Transcriptome Profiling of Taproot Reveals Complex Regulatory Networks during Taproot Thickening in Radish (Raphanus sativus L.)

Abstract

Radish (Raphanus sativus L.) is one of the most important vegetable crops worldwide. Taproot thickening represents a critical developmental period that determines yield and quality in radish life cycle. To isolate differentially expressed genes (DGEs) involved in radish taproot thickening process and explore the molecular mechanism underlying taproot development, three cDNA libraries from radish taproot collected at pre-cortex splitting stage (L1), cortex splitting stage (L2), and expanding stage (L3) were constructed and sequenced by RNA-Seq technology. More than seven million clean reads were obtained from the three libraries, from which 4,717,617 (L1, 65.35%), 4,809,588 (L2, 68.24%) and 4,973,745 (L3, 69.45%) reads were matched to the radish reference genes, respectively. A total of 85,939 transcripts were generated from three libraries, from which 10,450, 12,325, and 7392 differentially expressed transcripts (DETs) were detected in L1 vs. L2, L1 vs. L3, and L2 vs. L3 comparisons, respectively. Gene Ontology and pathway analysis showed that many DEGs, including EXPA9, Cyclin, CaM, Syntaxin, MADS-box, SAUR, and CalS were involved in cell events, cell wall modification, regulation of plant hormone levels, signal transduction and metabolisms, which may relate to taproot thickening. Furthermore, the integrated analysis of mRNA-miRNA revealed that 43 miRNAs and 92 genes formed 114 miRNA-target mRNA pairs were co-expressed, and three miRNA-target regulatory networks of taproot were constructed from different libraries. Finally, the expression patterns of 16 selected genes were confirmed using RT-qPCR analysis. A hypothetical model of genetic regulatory network associated with taproot thickening in radish was put forward. The taproot formation of radish is mainly attributed to cell differentiation, division and expansion, which are regulated and promoted by certain specific signal transduction pathways and metabolism processes. These results could provide new insights into the complex molecular mechanism underlying taproot thickening and facilitate genetic improvement of taproot in radish.

Integrated mRNA and miRNA transcriptome analysis reveals a regulatory network for tuber expansion in Chinese yam (Dioscorea opposita)

“…In this study, alpha-amylase, betaamylase, and isoamylase were up-regulated (Additional file 2: Table S1), which is similar to increase in beta-amylase activity in swollen taproot in radish [35], where starch content decreased during the tuber expansion stage [15], and some sucrose metabolism genes were detected during expansion stage, including SuSy, SPS, INV, and invertase inhibitor (Additional file 2: Table S1). Evidence shows that sucrose can be converted to starch in storage root by SuSy and AGPase, which means that they play a vital role in the early stage of radish expansion [35]. The SuSy gene was down-regulated during expansion stage.…”

“…In this study, based on our RNA-Seq and small RNA analysis, previous transcriptomics analysis and results of other tuber crops, a putative model of regulatory network associated with yam tuber expansion was proposed (Fig. 8) [35,36,52]. DELLA controls cell expansion and cell division in hypocotyl, shoot, root, and floral induction [57].…”

“…Starch and sucrose are considered to be one of the significant carbohydrates source, in which expansion tubers are highly coordinated with starch and sucrose metabolism genes in potato, radish, and lotus identified by transcriptome analysis [22,35,37]. In this study, alpha-amylase, betaamylase, and isoamylase were up-regulated (Additional file 2: Table S1), which is similar to increase in beta-amylase activity in swollen taproot in radish [35], where starch content decreased during the tuber expansion stage [15], and some sucrose metabolism genes were detected during expansion stage, including SuSy, SPS, INV, and invertase inhibitor (Additional file 2: Table S1). Evidence shows that sucrose can be converted to starch in storage root by SuSy and AGPase, which means that they play a vital role in the early stage of radish expansion [35].…”

“…In this study, XTH, expansin, extension, CKS, ftsHs, CDC5, CDC, CDKs, and CDKIs involved in cell division, cell expansion and cell cycles were differentially regulated during expansion stage. These differentially regulated genes involved in cell wall and cell cycle metabolism were identified in Arabidopsis, Rehmannia glutinosa, and radish[35,36,52].Transcription factors regulationTranscription factors have been identified to play an essential role in the regulation of plant growth, development, and secondary metabolism. Most transcription factors have been identified to play critical roles in organogenesis, including MADS, bHLH, and GRAS.…”

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.…”