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Journal of Integrative Agriculture  2026, Vol. 25 Issue (8): 3282-3294    DOI: 10.1016/j.jia.2025.12.070
Horticulture Advanced Online Publication | Current Issue | Archive | Adv Search |
Multi-omics analysis reveals dynamic metabolic and transcriptomic changes during potato tuber swelling

Jiangyue Long1*, Wei Tan1*, Chunzhi Zhang2, Guangtao Zhu1#, Zhong Zhang2, 1#

1 Yunnan Key Laboratory of Potato Biology/Engineering Research Center for Valorization of Unique Bio-Resources in Yunnan of Ministry of Education, School of Life Sciences, Yunnan Normal University/Southwest United Graduate School, Kunming 650500, China

2 State Key Laboratory of Genome and Multi-omics Technologies/Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture/Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs/Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China

 Highlights 
Metabolic and transcriptional dynamics during potato tuber development are revealed.
Stage and genotype-specific metabolic patterns are identified in two genotypes.
Novel genes involved in steroidal glycoalkaloid (SGA) and phenylpropanoid biosynthesis are discovered.
MYB113 positively regulates phenolic acid biosynthesis in tuber flesh.
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摘要  

马铃薯作为全球重要的粮食作物,为人类提供关键的膳食能量与营养。然而,块茎发育过程中的代谢动态变化及其潜在的转录调控机制尚未明确。本研究整合野生与栽培马铃薯块茎的时序代谢组和转录组分析,鉴定出 849 种代谢物呈现 10 种不同的时序积累模式,其中 6 种为两种基因型共有的积累模式,4 种为基因型特异模式。野生种质块茎膨大早期脂质含量显著减少,后期酚酸含量显著增加;栽培种质则在膨大早期酚酸含量显著增加,后期酚酸、氨基酸及类黄酮含量显著减少。代谢物差异比较分析进一步显示,与野生种质相比,栽培种质块茎的甾体糖苷生物碱(SGA)含量显著降低,类黄酮含量显著提高,这与栽培种质苦味减轻、薯肉着色增强的性状表现一致。共表达网络分析鉴定出 35 个与 SGA 含量、57 个与苯丙烷类代谢物含量高度相关的候选基因。转基因功能验证表明,候选转录因子 MYB113 可通过调控关键合成基因(PAL、C3H 和 HCT)的表达,促进块茎中酚酸的生物合成。本研究阐明了块茎发育过程中的代谢与转录动态规律,为通过分子育种改良块茎代谢品质提供了理论依据。

 



Abstract  

Potato is a vital global food source, yet the metabolic and transcriptional regulation governing tuber development and quality remains poorly understood.  Here, we performed integrated metabolomic and transcriptomic analyses in wild and cultivated potato tubers, revealing dynamic and distinct metabolic accumulation patterns.  The 849 metabolites exhibited 10 distinct temporal accumulation patterns, including six shared patterns between accessions and four genotype-specific patterns.  The wild genotype exhibited an early decrease in lipids, followed by an increase in phenolic acids, whereas the cultivated genotype displayed an early increase in phenolic acids, accompanied by a decrease in some phenolic acids, amino acids, and flavonoids.  A comparative analysis highlighted the cultivated genotype exhibited significantly lower levels of bitter steroidal glycoalkaloids (SGAs) but higher levels of beneficial flavonoids compared with its wild relative.  Co-expression network analysis revealed 35 SGA-related and 57 phenylpropanoid-related genes that underlie metabolite dynamics.  Notably, we functionally validated that the transcription factor StMYB113 plays a previously unknown role in positively regulating phenolic acid biosynthesis in tuber flesh.  Our work provides a comprehensive map of tuber metabolism and a valuable resource for accelerating the genetic improvement of key potato quality traits.

Keywords:   potato       multi-omics        steroidal glycoalkaloid        phenylpropanoid        transcriptional regulation  
Received: 01 April 2025   Accepted: 25 September 2025 Online: 31 December 2025  
Fund: 

This work was financially supported by the Guangdong Major Project of Basic and Applied Basic Research, China (2021B03
01030004), the National Natural Science Foundation of China (32272725, 32488302), and the China Postdoctoral Science Foundation (2022M723463).

About author:  Jiangyue Long, E-mail: 2223120031@ynnu.edu.cn, Wei Tan, E-mail: 2223120009@ynnu.edu.cn; #Correspondence Guangtao Zhu, Tel: +86-871-65941387, E-mail: zhuguangtao@ynnu.edu.cn; Zhong Zhang, Tel: +86-755-23250158, E-mail: zhangzhong@caas.cn *These authors contributed equally to this study.

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