Genetic diversity and comprehensive evaluation of physicochemical traits in Phyllanthus emblica L. for breeding and resource utilization

Abstract

Phyllanthus emblica L. is a nutritionally and medicinally valuable fruit tree with extensive germplasm diversity. This study evaluated 61 genetically diverse accessions collected from China and South Asia for 27 physicochemical traits, including 13 physical and 14 chemical attributes, to assess genetic diversity and identify elite germplasm for breeding. Substantial phenotypic variation was observed, with coefficients of variation (CV) ranging from 5.13 to 98.09% for physical traits and 1.51-59.82% for biochemical traits. Notably, single fruit weight (CV: 98.09%), flesh stickiness (63.65%), crude fat (59.82%), and polysaccharide content (50.12%) exhibited high variability. Fifteen traits conformed to a normal distribution and were categorized into five probability-based grades. Correlation analysis showed that pericarp strength was significantly positively correlated with soluble solids, titratable acid, total flavonoids, polyphenols, and tannin content, while flesh hardness correlated positively with crude fiber and total sugar. Principal component analysis (PCA) reduced the 27 traits to 12 representative indicators, accounting for 82.54% of total variation. Hierarchical clustering grouped the germplasms into three classes: Class I (19 accessions) with high antioxidant contents and strong textures; Class II (2 accessions) with the largest fruit size and high flesh toughness; and Class III (40 accessions) with high moisture content and lower values for most traits, suitable for juice processing. A comprehensive biochemical evaluation model was constructed using PCA-derived weights, and the top-performing accessions-PEF30, PEF41, PEF35, PEF17, and PEF31-demonstrated superior nutritional quality based on total sugar, polyphenols, vitamin C, and flavonoid contents. These accessions are promising candidates for functional food development, fresh consumption, and cultivar improvement. This study provides a robust analytical framework and theoretical foundation for the classification, conservation, and targeted utilization of P. emblica germplasm in breeding programs.

Keywords: Amla; Diversity analysis; Fruit quality; Resource conservation; Tropical and subtropical fruit.

Fig. 1

Fruit morphological diversity observed among 61 different germplasm accessions of Phyllanthus emblica. Each fruit, labeled from PEF1 to PEF61, exhibits variation in size, shape, and surface characteristics, highlighting the genetic diversity present within the evaluated accessions

Fig. 2

Fruit texture characteristic curve of P. emblica fruit. A is pericarp texture characterization curve; B is flesh texture characterization curve

Fig. 3

Physicochemical quality frequency distribution histogram of normal distribution

Fig. 4

Correlation analysis of physicochemical qualities of P. emblica fruit. Different colors in the figure represent the Pearson correlation coefficient. Red indicates a strong positive correlation, and blue indicates a strong negative correlation. The deeper the color in the circle and the larger the area, the greater the absolute value of the correlation coefficient between the qualities

Fig. 5

Heat map and hierarchical clustering of P. emblica fruit physicochemical attributes and samples. The hierarchical clustering tree for physicochemical attributes is displayed on the left, while the clustering tree for samples is shown at the top. The names of physicochemical attributes are listed on the right, and sample names are located at the bottom. The heat map uses a color gradient where red indicates high values and blue represents low values, with more intense red and blue shades corresponding to higher and lower values, respectively

Fig. 6

Principal component score plot A and loading diagram B of P. emblica fruit physicochemical qualities. A The principal component score plot, where different colors represent distinct categories, corresponding to Groups 1–3 identified in the cluster analysis. B The loading diagram illustrating the contribution of physical and chemical quality indices to the principal components

Fig. 7

OPLS-DA score plot A and permutation test B. Panel A shows the OPLS-DA score plot, where the first principal component (PC1) is plotted on the x-axis and the first orthogonal component (PC2) on the y-axis. Different colors represent distinct categories, with the legends Group 1, Group 2, and Group 3 corresponding to the first, second, and third groups identified in the cluster analysis. Panel B illustrates the OPLS-DA permutation test, with the x-axis representing the similarity between the actual sample group and 200 randomly generated groups, and the y-axis indicating the model evaluation parameters. Points in the upper-right corner, labeled Q2 and R2, correspond to the evaluation parameters of the actual sample group. The reliability of the OPLS-DA model is validated when all green and blue points on the left are positioned lower than the actual R2 and Q2 points in the upper-right corner

Fig. 8

VIP values of physicochemical properties of P. emblica fruit. The VIP values of each trait are arranged in descending order from left to right. Traits with VIP values greater than 1 include single fruit weight, longitudinal diameter, transverse diameter, total polyphenols, total flavonoids, moisture, soluble solids, flesh toughness, tannins, flesh stickiness, flesh adhesion, and flesh brittleness

Fig. 9

Physicochemical properties box plot of P. emblica fruit. A to L show the box plots representing the differences in single fruit weight, longitudinal diameter, transverse diameter, total polyphenols, total flavonoids, moisture, soluble solids, flesh toughness, flesh stickiness, tannin content, flesh adhesion, and flesh brittleness

Fig. 10

Comprehensive evaluation score of nutritional quality of P. emblica fruit. The comprehensive scores of nutritional quality of various quality samples decreased from left to right

Fig. 11

Cluster analysis of nutritional quality a and PCA score plot b of P. emblica fruit. Panel a shows the cluster diagram of 61 samples based on their nutritional quality, with different colored clusters representing Groups A, B, and C. Panel b presents the principal component score plot, where colors correspond to Groups A, B, and C, as shown in the cluster diagram. The ellipses represent the 95% confidence intervals for each group