Transcriptomic analysis reveals the gene expression profile that specifically responds to IBA during adventitious rooting in mung bean seedlings

Abstract

BackgroundAuxin plays a critical role in inducing adventitious rooting in many plants. Indole-3-butyric acid (IBA) is the most widely employed auxin for adventitious rooting. However, the molecular mechanisms by which auxin regulate the process of adventitious rooting are less well known.ResultsThe RNA-Seq data analysis indicated that IBA treatment greatly increased the amount of clean reads and the amount of expressed unigenes by 24.29 % and 27.42 % and by 4.3 % and 5.04 % at two time points, respectively, and significantly increased the numbers of unigenes numbered with RPKM = 10-100 and RPKM = 500-1000 by 13.04 % and 3.12 % and by 24.66 % and 108.2 % at two time points, respectively. Gene Ontology (GO) enrichment analysis indicated that the enrichment of down-regulated GOs was 2.87-fold higher than that of up-regulated GOs at stage 1, suggesting that IBA significantly down-regulated gene expression at 6 h. The GO functional category indicated that IBA significantly up- or down-regulated processes associated with auxin signaling, ribosome assembly and protein synthesis, photosynthesis, oxidoreductase activity and extracellular region, secondary cell wall biogenesis, and the cell wall during the development process. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment indicated that ribosome biogenesis, plant hormone signal transduction, pentose and glucuronate interconversions, photosynthesis, phenylpropanoid biosynthesis, sesquiterpenoid and triterpenoid biosynthesis, ribosome, cutin, flavonoid biosynthesis, and phenylalanine metabolism were the pathways most highly regulated by IBA. A total of 6369 differentially expressed (2-fold change > 2) unigenes (DEGs) with 3693 (58 %) that were up-regulated and 2676 (42 %) down-regulated, 5433 unigenes with 2208 (40.6 %) that were up-regulated and 3225 (59.4 %) down-regulated, and 7664 unigenes with 3187 (41.6 %) that were up-regulated and 4477 (58.4 %) down-regulated were detected at stage 1, stage 2, and between stage 1 and stage 2, respectively, suggesting that IBA treatment increased the number of DEGs. A total of 143 DEGs specifically involved in plant hormone signaling and 345 transcription factor (TF) genes were also regulated by IBA. qRT-PCR validation of the 36 genes with known functions indicated a strong correlation with the RNA-Seq data.ConclusionsThe changes in GO functional categories, KEGG pathways, and global DEG profiling during adventitious rooting induced by IBA were analyzed. These results provide valuable information about the molecular traits of IBA regulation of adventitious rooting.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2372-4) contains supplementary material, which is available to authorized users.

De novo sequencing and comparative transcriptome analysis of adventitious root development induced by exogenous indole-3-butyric acid in cuttings of tetraploid black locust

“…Among these, several genes were differentially expressed in the AR formation phase, with higher expression in IBA-treated cuttings than in CK, including ACC oxidase 1 (ACO1). Interestingly, the expression of these genes is induced by exogenous auxin in the rooting-competent cuttings of two distantly related forest species, and there are some similar reports that ACO genes lead to AR formation in mung bean and tomato [ 46 , 47 ]. It appears that IBA-induced ethylene production may contribute to the stimulation of adventitious rooting [ 47 ].…”

Dynamic Transcriptome Analysis Reveals Uncharacterized Complex Regulatory Pathway Underlying Dose IBA-Induced Embryogenic Redifferentiation in Cotton

“…Chen et al [18] found that an MSB (MS inorganic salt + B5 vitamin) medium supplemented with IBA could directly induce embryogenic calli and that appropriate concentrations of KT could promote the effect of IBA. IBA is used to induce root organogenesis [19], but studies have found that either IBA alone or in combination with KT can directly induce a certain amount of embryogenic callus from the hypocotyl segment. More extensive experiments are yet to be done to determine the mechanism through which IBA acts.…”

Transcriptomic profiling provides molecular insights into hydrogen peroxide-induced adventitious rooting in mung bean seedlings

“…In this experiment, the hypocotyl tissues that were treated with 10 mM H 2 O 2 for 6 h or 24 h, designated as HO6 and HO24, which represent the induction stage and initiation stage of adventitious root development in mung bean seedlings, respectively [ 29 , 30 ], were separately sampled for total RNA extraction, cDNA library construction, and Illumina Solexa RNA paired-end sequencing. The sequencing data and mapping results are listed in Table 1 .…”

“…The sequencing data and mapping results are listed in Table 1 . This sequencing generated approximately 93% of the high-quality reads from the samples, and approximately 93% of the quality reads mapped uniquely to the reference sequences that were constructed in our previous study [ 29 , 30 ]. Using the Chrysalis cluster module of TRINITY, we identified a total of 78,697 unigenes from all the samples [ 29 , 30 ].…”

“…In our previous studies, we reported that exogenous H 2 O 2 strongly promoted adventitious rooting in mung bean hypocotyl cuttings [ 6 ]. Recently, we characterized the mung bean transcriptome and gene expression profiles during the induction and initiation stages of adventitious rooting in water-treated [ 29 ] or IBA-treated [ 30 ] mung bean hypocotyl cuttings using RNA-Seq technology. In the present study, RNA-Seq technology and qRT-PCR were exploited to reveal the transcriptome of H 2 O 2 promotion adventitious rooting in mung bean hypocotyl cuttings.…”