Comparative transcriptome analysis reveals the role of auxin in the regulation of turnip hypocotyl-tuber formation

Brassica rapa is a plant comprising of numerous commonly grown subspecies with distinct morphological or physiological characteristics. Among them, the unique hypocotyl-tuber of turnip (Brassica rapa ssp. rapifera) is an important agronomic trait, but the molecular mechanisms underlying development of turnip hypocotyl-tuber has rarely been explored. Here, we compared the difference in morphological and anatomical characteristics between turnip and pak choi (Brassica rapa ssp. chinensis). Comparative transcriptomic analyses of hypocotyls at different growth stages between these two subspecies revealed that the expression pattern of auxin-related genes was closely related to the formation of the hypocotyl-tuber. The immunolocalization of IAA showed that the local distribution of auxin differed from the two subspecies at different growth stages, and the exogenous auxin treatments further confirmed the effect of auxin in turnip hypocotyl enlargement. We propose a possible mechanism that auxin regulates the expansion of secondary xylem through uneven distribution among different tissues to affect the developmental direction of hypocotyl. These results provided new information about the mechanism of auxin underlying turnip hypocotyl enlargement and enabled a more comprehensive understanding of plant storage organ development.