The Theobroma cacao presents a wide diversity in pod color among different cultivars. Although flavonoid biosynthesis has been studied in many plants, molecular mechanisms governing the diversity of coloration in cacao pods are largely unknown. The flavonoid metabolite profiles and flavonoid biosynthetic gene expression in the pod exocarps of light green pod ‘TAS 410’ (GW), green pod ‘TAS 166’ (GF), and mauve pod ‘TAS 168’ (PF) were determined. Changes in flavonoid metabolites, particularly the anthocyanins (cyanidin 3-O-galactoside, cyanidin 3-O-glucoside, and cyanidin O-syringic acid) were significantly up-accumulated in the mauve phenotype (PF) compared to the light green or green phenotypes, endowing the pod color change from light green or green to mauve. Consistently, the PF phenotype showed different expression patterns of flavonoid biosynthetic structural genes in comparison with GW/GF phenotypes. The expression level of LAR and ANR in GW/GF was significantly higher than PF, while the expression level of UFGT in GW/GF was lower than PF. These genes likely generated more anthocyanins in the exocarps samples of PF than that of GW/GF. Simultaneously, colorless flavan-3-ols (catechin, epicatechin and proanthocyanidin) content in the exocarp samples of PF was lower than GW/GF. Additionally, MYB (gene18079) and bHLH (gene5045 and gene21575) may participate in the regulation of the pod color. This study sheds light on the molecular basis of cacao pod color variation, which will contribute to breeding cacao varieties with enhanced flavonoid profiles for nutritional applications.

在可可呈现出广泛的多样性在不同品种间荚色。尽管已经在许多植物中研究了类黄酮生物合成，但控制可可豆荚颜色多样性的分子机制在很大程度上是未知的。测定了浅绿色豆荚“TAS 410”（GW）、绿色豆荚“TAS 166”（GF）和紫红色豆荚“TAS 168”（PF）的豆荚外果皮中的类黄酮代谢物谱和类黄酮生物合成基因表达。黄酮类代谢物的变化，特别是花青素（花青素 3- O-半乳糖苷、花青素 3- O-葡萄糖苷和花青素O-丁香酸）与浅绿色或绿色表型相比，在紫红色表型 (PF) 中显着累积，使豆荚颜色从浅绿色或绿色变为紫红色。一致地，与 GW/GF 表型相比，PF 表型显示出不同的类黄酮生物合成结构基因的表达模式。GW/GF中LAR和ANR的表达水平显着高于PF，而UFGT在GW/GF中的表达水平低于PF。这些基因可能在 PF 的外果皮样品中产生比 GW/GF 更多的花青素。同时，PF 外果皮样品中的无色 flavan-3-ols（儿茶素、表儿茶素和原花青素）含量低于 GW/GF。此外，MYB（gene18079）和bHLH（gene5045和gene21575）可能参与了豆荚颜色的调节。这项研究揭示了可可豆荚颜色变化的分子基础，这将有助于培育具有增强类黄酮特征的可可品种，以用于营养应用。