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Background  Taproot is the main edible organ and ultimately determines radish yield and quality. However, the precise molecular mechanism underlying taproot thickening awaits further investigation in radish. Here, RNA-seq was performed to identify critical genes involved in radish taproot thickening from three advanced inbred lines with different root size.    Results  A total of 2606 differentially expressed genes (DEGs) were shared between ‘NAU-DY’ (large acicular) and ‘NAU-YB’ (medium obovate), which were significantly enriched in ‘phenylpropanoid biosynthesis’, ‘glucosinolate biosynthesis’, and ‘starch and sucrose metabolism’ pathway. Meanwhile, a total of 16 differentially expressed miRNAs (DEMs) were shared between ‘NAU-DY’ and ‘NAU-YH’ (small circular), whereas 12 miRNAs exhibited specific differential expression in ‘NAU-DY’. Association analysis indicated that miR393a- bHLH77 , miR167c- ARF8 , and miR5658- APL  might be key factors to biological phenomenon of taproot type variation, and a putative regulatory model of taproot thickening and development was proposed. Furthermore, several critical genes including  SUS1 ,  EXPB3 , and  CDC5  were characterized and profiled by RT-qPCR analysis.    Conclusion  This integrated study on the transcriptional and post-transcriptional profiles could provide new insights into comprehensive understanding of the molecular regulatory mechanism underlying taproot thickening in root vegetable crops.

Genome-wide sRNA and mRNA transcriptomic profiling insights into dynamic regulation of taproot thickening in radish (Raphanus sativus L.)