Genotypic Diversity and Genome-Wide Association Study of Protein Content and Amino Acid Profile in Diverse Potato Accessions
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials and Preparation of Wholemeal Potato Powder
2.2. Determination of Protein Contents
2.3. Determination of Amino Acid Contents
2.4. SNP Calling and Population Structure Analysis
2.5. Genome-Wide Association Study
2.6. Statistical Analysis
3. Results
3.1. Genotypic Diversity of Potato Protein and Amino Acids Profile in 2019
3.2. Genotypic Diversity of Potato Protein and Amino Acids Profile in 2020
3.3. Genotype-by-Environment Interaction on Potato Protein and Amino Acids Diversity
3.4. Hierarchical Cluster Analysis
3.5. Principal Component Analysis
3.6. Correlation Analysis
3.7. Genome-Wide Association Study (GWAS) and Candidate Gene Analysis
4. Discussion
4.1. Genotypic Diversity of Protein Content and Amino Acids in Potatoes
4.2. Effect of Environments on Protein Content and Amino Acids
4.3. Genetic Basis of Potato Protein Contents and Amino Acids
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Environment-I | Environment-II | |||||
---|---|---|---|---|---|---|
Traits | Mean | Min. | Max. | Mean | Min. | Max. |
Essential amino acids | ||||||
Valine | 4.56 | 3.07 | 6.50 | 5.07 ** | 3.38 | 7.41 |
Isoleucine | 2.74 | 1.66 | 4.06 | 3.38 ** | 2.02 | 5.45 |
Leucine | 4.48 | 2.78 | 6.48 | 5.00 | 2.84 | 7.56 |
Threonine | 3.14 | 2.02 | 4.35 | 3.31 ** | 2.10 | 5.69 |
Phenylalanine | 3.44 | 2.26 | 5.00 | 4.21 | 2.00 | 6.13 |
Lysine | 4.84 | 2.99 | 7.27 | 5.25 ** | 3.21 | 7.77 |
Histidine | 1.43 | 0.79 | 2.27 | 1.74 ** | 1.04 | 3.17 |
Methionine | 0.93 | 0.27 | 1.85 | 0.98 ** | 0.21 | 1.91 |
Total EAA | 25.6 | 15.8 | 37.8 | 28.9 ** | 16.8 | 45.1 |
Non-Essential amino acids | ||||||
Aspartic acid | 19.8 | 9.86 | 36.8 | 23.3 ** | 10.5 | 39.1 |
Tyrosine | 2.19 | 1.30 | 3.36 | 2.95 ** | 1.61 | 4.63 |
Serine | 2.75 | 1.67 | 3.91 | 2.78 * | 1.62 | 4.31 |
Glutamic acid | 18.5 | 11.7 | 28.2 | 26.1 ** | 13.3 | 43.6 |
Glycine | 2.59 | 1.79 | 3.87 | 2.76 | 1.77 | 4.19 |
Alanine | 2.72 | 1.60 | 4.51 | 3.12 ** | 1.89 | 4.29 |
Cysteine | 0.69 | 0.35 | 1.18 | 0.76 ** | 0.02 | 1.51 |
Arginine | 4.32 | 2.01 | 9.70 | 6.17 | 2.27 | 19.3 |
Proline | 2.57 | 1.44 | 7.20 | 2.47 ** | 1.43 | 3.86 |
Total NEAA | 56.1 | 31.8 | 98.7 | 70.4 ** | 34.4 | 124.8 |
GABA | 2.32 | 0.94 | 4.30 | 2.28 ** | 0.17 | 5.21 |
Protein content (%) | 8.70 | 5.52 | 12.4 | 11.2 ** | 7.79 | 17.8 |
Source | df | Asp | Thr | Ser | Glu | Gly | Ala | Cys | Val | Met |
---|---|---|---|---|---|---|---|---|---|---|
Genotype | 89 | 41.2 ** | 0.59 ** | 0.34 ** | 39.2 ** | 0.31 ** | 0.34 ** | 0.05 ** | 1.02 ** | 0.08 |
Environment | 1 | 689.9 ** | 1.59 ** | 0.12 | 2882.8 ** | 1.39 ** | 8.71 ** | 0.26 ** | 14.6 ** | 0.22 * |
G × E | 89 | 25.0 ** | 0.26 ** | 0.24 ** | 16.1 ** | 0.14 ** | 0.19 ** | 0.04 ** | 0.52 ** | 0.09 |
Source | Ile | Leu | Tyr | Phe | GABA | Lys | His | Arg | Pro | Protein |
Genotype | 0.51 ** | 1.17 ** | 0.43 ** | 0.61 ** | 0.98 ** | 1.13 ** | 0.17 ** | 6.24 ** | 0.50 ** | 4.29 ** |
Environment | 21.1 ** | 14.2 ** | 29.7 ** | 29.9 ** | 0.02 | 10.5 ** | 4.95 ** | 171.7 ** | 0.61 * | 296.8 ** |
G × E | 0.28 ** | 0.59 ** | 0.27 ** | 0.42 ** | 0.30 | 0.63 ** | 0.11 ** | 2.36 ** | 0.37 ** | 2.67 ** |
Traits | Asp | Thr | Ser | Glu | Gly | Ala | Cys | Val | Met | Ile | Leu | Tyr | Phe | GABA | Lys | His | Arg | Pro | Protein |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Asp | 0.19 | 0.75 ** | 0.72 ** | 0.35 ** | 0.69 ** | 0.50 ** | 0.69 ** | 0.79 ** | 0.66 ** | 0.81 ** | 0.76 ** | 0.68 ** | 0.67 ** | 0.002 | 0.82 ** | 0.87 ** | 0.61 ** | 0.65 ** | 0.83 ** |
Thr | 0.73 ** | 0.37 ** | 0.85 ** | 0.34 ** | 0.85 ** | 0.56 ** | 0.78 ** | 0.75 ** | 0.64 ** | 0.80 ** | 0.87 ** | 0.66 ** | 0.66 ** | −0.09 | 0.81 ** | 0.80 ** | 0.69 ** | 0.80 ** | 0.81 ** |
Ser | 0.69 ** | 0.87 ** | 0.16 | 0.37 ** | 0.82 ** | 0.61 ** | 0.75 ** | 0.69 ** | 0.68 ** | 0.76 ** | 0.83 ** | 0.58 ** | 0.63 ** | −0.10 | 0.77 ** | 0.77 ** | 0.52 ** | 0.79 ** | 0.80 ** |
Glu | 0.51 ** | 0.49 ** | 0.36 ** | 0.39 ** | 0.23 * | 0.50 ** | 0.37 ** | 0.44 ** | 0.37 ** | 0.35 ** | 0.22 * | 0.29 ** | 0.18 | 0.16 | 0.40 ** | 0.47 ** | 0.35 ** | 0.20 | 0.64 ** |
Gly | 0.68 ** | 0.86 ** | 0.80 ** | 0.29 ** | 0.34 ** | 0.56 ** | 0.89 ** | 0.63 ** | 0.61 ** | 0.75 ** | 0.96 ** | 0.52 ** | 0.63 ** | −0.07 | 0.79 ** | 0.70 ** | 0.51 ** | 0.96 ** | 0.70 ** |
Ala | 0.75 ** | 0.82 ** | 0.81 ** | 0.50 ** | 0.75 ** | 0.26 * | 0.57 ** | 0.68 ** | 0.60 ** | 0.67 ** | 0.61 ** | 0.49 ** | 0.60 ** | 0.15 | 0.65 ** | 0.57 ** | 0.38 ** | 0.47 ** | 0.63 ** |
Cys | 0.63 ** | 0.69 ** | 0.62 ** | 0.25 * | 0.85 ** | 0.63 ** | 0.14 | 0.68 ** | 0.70 ** | 0.78 ** | 0.89 ** | 0.59 ** | 0.66 ** | −0.06 | 0.82 ** | 0.74 ** | 0.61 ** | 0.83 ** | 0.74 ** |
Val | 0.82 ** | 0.75 ** | 0.67 ** | 0.68 ** | 0.57 ** | 0.77 ** | 0.52 ** | 0.26 * | 0.65 ** | 0.94 ** | 0.74 ** | 0.82 ** | 0.82 ** | 0.12 | 0.88 ** | 0.88 ** | 0.68 ** | 0.57 ** | 0.83 ** |
Met | 0.52 ** | 0.54 ** | 0.44 ** | 0.43 ** | 0.39 ** | 0.53 ** | 0.48 ** | 0.63 ** | −0.03 | 0.68 ** | 0.64 ** | 0.58 ** | 0.61 ** | −0.18 | 0.65 ** | 0.70 ** | 0.65 ** | 0.50 ** | 0.71 ** |
Ile | 0.83 ** | 0.85 ** | 0.77 ** | 0.56 ** | 0.76 ** | 0.83 ** | 0.67 ** | 0.92 ** | 0.62 ** | 0.23 * | 0.84 ** | 0.80 ** | 0.85 ** | 0.07 | 0.91 ** | 0.88 ** | 0.67 ** | 0.69 ** | 0.81 ** |
Leu | 0.68 ** | 0.87 ** | 0.79 ** | 0.29 ** | 0.97 ** | 0.79 ** | 0.81 ** | 0.58 ** | 0.47 ** | 0.79 ** | 0.29 ** | 0.63 ** | 0.75 ** | −0.04 | 0.86 ** | 0.77 ** | 0.56 ** | 0.93 ** | 0.75 ** |
Tyr | 0.75 ** | 0.67 ** | 0.61 ** | 0.47 ** | 0.49 ** | 0.65 ** | 0.51 ** | 0.80 ** | 0.62 ** | 0.77 ** | 0.50 ** | 0.15 | 0.81 ** | −0.01 | 0.79 ** | 0.75 ** | 0.63 ** | 0.44 ** | 0.66 ** |
Phe | 0.83 ** | 0.83 ** | 0.79 ** | 0.43 ** | 0.80 ** | 0.79 ** | 0.68 ** | 0.82 ** | 0.59 ** | 0.91 ** | 0.81 ** | 0.75 ** | 0.13 | 0.02 | 0.80 ** | 0.69 ** | 0.53 ** | 0.55 ** | 0.62 ** |
GABA | 0.12 | 0.20 | 0.17 | 0.07 | 0.21 * | 0.26 ** | 0.27 ** | 0.16 | 0.20 | 0.16 | 0.20 * | 0.14 | 0.13 | 0.55 ** | 0.03 | 0.03 | −0.09 | −0.05 | −0.04 |
Lys | 0.89 ** | 0.84 ** | 0.78 ** | 0.52 ** | 0.77 ** | 0.83 ** | 0.66 ** | 0.88 ** | 0.56 ** | 0.93 ** | 0.78 ** | 0.78 ** | 0.93 ** | 0.16 | 0.24 * | 0.89 ** | 0.69 ** | 0.72 ** | 0.84 ** |
His | 0.90 ** | 0.77 ** | 0.71 ** | 0.54 ** | 0.69 ** | 0.79 ** | 0.61 ** | 0.88 ** | 0.58 ** | 0.91 ** | 0.72 ** | 0.79 ** | 0.90 ** | 0.12 | 0.93 ** | 0.13 | 0.78 ** | 0.68 ** | 0.91 ** |
Arg | 0.73 ** | 0.66 ** | 0.52 ** | 0.54 ** | 0.51 ** | 0.64 ** | 0.46 ** | 0.74 ** | 0.54 ** | 0.72 ** | 0.53 ** | 0.72 ** | 0.68 ** | −0.02 | 0.75 ** | 0.79 ** | 0.53 ** | 0.48 ** | 0.72 ** |
Pro | 0.58 ** | 0.60 ** | 0.60 ** | 0.18 | 0.74 ** | 0.57 ** | 0.67 ** | 0.43 ** | 0.24 * | 0.53 ** | 0.70 ** | 0.30 ** | 0.59 ** | 0.21 * | 0.59 ** | 0.54 ** | 0.35 ** | 0.15 | 0.68 ** |
Protein | 0.86 ** | 0.73 ** | 0.64 ** | 0.63 ** | 0.60 ** | 0.72 ** | 0.57 ** | 0.84 ** | 0.54 ** | 0.82 ** | 0.60 ** | 0.69 ** | 0.78 ** | 0.16 | 0.86 ** | 0.86 ** | 0.76 ** | 0.53 ** | 0.19 |
Traits | Env | Chr | Pos | Polymorphism | Effect | p-Value |
---|---|---|---|---|---|---|
Val | E2 | 3 | 30,733,104 | G/T | 0.96 | 3.63 × 10−6 |
E2 | 5 | 29,423,795 | A/G | 0.94 | 2.74 × 10−6 | |
E2 | 7 | 16,612,597 | T/G | 1.02 | 6.00 × 10−7 | |
E2 | 8 | 8,200,367 | T/A | 1.00 | 3.93 × 10−6 | |
E2 | 10 | 11,259,467 | A/T | 1.05 | 9.13 × 10−7 | |
E2 | 10 | 42,742,706 | G/A | 0.93 | 3.62 × 10−6 | |
E2 | 12 | 46,651,522 | T/A | 1.07 | 7.08 × 10−7 | |
Ile | E1 | 11 | 4,251,833 | C/T | −0.62 | 6.45 × 10−7 |
Leu | E1 | 4 | 3,239,607 | G/A | 0.93 | 3.54 × 10−6 |
E1 | 6 | 32,861,578 | G/A | 1.07 | 2.57 × 10−6 | |
E1 | 11 | 4,245686 | A/G | −0.97 | 2.60 × 10−6 | |
Thr | E1 | 1 | 39,366,436 | A/T | 0.62 | 1.10 × 10−6 |
E1 | 6 | 32,861,578 | G/A | 0.70 | 3.82 × 10−6 | |
E1 | 7 | 31,045,779 | A/G | 0.67 | 7.82 × 10−7 | |
E1 | 11 | 4,251,833 | C/T | −0.63 | 1.16 × 10−6 | |
E2 | 1 | 27,557,136 | G/A | 0.89 | 3.17 × 10−6 | |
E2 | 5 | 16,789,000 | G/A | 0.95 | 1.75 × 10−6 | |
E2 | 7 | 22,826,824 | T/C | 0.84 | 2.90 × 10−6 | |
E2 | 9 | 17,445,526 | T/C | 1.02 | 9.33 × 10−7 | |
E2 | 9 | 39,339,902 | C/T | 1.13 | 7.08 × 10−7 | |
E2 | 11 | 15,170,078 | A/T | 0.87 | 1.02 × 10−6 | |
Lys | E1 | 11 | 38,266,005 | G/A | 1.13 | 2.30 × 10−6 |
Met | E1 | 5 | 30,125,638 | A/C | 0.36 | 1.89 × 10−6 |
E1 | 8 | 13,060,996 | A/G | 0.36 | 3.14 × 10−6 | |
E1 | 9 | 5,875,273 | G/T | 0.41 | 2.96 × 10−6 | |
E1 | 11 | 44,175,166 | T/C | 0.30 | 3.40 × 10−6 | |
E2 | 6 | 40,534,805 | C/A | 0.46 | 4.92 × 10−8 | |
Asp | E2 | 5 | 37,361,991 | G/C | 7.08 | 3.64 × 10−6 |
Tyr | E1 | 4 | 294,768 | G/T | 0.62 | 3.06 × 10−6 |
Ser | E1 | 6 | 32,861,578 | G/A | 0.72 | 4.49 × 10−7 |
E1 | 7 | 46,305,291 | A/G | 0.68 | 1.90 × 10−6 | |
E2 | 9 | 39,339,902 | C/T | 0.86 | 3.60 × 10−6 | |
Glu | E1 | 5 | 39,242,513 | C/G | 2.30 | 6.82 × 10−8 |
E1 | 6 | 25,501,358 | T/A | 4.56 | 1.22 × 10−15 | |
E1 | 7 | 4,581,613 | T/C | −1.99 | 1.95 × 10−6 | |
E1 | 7 | 34,579,854 | A/G | −2.39 | 1.19 × 10−8 | |
E1 | 7 | 50,675,253 | T/C | 3.52 | 5.62 × 10−12 | |
E1 | 10 | 33,124,500 | A/G | 6.29 | 1.31 × 10−29 | |
E1 | 12 | 43,292,118 | C/A | −2.23 | 1.95 × 10−7 | |
E1 | 12 | 45,133,407 | C/A | −3.54 | 1.64 × 10−9 | |
Gly | E1 | 3 | 43,175,911 | C/A | 0.50 | 1.33 × 10−6 |
E1 | 6 | 32,861,578 | G/A | 0.57 | 2.37 × 10−7 | |
E1 | 10 | 58,454,528 | A/T | 0.59 | 3.32 × 10−6 | |
E1 | 10 | 59,143,531 | T/TA | 0.57 | 2.90 × 10−6 | |
Ala | E1 | 6 | 42,964,473 | A/G | 0.59 | 3.97 × 10−6 |
E1 | 7 | 34,678,031 | A/T | 0.79 | 2.06 × 10−6 | |
E1 | 11 | 4,245,686 | A/G | −0.62 | 1.89 × 10−6 | |
E1 | 11 | 35,966,739 | G/A | 0.76 | 7.39 × 10−7 | |
E1 | 11 | 36,000,195 | G/A | 0.69 | 3.80 × 10−6 | |
Cys | E1 | 3 | 19,968,173 | A/G | 0.21 | 6.63 × 10−8 |
E1 | 4 | 17,072,661 | T/C | 0.23 | 1.82 × 10−6 | |
E1 | 6 | 29,637,957 | G/A | 0.22 | 3.45 × 10−6 | |
E1 | 6 | 32,861,578 | G/A | 0.22 | 7.46 × 10−7 | |
E1 | 8 | 1,880,790 | T/C | 0.20 | 3.92 × 10−6 | |
E2 | 9 | 42,997,248 | G/T | 0.25 | 3.27 × 10−6 | |
Arg | E1 | 1 | 43,629,349 | T/G | 0.66 | 3.40 × 10−6 |
E1 | 1 | 68,183,425 | C/T | 0.60 | 7.08 × 10−7 | |
E1 | 3 | 5,618,996 | G/A | 0.78 | 1.38 × 10−7 | |
E1 | 11 | 4,251,833 | C/T | −0.85 | 1.30 × 10−10 | |
E2 | 1 | 8,356,1178 | C/CTCGGAGAG | 6.91 | 3.13 × 10−6 | |
E2 | 3 | 50,092 | C/T | 3.77 | 1.54 × 10−6 | |
E2 | 3 | 50,723,334 | C/T | 6.53 | 1.09 × 10−6 | |
E2 | 7 | 22,826,824 | T/C | 3.08 | 1.75 × 10−6 | |
E2 | 8 | 5,211,660 | G/A | 3.87 | 3.26 × 10−6 | |
E2 | 9 | 6,548,662 | G/A | 5.20 | 1.90 × 10−6 | |
Pro | E1 | 5 | 2,070,162 | G/A | 2.77 | 3.00 × 10−7 |
GABA | E1 | 5 | 18,301,550 | A/T | 1.12 | 9.60 × 10−8 |
E1 | 6 | 32,053,243 | A/C | 0.92 | 3.47 × 10−6 | |
E1 | 8 | 12,848,702 | T/A | 0.96 | 2.97 × 10−6 | |
E1 | 8 | 48,733,124 | A/T | 1.19 | 5.57 × 10−7 | |
E1 | 12 | 54,214,307 | G/A | 1.17 | 4.99 × 10−7 | |
E2 | 6 | 36,283,158 | T/A | 1.26 | 3.85 × 10−6 | |
E2 | 6 | 53,447,217 | T/G | −1.42 | 2.43 × 10−6 | |
E2 | 9 | 6,605,261 | A/G | 1.13 | 1.79 × 10−6 | |
E2 | 9 | 56,125,912 | A/G | 1.25 | 1.80 × 10−6 | |
E2 | 12 | 6,262,001 | G/T | −1.06 | 4.01 × 10−6 | |
Protein | E2 | 5 | 2,601,172 | G/A | 2.32 | 3.50 × 10−6 |
E2 | 9 | 58,640,876 | A/T | 2.52 | 1.94 × 10−6 |
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Rasheed, H.; Ying, Y.; Ahmad, D.; Deng, B.; Bao, J. Genotypic Diversity and Genome-Wide Association Study of Protein Content and Amino Acid Profile in Diverse Potato Accessions. Foods 2025, 14, 2039. https://doi.org/10.3390/foods14122039
Rasheed H, Ying Y, Ahmad D, Deng B, Bao J. Genotypic Diversity and Genome-Wide Association Study of Protein Content and Amino Acid Profile in Diverse Potato Accessions. Foods. 2025; 14(12):2039. https://doi.org/10.3390/foods14122039
Chicago/Turabian StyleRasheed, Haroon, Yining Ying, Daraz Ahmad, Bowen Deng, and Jinsong Bao. 2025. "Genotypic Diversity and Genome-Wide Association Study of Protein Content and Amino Acid Profile in Diverse Potato Accessions" Foods 14, no. 12: 2039. https://doi.org/10.3390/foods14122039
APA StyleRasheed, H., Ying, Y., Ahmad, D., Deng, B., & Bao, J. (2025). Genotypic Diversity and Genome-Wide Association Study of Protein Content and Amino Acid Profile in Diverse Potato Accessions. Foods, 14(12), 2039. https://doi.org/10.3390/foods14122039