximum number stage/initial stage were involved in carbohydrate metabolism. All differentially expressed miRNAs associated with AR formation from the initial stage to maximum stage were also analyzed. The expression of 16 miRNAs was determined using qRT-PCR. This work provides a general insight into miRNA regulation during AR formation in lotus.