Comparative proteomic analysis provides insight into a complex regulatory network of taproot formation in radish ( Raphanus sativus L.)

Abstract

The fleshy taproot of radish is an important storage organ determining its yield and quality. Taproot thickening is a complex developmental process in radish. However, the molecular mechanisms governing this process remain unclear at the proteome level. In this study, a comparative proteomic analysis was performed to analyze the proteome changes at three developmental stages of taproot thickening using iTRAQ approach. In total, 1862 differentially expressed proteins (DEPs) were identified from 6342 high-confidence proteins, among which 256 up-regulated proteins displayed overlapped accumulation in S1 (pre-cortex splitting stage) vs. S2 (cortex splitting stage) and S1 vs. S3 (expanding stage) pairs, whereas 122 up-regulated proteins displayed overlapped accumulation in S1 vs. S3 and S2 vs. S3 pairs. Gene Ontology (GO) and pathway enrichment analysis showed that these DEPs were mainly involved in several processes such as “starch and sucrose metabolism”, “plant hormone signal transduction”, and “biosynthesis of secondary metabolites”. A high concordance existed between iTRAQ and RT-qPCR at the mRNA expression levels. Furthermore, association analysis showed that 187, 181, and 96 DEPs were matched with their corresponding differentially expressed genes (DEGs) in S1 vs. S2, S1 vs. S3, and S2 vs. S3 comparison, respectively. Notably, several functional proteins including cell division cycle 5-like protein (CDC5), expansin B1 (EXPB1), and xyloglucan endotransglucosylase/hydrolase protein 24 (XTH24) were responsible for cell division and expansion during radish taproot thickening process. These results could facilitate a better understanding of the molecular mechanism underlying taproot thickening, and provide valuable information for the identification of critical genes/proteins responsible for taproot thickening in root vegetable crops.

Root vegetables: tapping into root thickening for improved yields

An investigation into the proteins and genes responsible for taproot thickening in radish could help improve yields of root vegetables. The fleshy taproot of vegetables like radish are vital to food supplies worldwide, but the precise mechanisms behind healthy, high quality taproot formation, and thickening are unclear. Liwang Liu at Nanjing Agricultural University in Nanjing, China, and co-workers have identified several functional proteins and corresponding genes responsible for cell division in taproot growth and thickening. The team analyzed changes in protein expression at three different developmental stages of radish taproot. They identified 1862 differentially expressed proteins involved in several processes including sugar and starch metabolism, hormone signaling, and biosynthesis of metabolites. Their results provide fundamental insights into the regulation of taproot thickening in radish and could be expanded to other root vegetables.