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.
Highlights
Auxin plays a critical role in inducing adventitious rooting in many plants
Illumina Solexa RNA paired-end sequencing and mapped reads To provide a comprehensive overview of mung bean and adventitious rooting in the seedlings at a transcriptional level, five cDNA libraries were constructed and sequenced from the hypocotyl tissues of 5 day-old seedlings harvested separately at 0 h (Con), after primary root excision and incubation in water for 6 h (Wat6) or 10 μM Indole-3-butyric acid (IBA) for 6 h (IBA6), and after primary root excision and incubation in water for 24 h (Wat24) or IBA for 24 h (IBA24) (Fig. 1), of which, the Con, Wat6, and Wat24 were previously sequenced in our previous study [39]
The changes in gene expression in response to IBA are complex, analysis from our results indicates that antioxidative processes and water deprivation responses were highly up-regulated, while lipoperoxidation of membranes were strongly alleviated by IBA treatment during the early stages of adventitious rooting
Summary
Auxin 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. Adventitious rooting acts as an alternative or supplement to seed propagation and is an important mechanism in response to stresses [2]. This method of vegetative propagation in plants has been widely used for the commercial production of woody forest and horticultural species [3]. Auxin acts as an effective inducer of adventitious roots in many plants and may interact with other endogenous factors or environmental stimuli during this process [4,5,6]. Auxin plays a crucial role in inducing cell dedifferentiation and root primordium formation, the exact mechanism of its action is still poorly understood
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