Integration of metabolome and transcriptome analyses reveals the mechanism of anthocyanin accumulation in purple radish leaves

Pu, Quanming; He, Zihan; Xiang, Chengyong; Shi, Shun; Zhang, Lincheng; Yang, Peng

doi:10.1007/s12298-022-01245-w

Cited by 4 publications

(4 citation statements)

References 41 publications

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“…Furthermore, we pointed out the anthocyanin-related structural genes PAL, C4L, C4H, CHS, CHI, FLS, F3H, F3'H, DFR, LDOX, ANR, UGT, UFGT, ROMT, and 3GT that were associated with anthocyanin. Our result was consistent with Pu and co-workers showing that the expression pattern of structural genes (such as the ANS, DFR, CHS, F3H, PAL4, OMT1, and 4CL4) and key transcription factors (such as the TT8 and WRKYs) through RNA-seq and qRT-PCR analysis, was higher in purple radish leaves compared to green (Pu et al, 2022). Some genes may have several copies, as we identified different genes with the same annotation and coding for the same or similar products.…”

Section: Anthocyanin Accumulation Relatedness With Structural Gene Ex...supporting

confidence: 93%

Integrative HPLC profiling and transcriptome analysis revealed insights into anthocyanin accumulation and key genes at three developmental stages of black rice (Oryza sativa. L) caryopsis

Mackon,

Jeazet Dongho Epse Mackon,

Yao

et al. 2023

Front. Plant Sci.

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IntroductionAnthocyanins are plants' secondary metabolites belonging to the flavonoid class with potential health-promoting properties. They are greatly employed in the food industry as natural alternative food colorants for dairy and ready-to-eat desserts and pH indicators. These tremendous advantages make them economically important with increasing market trends. Black rice is a rich source of anthocyanin that can be used to ensure food and nutritional security around the world. However, research on anthocyanin accumulation and gene expression during rice caryopsis development is lacking.MethodsIn this study, we combined high-performance liquid chromatography (HPLC) and transcriptome analysis to profile the changes in anthocyanin content and gene expression dynamics at three developmental stages (milky, doughy, and mature).ResultsOur results showed that anthocyanin accumulation started to be visible seven days after flowering (DAF), increased rapidly from milky (11 DAF) to dough stage, then started decreasing after the peak was attained at 18 DAF. RNA-seq showed that 519 out of 14889, 477 out of 17914, and 1614 out of 18810 genes were uniquely expressed in the milky, doughy, and mature stages, respectively. We performed three pairwise comparisons: milky vs. dough, milky vs. mature, and dough vs. mature, and identified 6753, 9540, and 2531 DEGs, respectively. The DEGs' abundance was higher in milky vs. mature, with 5527 up-regulated genes and 4013 down-regulated genes, while it was smaller in dough vs. mature, with 1419 up-regulated genes and 1112 down-regulated DEGs. This result was consistent with the changes in anthocyanin profiling, and the expression of structural, regulatory, and transporter genes involved in anthocyanin biosynthesis showed their highest expression at the dough stage. Through the gene expression profile and protein interaction network, we deciphered six main contributors of the anthocyanin peak observed at dough stage, including OsANS, OsDFR, OsGSTU34, OsMYB3, OsbHLH015, and OsWD40-50.DiscussionThis study is the first to report the investigation of anthocyanin and gene expression at three developmental stages of black rice caryopsis. The findings of this study could aid in predicting the best harvesting time to achieve maximum anthocyanin content and the best time to collect samples for various gene expression analysis, laying the groundwork for future research into the molecular mechanisms underlying rice caryopsis coloration.

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Section: Anthocyanin Accumulation Relatedness With Structural Gene Ex...supporting

confidence: 93%

Integrative HPLC profiling and transcriptome analysis revealed insights into anthocyanin accumulation and key genes at three developmental stages of black rice (Oryza sativa. L) caryopsis

Mackon,

Jeazet Dongho Epse Mackon,

Yao

et al. 2023

Front. Plant Sci.

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“…This aligns with the previous research conducted by Muleke et al [ 17 ], which demonstrated that RsUFGT plays a crucial role in regulating anthocyanin synthesis during various developmental stages of radish. DFR has been identified as the pivotal regulator of anthocyanin synthesis in purple leaves [ 23 ]. Extensive research has been conducted by scientific and technological experts on radish skin and radish meat in fleshy roots.…”

Section: Discussionmentioning

confidence: 99%

“…Specifically, the expression patterns of the four copies of RsPAP1 exhibited variations across the four different tissues of radish, with no single copy showing significant and specific up-regulation across all four tissues. Previous studies have reported the involvement of MYB114 ( PAP1 homologous gene) in the development of purple leaves in radish, while MYB75 ( PAP1 ) is responsible for regulating anthocyanins in the red skin of radish [ 23 , 35 ]. Notably, our research has revealed, for the first time, that RsPAP1.7c2 exhibits specific and high expression levels in radish sprouts and leaves, RsPAP1.7c1 is specifically highly expressed in purple fleshy roots, and RsPAP1.5c is specifically expressed in purple radish petals.…”

Section: Discussionmentioning

confidence: 99%

“…Upon subjecting radish sprouts to UV-A treatment, there was a significant increase in anthocyanin content, through comparative transcriptome sequencing analysis, the transcript levels of transcriptional regulators related to the MYB-bHLH-WD40 complex were consistent with the observed concentration of anthocyanins [ 40 ]. In the study conducted by Pu et al [ 23 ], it was observed that the expression levels of the structural genes PAL4 , 4CL4 , CHS , F3H , DFR , ANS , OMT1 , as well as the transcription factors TT8 , CPC , and MYB114 , were significantly elevated in purple leaves. Similarly, Gao et al [ 8 ] found that in radish fleshy roots, the transcription factors RsMYB_9 , RsERF070 , and the anthocyanin synthesis-related genes RsCHS , RsCHI , RsANS , RsMT2-4 , RsUF3GT , RsUFGT78D2-like , and RsUDGT-75C1-like play crucial roles in anthocyanin biosynthesis in radish varieties.…”

Section: Introductionmentioning

confidence: 99%

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Comparative transcriptome analysis reveals transcriptional regulation of anthocyanin biosynthesis in purple radish (Raphanus sativus L.)

Liu,

Wang,

Chen

et al. 2024

BMC Genomics

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Radish exhibits significant variation in color, particularly in sprouts, leaves, petals, fleshy roots, and other tissues, displaying a range of hues such as green, white, red, purple, and black. Although extensive research has been conducted on the color variation of radish, the underlying mechanism behind the variation in radish flower color remains unclear. To date, there is a lack of comprehensive research investigating the variation mechanism of radish sprouts, leaves, fleshy roots, and flower organs. This study aims to address this gap by utilizing transcriptome sequencing to acquire transcriptome data for white and purple radish flowers. Additionally, the published transcriptome data of sprouts, leaves, and fleshy roots were incorporated to conduct a systematic analysis of the regulatory mechanisms underlying anthocyanin biosynthesis in these four radish tissues. The comparative transcriptome analysis revealed differential expression of the anthocyanin biosynthetic pathway genes DFR, UGT78D2, TT12 and CPC in the four radish tissues. Additionally, the WGCNA results identified RsDFR.9c and RsUGT78D2.2c as hub genes responsible for regulating anthocyanin biosynthesis. By integrating the findings from the comparative transcriptome analysis, WGCNA, and anthocyanin biosynthetic pathway-related gene expression patterns, it is hypothesized that genes RsDFR.9c and RsUGT78D2.2c may serve as pivotal regulators of anthocyanins in the four radish tissues. Furthermore, the tissue-specific expression of the four copies of RsPAP1 is deemed crucial in governing anthocyanin synthesis and accumulation. Our results provide new insights into the molecular mechanism of anthocyanin biosynthesis and accumulation in different tissues of radish.

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Anthocyanins: Biotechnological targets for enhancing crop tolerance to salinity stress

Mansour

2023

Scientia Horticulturae

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Integration of metabolome and transcriptome analyses reveals the mechanism of anthocyanin accumulation in purple radish leaves

Cited by 4 publications

References 41 publications

Integrative HPLC profiling and transcriptome analysis revealed insights into anthocyanin accumulation and key genes at three developmental stages of black rice (Oryza sativa. L) caryopsis

Integrative HPLC profiling and transcriptome analysis revealed insights into anthocyanin accumulation and key genes at three developmental stages of black rice (Oryza sativa. L) caryopsis

Comparative transcriptome analysis reveals transcriptional regulation of anthocyanin biosynthesis in purple radish (Raphanus sativus L.)

Anthocyanins: Biotechnological targets for enhancing crop tolerance to salinity stress

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