Comparative transcriptome analysis reveals key genes associated with pigmentation in radish (Raphanus sativus L.) skin and flesh

• Published in: Scientific reports Vol. 11; no. 1; p. 11434
• Main Authors: Zhang, Jifang, Zhao, Jian, Tan, Qunyun, Qiu, Xiaojun, Mei, Shiyong
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01-06-2021; Nature Publishing Group; Nature Portfolio
• Subjects: 631/337; 631/449; Anthocyanins; Anthocyanins - biosynthesis; Anthocyanins - genetics; Biosynthesis; Flavonoids; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Plant; Genetic diversity; Humanities and Social Sciences; Metabolites; multidisciplinary; Nutritive value; Pigmentation; Plant Proteins - biosynthesis; Plant Proteins - genetics; Raphanus - genetics; Raphanus - metabolism; Raphanus sativus; Science; Science (multidisciplinary); Skin; Skin pigmentation; Transcription factors; Transcriptomes
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-021-90633-5

Radish (
Raphanus sativus
) is an important vegetable worldwide that exhibits different flesh and skin colors. The anthocyanins responsible for the red and purple coloring in radishes possess nutritional value and pharmaceutical potential. To explore the structural and regulatory networks related to anthocyanin biosynthesis and identify key genes, we performed comparative transcriptome analyses of the skin and flesh of six colored radish accessions. The transcript profiles showed that each accession had a species-specific transcript profile. For radish pigmentation accumulation, the expression levels of anthocyanin biosynthetic genes (
RsTT4
,
RsC4H
,
RsTT7
,
RsCCOAMT
,
RsDFR
, and
RsLDOX
) were significantly upregulated in the red- and purple-colored accessions, but were downregulated or absent in the white and black accessions. The correlation test, combined with metabolome (PCC > 0.95), revealed five structural genes (
RsTT4
,
RsDFR
,
RsCCOAMT
,
RsF3H
, and
RsBG8L
) and three transcription factors (
RsTT8-1
,
RsTT8-2
, and
RsPAR1
) to be significantly correlated with flavonoids in the skin of the taproot. Four structural genes (
RsBG8L
,
RsDFR
,
RsCCOAMT
, and
RsLDOX
) and nine transcription factors (
RsTT8-1
,
RsTT8-2
,
RsMYB24L
,
RsbHLH57
,
RsPAR2L
,
RsbHLH113L
,
RsOGR3L
,
RsMYB24,
and
RsMYB34L
) were found to be significantly correlated with metabolites in the flesh of the taproot. This study provides a foundation for future studies on the gene functions and genetic diversity of radish pigmentation and should aid in the cultivation of new valuable radish varieties.