Genome-wide sRNA and mRNA transcriptomic profiling insights into dynamic regulation of taproot thickening in radish (Raphanus sativus L.)

Abstract

Background: Taproot 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. Results: A 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. Conclusion: This 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.

Integration of Physiological, Transcriptomic and Metabolomic Reveals Molecular Mechanism of Paraisaria dubia Response to Zn2+ Stress

“…RSEM (http://deweylab.biostat.wisc.edu/rsem/, accessed on 11 September 2022) was used to quantify the abundance of target genes. Differential expression analysis was performed using DEGs with |log2(foldchange)| ≥ 1 and p ≤ 0.05 as criteria for significantly differentially expressed genes [28]. In addition, the GO functional enrichment and KEGG pathway analyses were conducted (significantly enriched DEGs with Bonferroni-corrected p ≤ 0.05) using Goatools (https://github.com/tanghaibao/Goatools, accessed on 11 September 2022) and KOBAS (http://kobas.cbi.pku.edu.cn/home.do, accessed on 11 September 2022).…”

Radish (Raphanus Sativus): Potential antioxidant role of bioactive compounds extracted from radish leaves - A review

“…Since ancient times it has been used against many toxicants as a natural drug in folk medicine 13 . It has root part that is main edible organ 14 and leave part, which in dried form are effective as functional foods 15 . The Major nutritional components as g/100 g "fresh weight" and Micronutrients as μg/g of fresh weight of Radish are shown in Table 1 16 .…”

Transcriptomic analysis of succulent stem development of Chinese kale (Brassica oleracea var. alboglabra Bailey) and its synthetic allotetraploid via RNA sequencing

“…The genetic mechanism and regulation of succulent stem formation in Chinese kale is still unclear. Therefore, the genetic mechanism of stem formation of Chinese kale and its hybrids could reference from that of storage organ formation in other crops, e.g., potato tubers (Kondhare et al, 2020;Kolachevskaya et al, 2021;Kondhare et al, 2021;Saidi and Hajibarat, 2021), radish taproot (Yu et al, 2016;Xie et al, 2018;Xie et al, 2020), sweetpotato tuberous root (Zierer et al, 2021), lotus rhizomes (Yang et al, 2015), the bolting stem of flowering Chinese cabbage (Huang et al, 2017;Kou et al, 2021;Ou et al, 2022), etc. Plant hormones such as gibberellin (GA), abscisic acid (ABA), cytokinin (CTK) and auxin (AUX) are important regulatory factors of plant growth and development, and play an important role in the formation of storage organs (Pieterse et al, 2012). GA is a cyclic diterpenoid hormone, which is involved in the growth and development of stem, flowering and fruiting in higher plants during their entire life cycle (Hedden, 2008).…”

“…The genetic mechanism and regulation of succulent stem formation in Chinese kale is still unclear. Therefore, the genetic mechanism of stem formation of Chinese kale and its hybrids could reference from that of storage organ formation in other crops, e.g., potato tubers ( Kondhare et al., 2020 ; Kolachevskaya et al, 2021 ; Kondhare et al., 2021 ; Saidi and Hajibarat, 2021 ), radish taproot ( Yu et al., 2016 ; Xie et al., 2018 ; Xie et al., 2020 ), sweetpotato tuberous root ( Zierer et al., 2021 ), lotus rhizomes ( Yang et al., 2015 ), the bolting stem of flowering Chinese cabbage ( Huang et al., 2017 ; Kou et al., 2021 ; Ou et al., 2022 ), etc.…”

“…At the same time, RNA-seq has also been used to study the development mechanism of plant storage organs. For example, key genes for taproot thickening in radish were identified from three advanced inbred lines with different root diameters by analyzing transcriptome data ( Xie et al., 2020 ). RNA-seq was used to reveal that the formation of storage roots of sweet potato is related to cambium development, starch accumulation and endogenous hormones ( Dong et al., 2019 ).…”