# The Anthocyanin Composition and Key Regulatory Genes Underlying the Color Variation Between Potato Tuber Bud Eyes and Periderm

## TL;DR

This study explores the genetic and metabolic reasons behind color differences in potato tubers, identifying key genes and compounds involved in pigmentation.

## Contribution

The study identifies StbHLH14 as a negative regulator of anthocyanin biosynthesis in potato tubers through its interaction with StAN2.

## Key findings

- Cyanidin, pelargonidin, and malvidin are key anthocyanins responsible for pigmentation differences in potato tubers.
- StbHLH14 inhibits anthocyanin biosynthesis by suppressing structural genes like StCHS and StDFR via StAN2.

## Abstract

The pigmentation patterns of potato tubers are complex and diverse, often exhibiting significant tissue specificity. This study was conducted to elucidate the molecular mechanisms underlying the differential pigmentation in different parts of potato tubers using two cultivars, ‘Huashu 12’ and 15EM36-26, which exhibit opposite pigmentation patterns between the bud eyes and the tuber periderm. Metabolomic analysis revealed that cyanidin, pelargonidin, and malvidin are the key anthocyanin components responsible for the observed pigmentation differences. A total of 118 common differentially expressed genes in the differentially pigmented tissues of both cultivars were identified in transcriptomic analysis, including key structural genes of the anthocyanin biosynthesis pathway (such as StPAL, StCHS, and StDFR). Weighted gene co-expression network analysis was further employed to screen modules significantly correlated with pigmentation phenotypes, and 28 candidate genes associated with anthocyanin biosynthesis were identified. Expression validation demonstrated that the expression of StbHLH14 was significantly higher in non-pigmented tissues compared to pigmented tissues. Functional analysis revealed that StbHLH14 can inhibit the activation of structural gene promoters (such as StCHS and StDFR) via the MYB transcription factor StAN2, thereby negatively regulating anthocyanin biosynthesis. This study unveils the metabolic and transcriptional basis of tissue-specific pigmentation in potato tubers and clarifies the negative regulatory role of StbHLH14.