Integrated multi-omics analysis of flavonoid metabolism in soybean seeds of different colours reveals candidate regulatory networks associated with anthocyanin and isoflavone accumulation
- 1Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, 530007, China
Abstract
Soybean seed colour reflects divergence in flavonoid metabolism and is an important quality attribute for edamame and functional food ingredients. The transcript-metabolite patterns associated with anthocyanin and isoflavone accumulation across colour phenotypes remain incompletely characterised. We compared one black-seeded (B), one green-seeded (G), and one yellow-seeded (Y) accession using commercial colorimetric assays, widely targeted metabolomic profiling, and RNA sequencing. Whole-seed assays showed higher total anthocyanin contents in B and G than in Y and a higher total flavonoid content in B than in G and Y. B also showed higher relative abundances of several delphinidin derivatives, proanthocyanidins, and catechins. Selected cyanidin and pelargonidin derivatives were more abundant in Y, whereas daidzein and several triterpenoid saponins were more abundant in G. Transcriptome comparisons identified accession-associated differences in flavonoid-pathway genes, including members of the CHS, CHI, and DFR families. Several flavonoid-related transcripts and metabolites showed parallel patterns across the three accessions. Exploratory DIABLO analysis revealed coordinated variation among the phenotype, metabolite, pathway-gene, and transcription-factor datasets and retained 20 transcription factors across two model components. RT-qPCR mean patterns were broadly similar to the RNA-seq results for some selected genes. Together, these findings reveal distinct flavonoid profiles and associated transcriptional patterns among the three soybean accessions, providing candidate metabolites, genes, and transcription factors for further functional and biochemical investigation.
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BibTeX
@article{qin2026integrated,
title = {{Integrated multi-omics analysis of flavonoid metabolism in soybean seeds of different colours reveals candidate regulatory networks associated with anthocyanin and isoflavone accumulation}},
author = {Yan Qin and Wenjie Chen and Yuan Chen and Xiaohua Huang and Fuyue Tang and Xiaohong Guo and Qingyuan Wei and Xiayan Qin and Haifeng Yan and Shufang Chen and Xue Bai and Jiang Liang and Rongchang Wei},
journal = {Food Chemistry: Molecular Sciences},
year = {2026},
month = oct,
doi = {10.1016/j.fochms.2026.100466},
url = {https://doi.org/10.1016/j.fochms.2026.100466},
note = {CC BY-NC 4.0},
}
RIS
TY - JOUR
TI - Integrated multi-omics analysis of flavonoid metabolism in soybean seeds of different colours reveals candidate regulatory networks associated with anthocyanin and isoflavone accumulation
AU - Yan Qin
AU - Wenjie Chen
AU - Yuan Chen
AU - Xiaohua Huang
AU - Fuyue Tang
AU - Xiaohong Guo
AU - Qingyuan Wei
AU - Xiayan Qin
AU - Haifeng Yan
AU - Shufang Chen
AU - Xue Bai
AU - Jiang Liang
AU - Rongchang Wei
PY - 2026
DA - 2026/10/26
JO - Food Chemistry: Molecular Sciences
DO - 10.1016/j.fochms.2026.100466
UR - https://doi.org/10.1016/j.fochms.2026.100466
AB - Soybean seed colour reflects divergence in flavonoid metabolism and is an important quality attribute for edamame and functional food ingredients. The transcript-metabolite patterns associated with anthocyanin and isoflavone accumulation across colour phenotypes remain incompletely characterised. We compared one black-seeded (B), one green-seeded (G), and one yellow-seeded (Y) accession using commercial colorimetric assays, widely targeted metabolomic profiling, and RNA sequencing. Whole-seed assays showed higher total anthocyanin contents in B and G than in Y and a higher total flavonoid content in B than in G and Y. B also showed higher relative abundances of several delphinidin derivatives, proanthocyanidins, and catechins. Selected cyanidin and pelargonidin derivatives were more abundant in Y, whereas daidzein and several triterpenoid saponins were more abundant in G. Transcriptome comparisons identified accession-associated differences in flavonoid-pathway genes, including members of the CHS, CHI, and DFR families. Several flavonoid-related transcripts and metabolites showed parallel patterns across the three accessions. Exploratory DIABLO analysis revealed coordinated variation among the phenotype, metabolite, pathway-gene, and transcription-factor datasets and retained 20 transcription factors across two model components. RT-qPCR mean patterns were broadly similar to the RNA-seq results for some selected genes. Together, these findings reveal distinct flavonoid profiles and associated transcriptional patterns among the three soybean accessions, providing candidate metabolites, genes, and transcription factors for further functional and biochemical investigation.
SN - 2666-5662
ER -