ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2022
Multi-omics analysis reveals the mechanism of seed coat color formation in Brassica rapa L.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed, 22 citations in OpenAlex.
- Roles of Metabolites Unveiled by Metabolomics inMetabolites · 2026Review
- Comparative analysis ofFood chemistry: X · 2025Article
- Untargeted Metabolomics Analysis Reveals Differential Accumulation of Flavonoids Between Yellow-Seeded and Black-Seeded Rapeseed Varieties.Plants (Basel, Switzerland) · 2025Article
- Natural variations inProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Metabolic diversity in sorghum: Mechanism underlying grain color variation and fermentation quality.PloS one · 2025Article
- Multi-omics analysis reveals ThMYB6 regulation of flavonoid biosynthesis in differently colored tuberous roots ofFrontiers in plant science · 2025Article
- The introgression of BjMYB113 from Brassica juncea leads to purple leaf trait in Brassica napus.BMC plant biology · 2024Article
- Deep learning the cis-regulatory code for gene expression in selected model plants.Nature communications · 2024Article
- Integrated metabolomic and transcriptomic dynamic profiles of endopleura coloration during fruit maturation in three walnut cultivars.BMC plant biology · 2024Article
- Genome-wide identification and expression analysis of the anthocyanin-related genes during seed coat development in six Brassica species.BMC genomics · 2023Article
- Integration of multi-omics technologies for crop improvement: Status and prospects.Frontiers in bioinformatics · 2022Article
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Authors and funding
16 authors at 2 institutions in 3 countries.
Funding
Abstract
keymessageMulti-omics analysis of the transcriptome, metabolome and genome identified major and minor loci and candidate genes for seed coat color and explored the mechanism of flavonoid metabolites biosynthesis in Brassica rapa. Yellow seed trait is considered an agronomically desirable trait with great potential for improving seed quality of Brassica crops. Mechanisms of the yellow seed trait are complex and not well understood. In this study, we performed an integrated metabolome, transcriptome and genome-wide association study (GWAS) on different B. rapa varieties to explore the mechanisms underlying the seed coat color formation. A total of 2,499 differentially expressed genes and 116 differential metabolites between yellow and black seeds with strong association with the flavonoid biosynthesis pathway was identified. In addition, 330 hub genes involved in the seed coat color formation, and the most significantly differential flavonoids biosynthesis were detected based on weighted gene co-expression network analysis. Metabolite GWAS analysis using the contents of 42 flavonoids in developing seeds of 159 B. rapa lines resulted in the identification of 1,626 quantitative trait nucleotides (QTNs) and 37 chromosomal intervals, including one major locus on chromosome A09. A combination of QTNs detection, transcriptome and functional analyses led to the identification of 241 candidate genes that were associated with different flavonoid metabolites. The flavonoid biosynthesis pathway in B. rapa was assembled based on the identified flavonoid metabolites and candidate genes. Furthermore, BrMYB111 members (BraA09g004490.3C and BraA06g034790.3C) involved in the biosynthesis of taxifolin were functionally analyzed in vitro. Our findings lay a foundation and provide a reference for systematically investigating the mechanism of seed coat color in B. rapa and in the other plants.
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