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.

WITHDRAWN: Effect of Elevated CO2 on Photosynthetic Accumulation and Sucrose Metabolism-related Enzyme Activity and Gene Expression Patterns in Goji Berry (Lycium Barbarum L.)

“…However, after 120 days under eCO 2 , the activities of the above four sucrose metabolism-related enzymes increased signi cantly in leaves, whereas in fruit tissue, SS and SPS decreased signi cantly, AI increased, and NI showed no change. Sucrose and starch are the major end products of photosynthesis in most plants and they are also major carbon sources involved in the synthesis of other important structural and metabolic compounds, such as cellulose and proteins, respectively [27,38,39]. Additionally, only two types of enzyme can cleave sucrose in plants: sucrose invertase, and sucrose synthase (SS) [40].…”

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

“…XTH9, XTH7), and root cell elongation factor (e.g. COBRA) [35,39], which might determine cell size during taproot thickening. In addition, several transcription factors (TFs) were found to be involved in root development in other plants including rice, and Arabidopsis, and some TFs including bHLHs (e.g.…”

“…Meanwhile, CDC5 gene was crucial to cell cycle during the G2 period, and the phase transition of G2 to M (G2/ M) was affected in the AtCDC5-RNAi transformants [37], and AtCDC5-VIGS transformants died before bolting and accelerated cell death [38]. Interestingly, CDC5 was identified to be up-regulated during taproot thickening, whatever RNA-seq or iTRAQ-seq method, which would be play important role in cell division of taproot thickening in radish [13,35]. In this study, RT-qPCR validation result was approximately consistent with those of previous studies, and CDC5 showed high abundance expression at ES (Fig.…”

Characterization of the OFP Gene Family and its Putative Involvement of Tuberous Root Shape in Radish

“…Root shape and size are important traits that can influence the commercial quality of radishes, such as transportation efficiency, processing methods, and consumer appeal. Studies on radish tuberous root formation have been a hot topic recently, and have mainly focused on finding QTLs, differentially expressed genes or proteins related to storage root formation [5][6][7][8][9][10][11]. However, the developmental mechanisms underlying the beneficial alleles controlling root formation have not yet been fully elucidated.…”