Genotypic Diversity and Genome-Wide Association Study of Protein Content and Amino Acid Profile in Diverse Potato Accessions

Abstract

The genotypic diversity and genome-wide association study (GWAS) of potato proteins and amino acid content were investigated in two environments: 98 potato accessions in Environment I and 93 in Environment II. Results revealed that aspartic acid was the most abundant amino acid in environment I and glutamic acid in environment II. The limiting amino acids were cysteine in both environments. The environmental variance accounted for more than 40% of the total variance for all traits except for serine and gamma amino butyric acid (GABA), indicating that potato protein and most amino acids were affected by growing seasons. GWAS identified 78 significant loci associated with potato protein and amino acid contents. The pleiotropic loci, especially those located on chromosomes 6, 9, and 11, provide a strong genetic basis for quality improvement. This study provides genetic insights into potato proteins and amino acid diversity, thereby enhancing molecular breeding for nutritional qualities.

Keywords: amino acid; environment; genotypic diversity; nutritional quality; potato.

Figure 1

Diversity of potato protein and amino acids across two environments. E1, environment-I; E2, environment-II; result indicated amino acid as mg/g; protein in percentage.

Figure 2

Protein and amino acid profile clustering in diverse potato accessions in two environments. Hierarchical clustering analysis based on the two-way Ward method. (A) represents Environment I and (B) Environment II. Each row in the heat map represents an individual amino acid and protein content, while the column represents different potato accessions. The color scale in the heat map represents the relative concentrations of amino acids, where the red color indicates a higher concentration, while the blue color indicates a lower level of protein and amino acid profile.

Figure 3

Principal component (PCA) visualization of protein and amino acid response to the diversity of environments. PCA separates potato accessions across two environments based on (mean of two repeats), protein, and amino acid composition in a diversity of potato accessions. Each point represents two different environments (Black, Environment I, and Red, Environment II). The ellipse represents 95% confidence intervals around the centroid of each data cluster.

Figure 4

Genome-wide association study of potato protein and amino acid contents across two environments. (A) represents the pleiotropic gene on chromosome 6 (B) represents chromosome 11 with the pleiotropic gene. Each dot represents an SNP. The x-axis represents chromosomal numbers and SNP positions. The y-axis represents the negative logarithm p-value for individual SNPs. The broken red line represents the significant threshold 4.02 × 10⁻⁶. The heat maps at the bottom of each chromosome represent SNP density for potato protein contents and amino acids across two environments.

Figure 4

Genome-wide association study of potato protein and amino acid contents across two environments. (A) represents the pleiotropic gene on chromosome 6 (B) represents chromosome 11 with the pleiotropic gene. Each dot represents an SNP. The x-axis represents chromosomal numbers and SNP positions. The y-axis represents the negative logarithm p-value for individual SNPs. The broken red line represents the significant threshold 4.02 × 10⁻⁶. The heat maps at the bottom of each chromosome represent SNP density for potato protein contents and amino acids across two environments.