Abstract
Rehmannia glutinosa, an herb of the Scrophulariaceae family, is widely cultivated in the Northern part of China. The tuberous root has well-known medicinal properties; however, yield and quality are threatened by abiotic and biotic stresses. Understanding the molecular process of tuberous root development may help identify novel targets for its control. In the present study, we used Illumina sequencing and de novo assembly strategies to obtain a reference transcriptome that is relevant to tuberous root development. We then conducted RNA-seq quantification analysis to determine gene expression profiles of the adventitious root (AR), thickening adventitious root (TAR), and the developing tuberous root (DTR). Expression profiling identified a total of 6794 differentially expressed unigenes during root development. Bioinformatics analysis and gene expression profiling revealed changes in phenylpropanoid biosynthesis, starch and sucrose metabolism, and plant hormone biosynthesis during root development. Moreover, we identified and allocated putative functions to the genes involved in tuberous root development, including genes related to major carbohydrate metabolism, hormone metabolism, and transcription regulation. The present study provides the initial description of gene expression profiles of AR, TAR, and DTR, which facilitates identification of genes of interest. Moreover, our work provides insights into the molecular mechanisms underlying tuberous root development and may assist in the design and development of improved breeding schemes for different R. glutinosa varieties through genetic manipulation.
Highlights
Rehmannia glutinosa, commonly known as the Chinese foxglove (Scrophulariaceae), is native to China, Japan, and Korea
Establishment of a Root Reference Transcriptome for Rehmannia We generated a total of 81,003 unique sequences from the cDNA library constructed from the adventitious root (AR), thickening adventitious root (TAR), and developing tuberous root (DTR) of Rehmannia by using the Illumina sequencing platform
The global gene expression profiles of ARs, TARs, and DTRs (Supplementary Table S3) revealed the dynamic characteristics of the developing root transcriptome. This RNA-seq based transcriptome analysis provides an initial view of the tuberous root development process, assisting in the identification of candidate genes related to hormone biosynthesis, sugar metabolism, and Transcription Factors (TFs), paving the way for further elucidation of the molecular mechanism underlying tuberous root development
Summary
Commonly known as the Chinese foxglove (Scrophulariaceae), is native to China, Japan, and Korea. R. glutinosa has been commercially cultivated in China for over a thousand years, and several high yielding cultivars such as “Beijing No 1” and “85-5” were developed by Chinese breeders through cross breeding and selection. The cultivar “85-5,” which was developed in the 1980s, is characterized by big tuberous roots and high yield. It has an average fresh weight of 24.5 tons per hectare (Li et al, 2007), which is comparable with that of sweet potato, a globally important food crop. Understanding of the molecular process of tuberous root development will greatly facilitate the genetic improvement of Rehmannia in terms of yield, quality, and medicinal values
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