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

• Main Authors: Yang Xie, Jiali Ying, Liang Xu, Yan Wang, Junhui Dong, Yinglong Chen, Mingjia Tang, Cui Li, Everlyne M’mbone Muleke, Liwang Liu
• Format: Article
• Language: English
• Published: BMC 2020-08-01
• Series: BMC Plant Biology
• Subjects: DEGs; DEMs; Radish; RT-qPCR; Taproot thickening
• Online Access: http://link.springer.com/article/10.1186/s12870-020-02585-z

Abstract 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.