Radish (Raphanus sativus L.) is an important root vegetable crop belonging to the Brassicaceae family. Anthocyanin rich radish varieties are popular among consumers because of their bright color and high nutritional value. However, the underlying molecular mechanism responsible for skin and flesh induce anthocyanin biosynthesis in transient overexpression, gene silencing and transcriptome sequencing were used to verify its function in radish anthocyanin accumulation, radish remains unclear. Here, we identified a long noncoding RNA LINC15957, overexpression of LINC15957 was significantly increased anthocyanin accumulation in radish leaves, and the expression levels of structural genes related to anthocyanin biosynthesis were also significantly increased. Anthocyanin accumulation and expression levels of anthocyanin biosynthesis genes were significantly reduced in silenced LINC15957 flesh when compared with control. By the transcriptome sequencing of the overexpressed LINC15957 plants and the control, 5,772 differentially expressed genes were identified. A total of 3,849 differentially expressed transcription factors were identified, of which MYB, bHLH, WD40, bZIP, ERF, WRKY and MATE were detected and differentially expressed in the overexpressed LINC15957 plants. KEGG enrichment analysis revealed the genes were significant enriched in tyrosine, L-Phenylalanine, tryptophan, phenylpropanol, and flavonoid biosynthesis. RT-qPCR analysis showed that 8 differentially expressed genes (DEGs) were differentially expressed in LINC15957-overexpressed plants. These results suggested that LINC15957 involved in regulate anthocyanin accumulation and provide abundant data to investigate the genes regulate anthocyanin biosynthesis in radish.
Radish is an important root vegetable that is widely grown in Asia. The root-knot nematode (RKN) Meloidogyne incognita seriously affects the growth and development of radish root and causes poor appearance quality. However, the molecular mechanism of radish response to RKNs remains poorly understood. In this study, a total of 220 lncRNAs, 1144 mRNAs, 20 miRNAs and 153 proteins were differential expressed between the RKN-infected and WT samples. Correlation analysis of all DEPs compared with all DGEs showed that 8 mRNAs-DEPs showed a changed abundance. The results showed that 18 DEmiRNAs have 167 target DEGs in 220 miRNA-target modules and 29 DElncRNAs were predicted as putative targets of 16 DEmiRNAs in 37 miRNA-target modules. In all, 6 DGEs in the ABA pathway and 2 DGEs in the JA pathway were identified under RKN infection, respectively. The four regulatory networks of lncRNA-miRNA-mRNA were constructed in response to RKN infection. qRT-PCR analysis found that the expression pattern of 6 DElncRNAs, 6 DEmRNAs, 6 DEmiRNAs and 6 DEPs were consistent with sequencing results. These results provide a theoretical basis for studying the molecular mechanism of radish in response to M. incognita and breeding resistant varieties to this nematode.
Abstract Background The transition from the vegetative to reproductive growth is an important stage in radish life cycle ( Raphanus sativus L.). However, the molecular mechanism of radish bolting and flowering is still unclear. To obtain new insight into the genomic variation, population structure, genetic diversity and molecular regulation mechanism of flowering time, genome resequencing and transcriptome sequencing were conducted between two cultivars with extreme differences in flowering time. Results In this study, a total of 366,679 single nucleotide polymorphisms (SNPs) and 97,973 insertion-deletion (InDel) markers were identified based on genome sequences between ‘YZH’ and ‘XHT’. In all, 53,343 SNPs and 4,257 InDels were detected in two cultivars by transcriptome. Among the InDel variations, 85 genomic and 15 transcriptomic InDels were newly developed and validated PCR. Population structure and phylogenetic relationship revealed that the radish cultivars from northern China were clustered together and the southwest China cultivars were clustered together. RNA-Seq analysis revealed that 10,983 differentially expressed genes (DEGs) were identified between the two cultivars, of which 5,020 were upregulated and 5,983 were downregulated. In total, 145 flowering time-related DGEs were detected, most of which were involved in flowering time integrator, circadian clock/photoperiod autonomous, and vernalization pathways. In flowering time-related DGEs region, 150 transcriptomic SNPs and 9 InDels were obtained. RT-qPCR displayed that the expression pattern of ten DEGs were consistent with the results obtained by RNA-Seq analysis. Conclusions The large amount of SNPs and InDels identified in this study will provide a valuable marker resource for radish genetic and genomic studies. The detected flowering time-related DGEs could provide fundamental insight into bolting and flowering regulatory networks and accelerate further investigating molecular mechanisms underlying the transition from vegetative to reproductive growth in radish.
The yield and quality of radish is seriously affect by the premature bolting and flowering, the identification and characterization of long non-coding RNAs (lncRNAs) have yet not been explored. A total of 5315 differentially expressed genes (DGEs), 263 DElncRNAs and 38 DEmiRNAs were detected in two stages. GO analysis found that many flower DGEs associated with reproductive process, response to hormone and pollination were enriched. In total, 202 DElncRNAs and 257 DElncRNAs were found to have potential cis and trans-regulatory effects on 572 DEmRNAs and 3902 DGEs, respectively. A total of 93 and 82 DEGs were predicted as putative targets of 31 DEmiRNAs and 29 DEmiRNAs, respectively. Five mRNA-lncRNA-miRNA regulatory pairs involved in flowering time regulation were constructed, including miRNA156a-5p, miRNA399b, miRNA novel-23, miRNA164c-5p and miRNA165a-5p. These findings provide a theoretical foundation for further elucidating the molecular regulation mechansim of mRNAs, lncRNAs and miRNAs in bolting and flowering in radish.
Single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) are the most abundant genetic variations and widely distribute across the genomes in plant. Development of SNP and InDel markers is a valuable tool for genetics and genomic research in radish (Raphanus sativus L.).In this study, a total of 366,679 single nucleotide polymorphisms (SNPs) and 97,973 insertion-deletion (InDel) markers were identified based on genome resequencing between 'YZH' and 'XHT'. In all, 53,343 SNPs and 4,257 InDels were detected in two cultivars by transcriptome sequencing. Among the InDel variations, 85 genomic and 15 transcriptomic InDels were newly developed and validated PCR. The 100 polymorphic InDels markers generated 207 alleles among 200 Chinese radish germplasm, with an average 2.07 of the number of alleles (Na) and with an average 0.33 of the polymorphism information content (PIC). Population structure and phylogenetic relationship revealed that the radish cultivars from northern China were clustered together and the southwest China cultivars were clustered together. RNA-Seq analysis revealed that 11,003 differentially expressed genes (DEGs) were identified between the two cultivars, of which 5,020 were upregulated and 5,983 were downregulated. In total, 145 flowering time-related DGEs were detected, most of which were involved in flowering time integrator, circadian clock/photoperiod autonomous, and vernalization pathways. In flowering time-related DGEs region, 150 transcriptomic SNPs and 9 InDels were obtained.The large amount of SNPs and InDels identified in this study will provide a valuable marker resource for radish genetic and genomic studies. The SNPs and InDels within flowering time-related DGEs provide fundamental insight into for dissecting molecular mechanism of bolting and flowering in radish.
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