Abstract
BackgroundYam 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.ResultsA 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.ConclusionThe 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.
Highlights
Yam tuber is a storage organ, derived from the modified stem
Overview of RNA-Seq dynamics and small RNA sequencing To identify the regulation of mRNA and miRNAs coregulatory network during tuber expansion, the RNA-Seq and small RNA were examined during tuber initiation stage (GH16_I) and expansion stage (GH16_E) (Fig. 1)
Similar species distributions were observed for yam tuber in previous research [25], 8229 (16.2%) genes in D. zingiberensis had the most hits from Elaeis guineensis, followed by Phoenix dactylifera (6857, 13.5%), Musa acuminate (2692, 5.3%)
Summary
Yam tuber is a storage organ, derived from the modified stem. 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. Yams (Dioscorea spposita) are monocotyledonous plants belonging to the family Dioscoreaceae, and tuber is its harvested organ. Endogenous hormones including gibberellins (GA), acetic acid (IAA) and abscisic acid (ABA) performed a key role at the beginning of tuber expansion stage, and trans-zeatin (tZ), jasmonic acid (JA) were involved in tuber expansion [2, 7, 8]. Exogenous hormones have been used to study the mechanism of tuber expansion, GAs could promote tuber expansion and yield through in vitro and in vivo treatment [9, 10]. Fundamental knowledges of endogenous metabolic networks are poor in tuber expansion
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