2. Academic Validation
  3. Metabolomic remodeling and genetic regulation in potato tubers during domestication

Metabolomic remodeling and genetic regulation in potato tubers during domestication

  • Mol Plant. 2025 Dec 13:S1674-2052(25)00435-6. doi: 10.1016/j.molp.2025.12.005.
Zhong Zhang 1,  Wei Tan 2,  Jintao Liu 2,  Jiangyue Long 2,  Zefeng Zhai 3,  Yang Feng 2,  Lingling Wei 2,  Hui Du 3,  Qi Fu 2,  Yanan Pu 2,  Pei Wang 3,  Chunzhi Zhang 4,  Guangtao Zhu 5
Affiliations

Affiliations

  • 1 School of Life Sciences, Yunnan Key Laboratory of Potato Biology, Engineering Research Center for Valorization of Unique Bio-Resources in Yunnan, Ministry of Education, Yunnan Normal University, Southwest United Graduate School, Kunming 650500, Yunnan Province, China; 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 518000, Guangdong Province, China.
  • 2 School of Life Sciences, Yunnan Key Laboratory of Potato Biology, Engineering Research Center for Valorization of Unique Bio-Resources in Yunnan, Ministry of Education, Yunnan Normal University, Southwest United Graduate School, Kunming 650500, Yunnan Province, China.
  • 3 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 518000, Guangdong Province, China.
  • 4 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 518000, Guangdong Province, China. Electronic address: [email protected].
  • 5 School of Life Sciences, Yunnan Key Laboratory of Potato Biology, Engineering Research Center for Valorization of Unique Bio-Resources in Yunnan, Ministry of Education, Yunnan Normal University, Southwest United Graduate School, Kunming 650500, Yunnan Province, China. Electronic address: [email protected].
PMID: 41392480 DOI: 10.1016/j.molp.2025.12.005
Abstract

The potato is an important crop for ensuring global food and nutritional security. The metabolic transitions and underlying genetic mechanisms that occurred during domestication from wild progenitors remain not fully understood. Here, we used a multi-omics approach to decipher its domestication footprint. The metabolomic remodeling of tubers was featured with the decrease in the diversity and content of bitter steroidal glycoalkaloids (SGAs) and the increase in the nutritional flavonoid content. Two biosynthesis genes affecting the structural divergence of SGAs and two transcription factors regulating the SGA content were characterized. Two tandem MYBs were shown to modulate the phenylpropanoid flux between phenolic acids and Flavonoids. Our findings demonstrate that selection of coding and cis-regulatory variations has substantially reshaped tuber metabolite diversity and content, respectively. The dissection of the genetic architecture of 2,046 loci for 568 metabolites, involving 2,745 epistatic interactions and 268 pleiotropic effects, provides a roadmap for metabolic manipulation in tubers. These findings deepen our understanding of potato domestication and offer genetic strategies for developing cultivars with improved quality.

Keywords

domestication; genetic interaction; mGWAS; potato; secondary metabolism; transcription regulation.

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