Comparative Metabolomics Analysis of Four Pineapple (Ananas comosus L. Merr) Varieties with Different Fruit Quality

Abstract

Understanding the metabolic characteristics of pineapple varieties is crucial for market expansion and diversity. This study performed comparative metabolomic analysis on the "Comte de Paris" (BL) and three Taiwan-introduced varieties: "Tainong No. 11" (XS), "Tainong No. 23" (MG), and "Tainong No. 13" (DM). A total of 551 metabolites were identified across the four varieties, with 231 metabolites exhibiting no significant differences between all varieties. This included major sugars such as sucrose, glucose, and fructose, as well as key acids like citric, malic, and quinic acids, indicating that the in-season maturing fruits of different pineapple varieties can all achieve good sugar-acid accumulation under suitable conditions. The differentially accumulated metabolites (DAMs) that were identified among the four varieties all primarily belonged to several major subclasses, including phenolic acids, flavonoids, amino acids and derivatives, and alkaloids, but the preferentially accumulated metabolites in each variety varied greatly. Specifically, branched-chain amino acids (L-leucine, L-isoleucine, and L-valine) and many DAMs in the flavonoid, phenolic acid, lignan, and coumarin categories were most abundant in MG, which might contribute to its distinct and enriched flavor and nutritional value. XS, meanwhile, exhibited a notable accumulation of aromatic amino acids (L-phenylalanine, L-tryptophan), various phenolic acids, and many lignans and coumarins, which may be related to its unique flavor profile. In DM, the dominant accumulation of jasmonic acid might contribute to its greater adaptability to low temperatures during autumn and winter, allowing off-season fruits to maintain good quality. The main cultivar BL exhibited the highest accumulation of L-ascorbic acid and many relatively abundant flavonoids, making it a good choice for antioxidant benefits. These findings offer valuable insights for promoting different varieties and advancing metabolome-based pineapple improvement programs.

Keywords: comparative analysis; fruit quality; metabolome; pineapple.

Figure 1

Pineapple fruit phenotyping and metabolite profiling. (A) Fruit of the four representative pineapple varieties; (B) Classification of all identified metabolites.

Figure 2

Principal component analysis (PCA) and hierarchical clustering heatmap of all pineapple samples. (A) PCA score plot of all pineapple samples with three quality control (mix 01–03); (B) Total metabolite clustering heatmap of all samples. Each column is a different sample, and each row is an identified metabolite. The heatmap was created based on the relative content value of identified metabolites and normalized by row. Differences in metabolite accumulation changes are shown in color as the scale, red for high abundance and green for low abundance.

Figure 3

OPLS-DA analyses of three comparison groups with BL pineapple. (A–C) OPLS-DA score plots for BL vs. DM (A), BL vs. MG (B), and BL vs. XS (C), respectively. The abscissa represents the predicted principal component, and the ordinate represents the orthogonal principal components. The percentage indicates how well the component explains the data set. (D–F) Permutation test of the OPLS-DA model for BL vs. DM (D), BL vs. MG (E), and BL vs. XS (F), respectively. The abscissa represents the accuracy of the model, and the ordinate is the frequency of the model classification effect.

Figure 4

DAMs identified in different categories between four varieties. (A–C) Numbers of DAMs in different categories between BL vs. DM (A), BL vs. MG (B), and BL vs. XS (C), respectively. (D) Venn diagram of the common more-accumulated metabolites of BL vs. DM, BL vs. MG, and BL vs. XS. (E) Venn diagram of less-accumulated metabolites of BL vs. DM, BL vs. MG, and BL vs. XS. (F) Number of the common DAMs in different categories between BL vs. DM, BL vs. MG, and BL vs. XS. (G–I) Numbers of DAMs in different categories between DM vs. MG (G), DM vs. XS (H), and MG vs. XS (I), respectively.

Figure 5

K-means clustering of the metabolites between four pineapple varieties. Nine classes (Sub class 1–9) of 320 metabolites were grouped based on the dynamic changes of metabolites between four pineapple varieties. Colored lines represent the standardized expression patterns of individual metabolites, while the black line indicates the mean trend of each subclass.