Abstract
BackgroundTaproot is the main edible organ and ultimately determines radish yield and quality. However, the precise molecular mechanism underlying taproot thickening awaits further investigation in radish. Here, RNA-seq was performed to identify critical genes involved in radish taproot thickening from three advanced inbred lines with different root size.ResultsA total of 2606 differentially expressed genes (DEGs) were shared between ‘NAU-DY’ (large acicular) and ‘NAU-YB’ (medium obovate), which were significantly enriched in ‘phenylpropanoid biosynthesis’, ‘glucosinolate biosynthesis’, and ‘starch and sucrose metabolism’ pathway. Meanwhile, a total of 16 differentially expressed miRNAs (DEMs) were shared between ‘NAU-DY’ and ‘NAU-YH’ (small circular), whereas 12 miRNAs exhibited specific differential expression in ‘NAU-DY’. Association analysis indicated that miR393a-bHLH77, miR167c-ARF8, and miR5658-APL might be key factors to biological phenomenon of taproot type variation, and a putative regulatory model of taproot thickening and development was proposed. Furthermore, several critical genes including SUS1, EXPB3, and CDC5 were characterized and profiled by RT-qPCR analysis.ConclusionThis integrated study on the transcriptional and post-transcriptional profiles could provide new insights into comprehensive understanding of the molecular regulatory mechanism underlying taproot thickening in root vegetable crops.
Highlights
Taproot is the main edible organ and determines radish yield and quality
Heatmap clustering of differentially expressed miRNAs (DEMs) was shown in Additional file 1: Figure S1, and the results indicated that the expression levels of those miRNAs exhibited characteristics of dynamic change during radish taproot thickening
In this study, all COBRA genes were up-regulated, whereas all COBRA-like genes were down-regulated in S3 vs S1 pair comparison between ‘NAU-DY’ and ‘NAU-YB’, suggesting that COBRA might play a critical role on cell elongation for taproot thickening in radish. This is the first report on integrative analysis of transcriptome and miRNA in three radish advanced inbred lines during taproot thickening
Summary
Taproot is the main edible organ and determines radish yield and quality. The precise molecular mechanism underlying taproot thickening awaits further investigation in radish. RNA-seq was performed to identify critical genes involved in radish taproot thickening from three advanced inbred lines with different root size. With the rapid development of ‘omics’ methodology, RNA-seq has become a valuable strategy for systematical identification of differentially regulated genes, miRNAs, and regulation pathways in different tissues, organs, and developmental stages in several plant species, such as Rosa chinensis [8], Glycine max [9], Citrus sinensis [10], Myrica rubra [11], Solanum lycopersicum [12], and R. sativus [13]. There is no report on identification of genes involved in taproot development in different cultivars, which limits the genetic improvement and germplasm innovation of radish cultivars
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