Abstract
Background
Taproot skin color is a major trait for assessing the commercial and nutritional quality of radish, and red-skinned radish is confirmed to improve consumer’s interest and health. However, little is known about the molecular mechanisms responsible for controlling the formation of red-skinned radish.
Objective
This study aimed to identify the differentially expressed anthocyanin biosynthetic genes between red- and white-skinned radishes and understand the molecular regulatory mechanism underlying red-skinned radish formation.
Methods
Based on the published complete genome sequence of radish, the digital gene expression profiles of Yangzhouyuanbai (YB, white-skinned) and Sading (SD, red-skinned) were analyzed using Illumina sequencing.
Results
A total of 3666 DEGs were identified in SD compared with YB. Interestingly, 46 genes encoded enzymes related to anthocyanin biosynthesis and 241 genes encoded transcription factors were identified. KEGG pathway analysis showed that the formation of red-skinned radish was mainly controlled by pelargonidin-derived anthocyanin biosynthetic pathway genes. This process included the upregulation of PAL, C4H, 4CL, CHS, CHI, F3H, DFR, LDOX, and UGT enzymes in SD. CHS genes were specifically expressed in SD, and it might be the key point for red pigment accumulation in red-skinned radish. Furthermore, MYB1/2/75, bHLH (TT8), and WD 40 showed higher expression in SD than in YB. Meanwhile, the corresponding low-abundance anthocyanin biosynthesis enzymes and upregulation of MYB4 might be the factors influencing the formation of white-skinned radish.
Conclusion
These findings provide new insights into the molecular mechanisms and regulatory network of anthocyanin biosynthesis in red-skinned radish.
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Abbreviations
- DEG:
-
Differentially expressed gene
- GO:
-
Gene ontology
- KEGG:
-
Kyoto encyclopedia of genes and genomes
- RT-qPCR:
-
Reverse-transcription quantitative PCR
- CHS:
-
Chalcone synthase
- CHI:
-
Chalcone isomerase
- F3′H:
-
Flavanone 3′-hydroxylase
- F3H:
-
Flavanone 3-hydroxylase
- F3′5′H:
-
Flavanone 3′,5′-hydroxylase
- DFR:
-
Dihydroflavonol 4-reductase
- LDOX/ANS:
-
Leucoanthocyanidin dioxygenase/anthocyanidin synthase
- UFGT:
-
UDP flavonoid glucosyltransferase
- MYB:
-
Myeloblastosis
- bHLH:
-
Basic helix-loop-helix
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Acknowledgements
This work was in part supported by grants from the Natural Science Foundation of Anhui Province of China (1708085MC55) and the Science Research Foundation of the Education Bureau of Anhui Province of China (KJ2016B014), and also supported by Anhui Province Key Labratory of Pollutant Sensitive Materials and Environmental Remediation.
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Yu, R., Du, X., Li, J. et al. Identification and differential expression analysis of anthocyanin biosynthetic genes in root-skin color variants of radish (Raphanus sativus L.). Genes Genom 42, 413–424 (2020). https://doi.org/10.1007/s13258-020-00915-x
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DOI: https://doi.org/10.1007/s13258-020-00915-x