Integrated metabolomic and transcriptomic analyses reveal tissue-specific distribution and gene-metabolite associations of quality-related metabolites in the Tibetan Plateau turnip landrace "Yushuyuangen" (Brassica rapa ssp. rapa).
- 1Laboratory of Research and Utilization of Germplasm Resources in Qinghai-Tibet Plateau, Academy of Agriculture and Forestry Sciences of Qinghai Province, Qinghai University, Xining, Qinghai, China.
- 2Key Laboratory of Germplasm Resources Protection and Genetic Improvement of the Qinghai-Tibet Plateau in Ministry of Agriculture and Rural, Xining, Qinghai, China.
Abstract
Yushuyuangen (Brassica rapa ssp. rapa) is a characteristic turnip landrace cultivated on the Qinghai-Tibet Plateau and valued for its nutritional and flavor qualities. However, the tissue-specific distribution of quality-related metabolites and the gene-expression patterns associated with their accumulation remain poorly understood. Here, metabolomics and transcriptomics were integrated with weighted gene co-expression network analysis (WGCNA) to investigate three root tissues in two varieties, YPW (purple-white) and YGW (green-white): the upper colored peel (purple in YPW and green in YGW), lower white peel, and root flesh. A total of 775 metabolites were identified, showing clear tissue-dependent metabolic differentiation. Sugar-phosphate intermediates and aromatic/aspartate-family amino acids accumulated mainly in root flesh (glucose-6-phosphate, fructose-6-phosphate, phenylalanine, and homoserine), whereas branched-chain amino acids were abundant in colored peel (valine and leucine). Purple peel accumulated higher levels of p-coumaric acid and ferulic acid, while flavonoids differed markedly between purple and green peel, represented by phloretin and diosmetin in purple peel and trifolin and kaempferol-7-O-glucoside in green peel. Integrated WGCNA and correlation analyses further identified tissue-associated relationships among metabolites, structural genes, and transcription factors. Four candidate transcription factor-structural gene-metabolite associations were highlighted: NAC22-F16P2.1-D-fructose-6-phosphate, bHLH65/ARFD4-TRBP2.2-L-tryptophan, MYB62/AGL63-PAL1.2/C4H.2-p-coumaric acid, and MYB62-FLS1/F3'H1.2-trifolin/kaempferol-7-O-glucoside. These associations were inferred from co-expression and correlation patterns and represent candidate relationships for further functional validation.
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BibTeX
@article{li2026integrated,
title = {{Integrated metabolomic and transcriptomic analyses reveal tissue-specific distribution and gene-metabolite associations of quality-related metabolites in the Tibetan Plateau turnip landrace "Yushuyuangen" (Brassica rapa ssp. rapa).}},
author = {Caixia Li and Ruxue Qian and Quanhui Li and Yanjing Ren},
journal = {Frontiers in nutrition},
year = {2026},
month = oct,
doi = {10.3389/fnut.2026.1980490},
url = {https://europepmc.org/article/MED/42948060},
note = {CC BY},
}
RIS
TY - JOUR
TI - Integrated metabolomic and transcriptomic analyses reveal tissue-specific distribution and gene-metabolite associations of quality-related metabolites in the Tibetan Plateau turnip landrace "Yushuyuangen" (Brassica rapa ssp. rapa).
AU - Caixia Li
AU - Ruxue Qian
AU - Quanhui Li
AU - Yanjing Ren
PY - 2026
DA - 2026/10/13
JO - Frontiers in nutrition
DO - 10.3389/fnut.2026.1980490
UR - https://europepmc.org/article/MED/42948060
AB - Yushuyuangen (Brassica rapa ssp. rapa) is a characteristic turnip landrace cultivated on the Qinghai-Tibet Plateau and valued for its nutritional and flavor qualities. However, the tissue-specific distribution of quality-related metabolites and the gene-expression patterns associated with their accumulation remain poorly understood. Here, metabolomics and transcriptomics were integrated with weighted gene co-expression network analysis (WGCNA) to investigate three root tissues in two varieties, YPW (purple-white) and YGW (green-white): the upper colored peel (purple in YPW and green in YGW), lower white peel, and root flesh. A total of 775 metabolites were identified, showing clear tissue-dependent metabolic differentiation. Sugar-phosphate intermediates and aromatic/aspartate-family amino acids accumulated mainly in root flesh (glucose-6-phosphate, fructose-6-phosphate, phenylalanine, and homoserine), whereas branched-chain amino acids were abundant in colored peel (valine and leucine). Purple peel accumulated higher levels of p-coumaric acid and ferulic acid, while flavonoids differed markedly between purple and green peel, represented by phloretin and diosmetin in purple peel and trifolin and kaempferol-7-O-glucoside in green peel. Integrated WGCNA and correlation analyses further identified tissue-associated relationships among metabolites, structural genes, and transcription factors. Four candidate transcription factor-structural gene-metabolite associations were highlighted: NAC22-F16P2.1-D-fructose-6-phosphate, bHLH65/ARFD4-TRBP2.2-L-tryptophan, MYB62/AGL63-PAL1.2/C4H.2-p-coumaric acid, and MYB62-FLS1/F3'H1.2-trifolin/kaempferol-7-O-glucoside. These associations were inferred from co-expression and correlation patterns and represent candidate relationships for further functional validation.
SN - 2296-861X
ER -