Genetic Diversity and Genome-Wide Association Study of Total Phenolics, Flavonoids, and Antioxidant Properties in Potatoes (Solanum tuberosum L.)

Abstract

Genetic diversity of nutritional quality traits is crucial for potato breeding efforts to develop better varieties for the diverse market demands. In this study, the genetic diversity of 104 potato genotypes was estimated based on nutritional quality traits such as color parameters, total phenolic content, total flavonoid content, 2,2-Diphenyl-1-picrylhydrazyl (DPPH), and 2,2-azino-bis-(3-ethylbezothiazoline-6-sulphonic acid) radical scavenging potential across two environments. The results indicated that environment II, Hangzhou 2020, exhibited higher bioactive compounds and antioxidant properties than environment I, Hangzhou 2019. The colored potato accessions exhibited higher levels of total phenolic content, total flavonoid content, DPPH, and ABTS activities than the white potato accessions, indicating the superiority of the colored to white potato accessions. The genome sequencing identified 1,101,368 high-quality single-nucleotide polymorphisms (SNPs), and 141,656 insertion/deletions (Indels). A population structure analysis revealed that genotypes can be divided into two subpopulations. Genome-wide association studies (GWAS) identified 128 significant SNPs associated with potato's color, total phenolic content, total flavonoid content, and antioxidant properties. Thus, the study provides new opportunities for strategic breeding and marker-assisted selection of ideal varieties and favorable alleles to enhance bioactive compounds and health-beneficial properties.

Keywords: antioxidant properties; environment; genetic diversity; genome-wide association study; nutritional quality; potato.

Figure 1

Genetic diversity and population structure of 104 potato accessions. (A,B) SNP distribution and density in potato’s chromosomes. (C) ADMIXTURE analysis of cross-validation, K = 1 – 10. (D) Population structure based on K = 2 for the whole panel of potato accessions. (E) Linkage disequilibrium plot for the tested genotypes. (F) Principal component analysis (PCA) denotes the first two principal components of the population, subpopulation 1 (red dots) and subpopulation 2 (black dots). (G) Neighbor-joining tree constructed using a P-distance matrix for 104 accessions.

Figure 2

Mean distributions of total phenolic content, total flavonoid content, DPPH, and ABTS activities of potatoes. (A) TPC: total phenolic content expressed as mg GAE/100 g; (B) TFC: total flavonoid content expressed as mg/g CE/100 g; (C) DPPH: 2,2-Diphenyl-1-picrylhydrazyl; and (D) ABTS: 2,2-azino-bis-(3-ethylbenzothiazoline-6-sulphonic acid) expressed as µM TE/g of potato powder; W = Shapiro–Wilk test statistics; * p < 0.05.

Figure 3

Circular heat map based on Pearson’s correlation of 104 potato accessions in two environments. (A) environment I and (B) environment II. TFC, total flavonoid content; TPC, total phenolic content (mg/100 g); DPPH, 2,2-Diphenyl-1-picrylhydrazyl; and ABTS, 2,2-azino-bis-(3-ethylbenzothiazoline-6-sulphonic acid) (µM TE/g of potato powder). Color ranges from dark blue to dark red indicate lower to higher levels of color parameters, TPC, TFC, DPPH, and ABTS.

Figure 4

Manhattan plots represent a genome-wide association study regarding color parameters in 104 potato accessions across two growing seasons. E1 represents environment I and E2 represents environment II. (A) Color parameters on a fresh basis of potatoes and (B) color parameters of potato fine powder (L* = lightness, a* = redness, b* = yellowness, C* = chroma, and H° = hue angle). The x-axis represents the chromosome number and the position of each SNP, while the y-axis represents the negative logarithm (−log10) of the p-values for each SNP. The broken lines represent significant thresholds 4.02 × 10⁻⁶. The heat maps at the bottom of each chromosome represent SNP density. The QQ plot on the left shows the observed vs. expected −log10 values. The diagonal line shows the predicted distribution whereas the other line indicates the observed p-values. The deviation from the diagonal line indicates a significant association.

Figure 5

Manhattan plots represent a genome-wide association study regarding nutritional quality traits in 104 potato accessions across two growing seasons. E1 represents environment I and E2 represents environment II. Significant SNPs are plotted on the right for DPPH and ABTS activity along with total phenolic content and total flavonoid content. The x-axis represents each SNP’s chromosome number and position, while the y-axis represents the negative logarithm (−log10) of the p-values for each SNP in the Manhattan plot. The broken lines represent significant thresholds 4.02 × 10⁻⁶. The heat maps at the bottom of each chromosome represent SNP density. The QQ plot on the left shows the observed vs. expected −log10 values.