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 14,238 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

“…4a). 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.…”

Next-Generation Sequencing Identification and Characterization of MicroRNAs in Dwarfed Citrus Trees Infected With Citrus Dwarfing Viroid in High-Density Plantings

“…Members of this transcription factor family are known to play important roles in flower and fruit development, plant architecture, and in the transitions from juvenile to adult stages and to flowering Yu et al, 2012). Even though miR535 is also known to target squamosa promoter-binding-like protein 3 (Shi et al, 2017;Zhou et al, 2020), our study identified rhomboid-like protein 1 as the target of miR535 in the roots (P_trifoliata_00066_mRNA_51.1). In Arabidopsis, a rhomboidlike protein was identified, providing evidence for the existence of regulated intramembrane proteolysis (RIP), a fundamental mechanism for controlling a wide range of cellular functions, in plants (Kanaoka et al, 2005).…”

Molecular Pharmacognosy in Daodi herbs

“…如NO处理下 石斛的DNA甲基化水平发生改变 [52] 、DNA甲基化水 平变异会影响菊花的生长和花的发育 [53] , DNA甲基化 通路在果实发育与成熟 [54] 、生物和非生物胁迫 [55,56] 、 根瘤发育和根瘤固氮 [57] 中也具有重要作用. 非编码 RNA也可参与生物表型、环境应激反应、代谢的调 控 [58,59] , 如茉莉酸甲酯处理下商陆miRNA可靶向茉莉 酸生物合成酶基因的转录 [60] ; 通过整合mRNA和miR-NA分析, 揭示山药块茎发育的基因调控模式, 发现 miRNA160、miRNA396、miRNA535和miRNA5021 可能参与了山药细胞分裂和分化的调控 [61] ; 并参与调 控萜类 [62] 、萜内酯类 [63] 、黄酮类 [64] 、皂苷类 [65] 成分 的生物合成. [66] .…”