RNA-Seq and iTRAQ reveal multiple pathways involved in storage root formation and development in sweet potato (Ipomoea batatas L.)

Abstract

Background Sweet potato ( Ipomoea batatas L.) is the sixth most important food crop in the world. The formation and development of storage roots in sweet potato is a highly complicated and genetically programmed process. However, the underlying mechanisms of storage root development have not yet been elucidated. Results To better understand the molecular mechanisms involved in storage root development, a combined analysis of the transcriptome and proteome of sweet potato fibrous roots (F) and storage roots at four different stages (D1, D3, D5 and D10) was performed in the present study. A total of 26,273 differentially expressed genes were identified in a comparison between the fibrous root library and four storage root libraries, while 2558 proteins showed a 1.0-fold or greater expression difference as indicated by isobaric tags for relative and absolute quantitation (iTRAQ) analysis. The combination of the transcriptome and proteome analyses and morphological and physiological data revealed several critical pathways involved in storage root formation and development. First, genes/proteins involved in the development of meristems/cambia and starch biosynthesis were all significantly upregulated in storage roots compared with fibrous roots. Second, multiple phytohormones and the genes related to their biosynthesis showed differential expression between fibrous roots and storage roots. Third, a large number of transcription factors were differentially expressed during storage root initiation and development, which suggests the importance of transcription factor regulation in the development of storage roots. Fourth, inconsistent gene expression was found between the transcriptome and proteome data, which indicated posttranscriptional regulatory activity during the development of storage roots. Conclusion Overall, these results reveal multiple events associated with storage root development and provide new insights into the molecular mechanisms underlying the regulatory networks involved in storage root development. Electronic supplementary material The online version of this article (10.1186/s12870-019-1731-0) contains supplementary material, which is available to authorized users.

Integrative Transcriptomic and Proteomic Analyses of Molecular Mechanism Responding to Salt Stress during Seed Germination in Hulless Barley

“…The GO and KEGG pathway analysis showed the complexity of molecular mechanisms in response to salt stress during the seed germination stage. The correlation between the transcriptome and proteome profiles varies with species, response environments, and different stages of growth and development [34][35][36]. In this study, the r values indicated a weak correlation between the transcriptome and proteome profiles under salt stress.…”

Comparative transcriptome analysis of roots at different development stages reveals the mechanism of root expansion of Callerya speciosa Champ.

“…Our transcriptome data showed 9 AP2-EREBP TFs were upregulated during the process of tuberous root development, especially at the late stage ( Fig. 3 [11]. In this study, obvious changes were detected in the expression of genes related to auxins, CKs, GA, ABA, ethylene, JA and BRs in TRs, and majority of these genes were up-regulated in more than one tuberous development stage (Table 2 and Additional file 11: Table S6).…”

“…The initiation and development of storage roots constitute a highly complicated process that involves multiple pathways, which regulate the development of secondary anomalous cambia and the accumulation of starch, sucrose and other chemical components [11]. Accordingly, our study showed that carbohydrate metabolism, which mainly involved metabolic pathways (ko01100), starch and sucrose metabolism (ko00500) and biosynthesis of secondary metabolites (ko01110), was identified to the most important pathway during tuberous root development ( Fig.…”

“…Endogenous phytohormones are also closely related to the initiation and development of tuberous roots. The synergistic actions of various phytohormones finally result in the bulking of tuberous roots, such as auxin (IAA), cytokinins (CKs), abscisic acid (ABA), gibberellin (GAs), ethylene and jasmonic acid (JA) [11].Auxins can be considered as a general coordinator of growth and development, who play an important role in tuberization and stress resistance [12], proliferation of metaxylem and cambium cells, cell expansion [13]. CKs control numerous developmental processes throughout the plant life cycle, including gametogenesis, root meristem specification, vascular development, shoot and root growth, meristem homeostasis, senescence, and so on [14].…”

“…Many key genes regulating storage root formation, especially transcription factors (TFs), have been intensively studied. Several MADS-box genes (IbMADS1, 3,4,10,79;IbMBP1~9;IbAGL17,20;StMADS1,3,11,13,16,29;SRD1) have been found to significantly express in root tissues of sweet potato and potato, and their possible functions in tuber development have subsequently been studied [13,17]. Three sweet potato class 1 knotted1-like homeobox (KNOX1) genes (Ibkn1, Ibkn2 and Ibkn3) all expressed in the storage roots, but only Ibkn1 and Ibkn2 were obviously up-regulated in storage roots [18].…”