Meta-Analysis of Genetic Factors for Potato Starch Phosphorylation
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Material
2.2. Starch Isolation
2.3. DNA Isolation and Genotyping
2.4. Phosphorus Content Analysis
2.5. PCA and Population Structure Analysis
2.6. Partial Least Squares (PLS) Analysis
2.7. Association Analysis
2.8. Meta-Analysis
2.9. Basic Local Alignment Tool (BLAST)
3. Results
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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SNP | p-Value (2017) | p-Value (2018) | p-Value (2019) | p-Value Meta-Analysis |
---|---|---|---|---|
solcap_snp_c2_55899 | 6.14 × 10−5 | 7.97 × 10−5 | 7.00 × 10−4 | 4.23 × 10−7 |
PotVar0091465 | 2.46 × 10−4 | 4.86 × 10−4 | 3.83 × 10−4 | 2.16 × 10−6 |
PotVar0001436 | 7.86 × 10−4 | 5.98 × 10−5 | 1.20 × 10−3 | 2.46 × 10−6 |
solcap_snp_c2_50231 | 3.49 × 10−4 | 9.93 × 10−5 | 1.87 × 10−3 | 2.69 × 10−6 |
2017 | 2018 | 2019 | |
---|---|---|---|
2017 | 1 | ||
2018 | 0.72 * | 1 | |
2019 | 0.80 * | 0.75 * | 1 |
Axis | Sing.Val. | % Covar |
---|---|---|
1 | 5.5948 | 91.503 |
2 | 1.3609 | 5.4137 |
3 | 1.027 | 3.0835 |
Year | First Bicomponent | Second Bicomponent | Third Bicomponent | |||
---|---|---|---|---|---|---|
Phenotype | Genotype | Phenotype | Genotype | Phenotype | Genotype | |
2017 | 0.93 * | 0.78 * | 0.14 | 0.09 | 0.36 * | 0.27 * |
2018 | 0.89 * | 0.74 * | 0.47 * | 0.32 * | 0.11 | 0.06 |
2019 | 0.94 * | 0.79 * | 0.22 | 0.21 | 0.20 | 0.21 |
N | SNP | Ch | Position | Threshold | p-Value | Polymorphysm | Minor Allele | Minor Allele Frequency | ||
---|---|---|---|---|---|---|---|---|---|---|
Current Study | Article [2] | Current Study, Meta-Analysis | Article [2] | |||||||
1 | solcap_snp_c2_55899 | 5 | 9,639,637 | Bonferroni | FDR | 4.23 × 10−7 | 9.01 × 10−6 | T/G | G | 0.30 |
2 | PotVar0091465 | 5 | 9,834,091 | Bonferroni | Below FDR | 2.16 × 10−6 | -- | A/G | G | 0.34 |
3 | PotVar0001436 | 5 | 20,274,370 | Bonferroni | Below FDR | 2.46 × 10−6 | -- | T/C | C | 0.38 |
4 | solcap_snp_c2_50231 | 5 | 36,834,630 | Bonferroni | FDR | 2.69 × 10−6 | 2.70 × 10−5 | T/C | C | 0.33 |
N | SNP | Gene Code | Gene Statistics | Protein Name | Protein Statistics |
---|---|---|---|---|---|
1 | solcap_snp_c2_50231 | -- | -- | -- | -- |
2 | solcap_snp_c2_55899 | PGSC0003DMG401016989 | Exons: 2, Coding exons: 1, Transcript length: 2961 bps, Translation length: 212 residues | LescPth4, or protein serine/threonine kinase | Ave. residue weight: 113.766 g/mol Charge: 0.0 Isoelectric point: 6.4888 Molecular weight: 24,118.36 g/mol Number of residues: 212 aa |
PGSC0003DMG402016989 | Exons: 1, Coding exons: 1, Transcript length: 1372 bps, Translation length: 68 residues | Protein kinase family protein | Ave. residue weight: 115.902 g/mol Charge: 2.5 Isoelectric point: 8.0567 Molecular weight: 7,881.32 g/mol Number of residues: 68 aa | ||
PGSC0003DMG400016991 | Exons: 1, Coding exons: 1, Transcript length: 1101 bps, Translation length: 205 residues | LescPth2, protein kinase | Ave. residue weight: 113.319 g/mol Charge: −5.0 Isoelectric point: 5.4433 Molecular weight: 36,375.41 g/mol Number of residues: 321 aa | ||
PGSC0003DMG400016992 | Exons: 1, Coding exons: 1, Transcript length: 1448 bps, Translation length: 120 residues | LescPth2, protein kinase | Ave. residue weight: 113.414 g/mol Charge: 7.0 Isoelectric point: 10.3705 Molecular weight: 15,991.43 g/mol Number of residues: 141 aa | ||
3 | PotVar0091465 | PGSC0003DMG400007677 | Exons: 34, Coding exons: 33, Transcript length: 5008 bps, Translation length: 1464 residues | GWD, or Starch-granule-bound R1 protein | Ave. residue weight: 111.535 g/mol Charge: −10.0 Isoelectric point: 5.8464 Molecular weight: 163,287.07 g/molNumber of residues: 1464 aa |
4 | PotVar0001436 | -- | -- | -- | -- |
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Khlestkin, V.; Erst, T.; Igoshin, A.; Rozanova, I.; Khlestkina, E. Meta-Analysis of Genetic Factors for Potato Starch Phosphorylation. Agronomy 2022, 12, 1343. https://doi.org/10.3390/agronomy12061343
Khlestkin V, Erst T, Igoshin A, Rozanova I, Khlestkina E. Meta-Analysis of Genetic Factors for Potato Starch Phosphorylation. Agronomy. 2022; 12(6):1343. https://doi.org/10.3390/agronomy12061343
Chicago/Turabian StyleKhlestkin, Vadim, Tatyana Erst, Alexander Igoshin, Irina Rozanova, and Elena Khlestkina. 2022. "Meta-Analysis of Genetic Factors for Potato Starch Phosphorylation" Agronomy 12, no. 6: 1343. https://doi.org/10.3390/agronomy12061343
APA StyleKhlestkin, V., Erst, T., Igoshin, A., Rozanova, I., & Khlestkina, E. (2022). Meta-Analysis of Genetic Factors for Potato Starch Phosphorylation. Agronomy, 12(6), 1343. https://doi.org/10.3390/agronomy12061343