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

Abstract

Background Yam tuber is a storage organ, derived from the modified stem. Tuber expansion is a complex process, and depends on the expressions of genes that can be influenced by environmental and endogenous factors. However, little is known about the regulatory mechanism of tuber expansion. In order to identify the genes and miRNAs involved in tuber expansion, we examined the mRNAs and small RNAs in Dioscorea opposita (Chinese yam) cv. Guihuai 16 tuber during its initiation and expansion stages. Results A total of 14238 differentially expressed genes in yam tuber at its expansion stage were identified by using RNA sequencing technology. Among them, 5723 genes were up-regulated, and 8515 genes were down-regulated. Functional analysis revealed the coordination of tuber plant involved in processes of cell events, metabolism, biosynthesis, and signal transduction pathways at transcriptional level, suggesting that these differentially expressed genes are somehow involved in response to tuber expansion, including CDPK, CaM, CDL, SAUR, DELLA, SuSy, and expansin. In addition, 541 transcription factor genes showed differential expression during the expansion stage at transcriptional level. MADS, bHLH, and GRAS were involved in cell differentiation, division, and expansion, which may relate to tuber expansion. Noteworthy, data analysis revealed that 22 known tuber miRNAs belong to 10 miRNA families, and 50 novel miRNAs were identified. The integrated analysis of miRNA-mRNA showed that 4 known miRNAs and 11 genes formed 14 miRNA-target mRNA pairs were co-expressed in expansion stage. miRNA160, miRNA396, miRNA535 and miRNA5021 may be involved in complex network to regulate cell division and differentiation in yam during its expansion stage. Conclusion The mRNA and miRNA datasets presented here identified a subset of candidate genes and miRNAs that are putatively associated with tuber expansion in yam, a hypothetical model of genetic regulatory network associated with tuber expansion in yam was put forward, which may provide a foundation for molecular regulatory mechanism researching on tuber expansion in Dioscorea species.

Hormonal and transcriptional analyses provides new insights into the molecular mechanisms underlying root thickening and isoflavonoid biosynthesis in Callerya speciosa (Champ. ex Benth.) Schot

“…4 a). Overall, our result suggested that various phytohormones play roles at different ages of storage root development, which were supported by the previous studies in sweet potato 10 , radish 24 and yam 25 . Nevertheless, the synergistic effect of phytohormones on C. speciosa tuberous root formation and development warrants further investigation.…”

“…The activity of beta-amylase (BAMY) could decrease by silencing StBAM1 and StBAM9 in potato, and StBAM9 interacted with StBAM1 on the starch granules 33 . Genes encoding BAMY were highly expressed at the expansion stage of yam tuberous roots 25 . In this study, BAM9 was highly expressed at the mid-rapid thickening stage (18 MAG), whereas BAM1 had a higher expression at 6 MAG (Fig.…”

“…Most transcripts encoding Aux/IAA genes responsible for cambium secondary differentiation during radish taproot thickening were down-regulated, while those encoding ARFs genes and two SAUR transcripts were up-regulated at the cortex splitting and expanding stage 24 . Researchers suggested that the endogenous IAA content and genes involved in auxins signaling pathway, including Aux/IAAs and ARFs were highly expressed in expansion stage 20 , 25 . Congruent with previous studies, 6 Aux/IAAs , 4 SAURs, 2 ARFs and 2 CH3s , were highly expressed at the rapid thickening stage (12 and 18 MAG) in this study (Fig.…”

An underutilized orphan tuber crop—Chinese yam : a review

“…It is not yet clear if these genes also play a role in yam. Transcriptome analysis to compare tubers during initiation and expansion revealed several differentially expressed genes that may be involved in tuber expansion (Zhou et al 2020). These included genes related to MAP kinase signaling, starch and sucrose metabolism, hormone biosynthesis and signaling, as well as transcription factors and miRNAs involved in these processes (Zhou et al 2020).…”

Tumorous Stem Development of Brassica Juncea: A Complex Regulatory Network of Stem Formation and Identification of Key Genes in Glucosinolate Biosynthesis

“…For example, the single cell-type root hair transcriptome was less complex than the transcriptome of multiple cell-type primary roots without root hairs for maize [ 23 ]. mRNA and miRNA sequencing data also uncovered a regulatory network of tuber expansion in yam [ 24 ]. Moreover, the transcriptome sequencing technology provides a more comprehensive characterization and quantitative description compared with the gene chip technology [ 25 ].…”