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1. Additional file 10 of Genotyping and lipid profiling of 601 cultivated sunflower lines reveals novel genetic determinants of oil fatty acid content

Author

Chernova, Alina I., Gubaev, Rim F., Singh, Anupam, Sherbina, Katrina, Goryunova, Svetlana V., Martynova, Elena U., Goryunov, Denis V., Boldyrev, Stepan V., Vanyushkina, Anna A., Anikanov, Nikolay A., Stekolshchikova, Elena A., Yushina, Ekaterina A., Demurin, Yakov N., Mukhina, Zhanna M., Gavrilova, Vera A., Anisimova, Irina N., Karabitsina, Yulia I., Alpatieva, Natalia V., Chang, Peter L., Khaitovich, Philipp, Mazin, Pavel V., and Nuzhdin, Sergey V.

Subjects
lipids (amino acids, peptides, and proteins)
Abstract

Additional file 10: FigureS10. GWAS Manhattan plots for (a) Stearic acid; (b) Nonadecanoic acid; (c) Eicosenoic acid; (d) Docosanoic acid; (e) Tetracosanoic acid; (f) Nervonic acid; (g) Oleic acid; (h) Linoleic acid; (i) Ratio between oleic and linoleic acids. FDR and Bonferroni thresholds are shown by blue and red, respectively.

Published
2021
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2. Additional file 5 of Genotyping and lipid profiling of 601 cultivated sunflower lines reveals novel genetic determinants of oil fatty acid content

Author

Chernova, Alina I., Gubaev, Rim F., Singh, Anupam, Sherbina, Katrina, Goryunova, Svetlana V., Martynova, Elena U., Goryunov, Denis V., Boldyrev, Stepan V., Vanyushkina, Anna A., Anikanov, Nikolay A., Stekolshchikova, Elena A., Yushina, Ekaterina A., Demurin, Yakov N., Mukhina, Zhanna M., Gavrilova, Vera A., Anisimova, Irina N., Karabitsina, Yulia I., Alpatieva, Natalia V., Chang, Peter L., Khaitovich, Philipp, Mazin, Pavel V., and Nuzhdin, Sergey V.

Abstract

Additional file 5: FigureS5. (A) Multidimensional scaling plot (two dimensions, 1 - Spearman correlation coefficient between TAGs abundances measured using LC-MS with dilution 1:25 was used as distance). One sample is shown by one point; accessions are shown by different colors; different years are shown by points of different shapes. (B) Minus log10 p-values for the differences between lines (ANOVA) are shown, TAGs are ordered by p-value increase from top left to bottom right. Bonferroni adjusted 0.05 significance level is shown by red line; (C-G) abundances of five selected TAGs are shown across lines and years. Each point represents 1 sample, point shapes, and colors as in (A), lines show per-year averages. This figure complements main Fig. 3.

Published
2021
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3. Additional file 9 of Genotyping and lipid profiling of 601 cultivated sunflower lines reveals novel genetic determinants of oil fatty acid content

Author

Chernova, Alina I., Gubaev, Rim F., Singh, Anupam, Sherbina, Katrina, Goryunova, Svetlana V., Martynova, Elena U., Goryunov, Denis V., Boldyrev, Stepan V., Vanyushkina, Anna A., Anikanov, Nikolay A., Stekolshchikova, Elena A., Yushina, Ekaterina A., Demurin, Yakov N., Mukhina, Zhanna M., Gavrilova, Vera A., Anisimova, Irina N., Karabitsina, Yulia I., Alpatieva, Natalia V., Chang, Peter L., Khaitovich, Philipp, Mazin, Pavel V., and Nuzhdin, Sergey V.

Abstract

Additional file 9: FigureS9. Replication experiment on 6 accessions. (Left) Distributions of FAs (top) or TAGs (middle and bottom) by percentages of variance explained by genotype (G), environment (year, E), interaction between genotype and environment (G:E) or percentage of residual variance. Distribution of the same percentages divided by number of degrees of freedom of corresponding factor are shown on the right.

Published
2021
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4. Additional file 6 of Genotyping and lipid profiling of 601 cultivated sunflower lines reveals novel genetic determinants of oil fatty acid content

Author

Chernova, Alina I., Gubaev, Rim F., Singh, Anupam, Sherbina, Katrina, Goryunova, Svetlana V., Martynova, Elena U., Goryunov, Denis V., Boldyrev, Stepan V., Vanyushkina, Anna A., Anikanov, Nikolay A., Stekolshchikova, Elena A., Yushina, Ekaterina A., Demurin, Yakov N., Mukhina, Zhanna M., Gavrilova, Vera A., Anisimova, Irina N., Karabitsina, Yulia I., Alpatieva, Natalia V., Chang, Peter L., Khaitovich, Philipp, Mazin, Pavel V., and Nuzhdin, Sergey V.

Abstract

Additional file 6: FigureS6. Replication experiment on 6 accessions: relative abundances of all the fatty acids with significant (FDR

Published
2021
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5. Additional file 1 of Genotyping and lipid profiling of 601 cultivated sunflower lines reveals novel genetic determinants of oil fatty acid content

Author

Chernova, Alina I., Gubaev, Rim F., Singh, Anupam, Sherbina, Katrina, Goryunova, Svetlana V., Martynova, Elena U., Goryunov, Denis V., Boldyrev, Stepan V., Vanyushkina, Anna A., Anikanov, Nikolay A., Stekolshchikova, Elena A., Yushina, Ekaterina A., Demurin, Yakov N., Mukhina, Zhanna M., Gavrilova, Vera A., Anisimova, Irina N., Karabitsina, Yulia I., Alpatieva, Natalia V., Chang, Peter L., Khaitovich, Philipp, Mazin, Pavel V., and Nuzhdin, Sergey V.

Abstract

Additional file 1: FigS1. ((A) PCA plots reflecting the relationships between sunflower technical samples based on 15,068 SNPs segregating in the Russian collection. Each dot corresponds to a sunflower technical sample used in the study. Dots are colored by sequencing batch (A) or collection samples were obtained from (B) (C) Nei’s genetic distance matrix between each 2 samples.

Published
2021
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6. Additional file 6 of Genotyping and lipid profiling of 601 cultivated sunflower lines reveals novel genetic determinants of oil fatty acid content

Author

Chernova, Alina I., Gubaev, Rim F., Singh, Anupam, Sherbina, Katrina, Goryunova, Svetlana V., Martynova, Elena U., Goryunov, Denis V., Boldyrev, Stepan V., Vanyushkina, Anna A., Anikanov, Nikolay A., Stekolshchikova, Elena A., Yushina, Ekaterina A., Demurin, Yakov N., Mukhina, Zhanna M., Gavrilova, Vera A., Anisimova, Irina N., Karabitsina, Yulia I., Alpatieva, Natalia V., Chang, Peter L., Khaitovich, Philipp, Mazin, Pavel V., and Nuzhdin, Sergey V.

Abstract

Additional file 6: FigureS6. Replication experiment on 6 accessions: relative abundances of all the fatty acids with significant (FDR

Published
2021
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7. Additional file 3 of Genotyping and lipid profiling of 601 cultivated sunflower lines reveals novel genetic determinants of oil fatty acid content

Author

Chernova, Alina I., Gubaev, Rim F., Singh, Anupam, Sherbina, Katrina, Goryunova, Svetlana V., Martynova, Elena U., Goryunov, Denis V., Boldyrev, Stepan V., Vanyushkina, Anna A., Anikanov, Nikolay A., Stekolshchikova, Elena A., Yushina, Ekaterina A., Demurin, Yakov N., Mukhina, Zhanna M., Gavrilova, Vera A., Anisimova, Irina N., Karabitsina, Yulia I., Alpatieva, Natalia V., Chang, Peter L., Khaitovich, Philipp, Mazin, Pavel V., and Nuzhdin, Sergey V.

Abstract

Additional file 3: FigureS3. Joint principal component analysis of sunflower accessions genotyped in this study and in Hübner (2019) based on 2345 shared SNPs. The first and the second (A) or the first and the third (B) PCs are shown. Each dot corresponds to a plant accession. Colors indicate the origin (wild/line/landrace). Shapes indicate species.

Published
2021
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8. Additional file 8 of Genotyping and lipid profiling of 601 cultivated sunflower lines reveals novel genetic determinants of oil fatty acid content

Author

Chernova, Alina I., Gubaev, Rim F., Singh, Anupam, Sherbina, Katrina, Goryunova, Svetlana V., Martynova, Elena U., Goryunov, Denis V., Boldyrev, Stepan V., Vanyushkina, Anna A., Anikanov, Nikolay A., Stekolshchikova, Elena A., Yushina, Ekaterina A., Demurin, Yakov N., Mukhina, Zhanna M., Gavrilova, Vera A., Anisimova, Irina N., Karabitsina, Yulia I., Alpatieva, Natalia V., Chang, Peter L., Khaitovich, Philipp, Mazin, Pavel V., and Nuzhdin, Sergey V.

Abstract

Additional file 8: FigureS8. Replication experiment on 6 genotypes: relative abundances of all TAGs detected by LC-MS with dilution 1:25 with significant (FDR

Published
2021
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9. Additional file 7 of Genotyping and lipid profiling of 601 cultivated sunflower lines reveals novel genetic determinants of oil fatty acid content

Author

Chernova, Alina I., Gubaev, Rim F., Singh, Anupam, Sherbina, Katrina, Goryunova, Svetlana V., Martynova, Elena U., Goryunov, Denis V., Boldyrev, Stepan V., Vanyushkina, Anna A., Anikanov, Nikolay A., Stekolshchikova, Elena A., Yushina, Ekaterina A., Demurin, Yakov N., Mukhina, Zhanna M., Gavrilova, Vera A., Anisimova, Irina N., Karabitsina, Yulia I., Alpatieva, Natalia V., Chang, Peter L., Khaitovich, Philipp, Mazin, Pavel V., and Nuzhdin, Sergey V.

Abstract

Additional file 7: FigureS7. Replication experiment on 6 genotypes: relative abundances of all TAGs detected by LC-MS with dilution 1:3 with significant (FDR

Published
2021
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10. Additional file 2 of Genotyping and lipid profiling of 601 cultivated sunflower lines reveals novel genetic determinants of oil fatty acid content

Author

Chernova, Alina I., Gubaev, Rim F., Singh, Anupam, Sherbina, Katrina, Goryunova, Svetlana V., Martynova, Elena U., Goryunov, Denis V., Boldyrev, Stepan V., Vanyushkina, Anna A., Anikanov, Nikolay A., Stekolshchikova, Elena A., Yushina, Ekaterina A., Demurin, Yakov N., Mukhina, Zhanna M., Gavrilova, Vera A., Anisimova, Irina N., Karabitsina, Yulia I., Alpatieva, Natalia V., Chang, Peter L., Khaitovich, Philipp, Mazin, Pavel V., and Nuzhdin, Sergey V.

Abstract

Additional file 2: FigureS2. Linkage disequilibrium (LD) decay plot. (A) Genome-wide LD. Gray dots correspond to a SNP pair, y-axis show r2 between two SNPs calculated using whole dataset. SNP pairs with distance less than 5 Mb are shown. (B) LD per each chromosome. Lines correspond to loess curves; 95% confidence intervals are shown by shades.

Published
2021
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11. Additional file 4 of Genotyping and lipid profiling of 601 cultivated sunflower lines reveals novel genetic determinants of oil fatty acid content

Author

Chernova, Alina I., Gubaev, Rim F., Singh, Anupam, Sherbina, Katrina, Goryunova, Svetlana V., Martynova, Elena U., Goryunov, Denis V., Boldyrev, Stepan V., Vanyushkina, Anna A., Anikanov, Nikolay A., Stekolshchikova, Elena A., Yushina, Ekaterina A., Demurin, Yakov N., Mukhina, Zhanna M., Gavrilova, Vera A., Anisimova, Irina N., Karabitsina, Yulia I., Alpatieva, Natalia V., Chang, Peter L., Khaitovich, Philipp, Mazin, Pavel V., and Nuzhdin, Sergey V.

Abstract

Additional file 4 (A) Multidimensional scaling plot (two dimensions, 1 - Spearman correlation coefficient between TAGs abundances measured using LC-MS with dilution 1:3 was used as distance). One sample is shown by one point; accessions are shown by different colors; different years are shown by points of different shapes. (B) Minus log10 p-values for the differences between lines (ANOVA) are shown, TAGs are ordered by p-value increase from top left to bottom right. Bonferroni adjusted 0.05 significance level is shown by red line; (C-G) abundances of five selected TAGs are shown across lines and years. Each point represents 1 sample, point shapes, and colors as in (A), lines show per-year averages. This figure complements main Fig. 3.

Published
2021
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12. Additional file 9 of Genotyping and lipid profiling of 601 cultivated sunflower lines reveals novel genetic determinants of oil fatty acid content

Author

Chernova, Alina I., Gubaev, Rim F., Singh, Anupam, Sherbina, Katrina, Goryunova, Svetlana V., Martynova, Elena U., Goryunov, Denis V., Boldyrev, Stepan V., Vanyushkina, Anna A., Anikanov, Nikolay A., Stekolshchikova, Elena A., Yushina, Ekaterina A., Demurin, Yakov N., Mukhina, Zhanna M., Gavrilova, Vera A., Anisimova, Irina N., Karabitsina, Yulia I., Alpatieva, Natalia V., Chang, Peter L., Khaitovich, Philipp, Mazin, Pavel V., and Nuzhdin, Sergey V.

Abstract

Additional file 9: FigureS9. Replication experiment on 6 accessions. (Left) Distributions of FAs (top) or TAGs (middle and bottom) by percentages of variance explained by genotype (G), environment (year, E), interaction between genotype and environment (G:E) or percentage of residual variance. Distribution of the same percentages divided by number of degrees of freedom of corresponding factor are shown on the right.

Published
2021
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13. Additional file 22 of Genotyping and lipid profiling of 601 cultivated sunflower lines reveals novel genetic determinants of oil fatty acid content

Author

Chernova, Alina I., Gubaev, Rim F., Singh, Anupam, Sherbina, Katrina, Goryunova, Svetlana V., Martynova, Elena U., Goryunov, Denis V., Boldyrev, Stepan V., Vanyushkina, Anna A., Anikanov, Nikolay A., Stekolshchikova, Elena A., Yushina, Ekaterina A., Demurin, Yakov N., Mukhina, Zhanna M., Gavrilova, Vera A., Anisimova, Irina N., Karabitsina, Yulia I., Alpatieva, Natalia V., Chang, Peter L., Khaitovich, Philipp, Mazin, Pavel V., and Nuzhdin, Sergey V.

Abstract

Additional file 22: Supporting experimental procedures. Method S1. Reagents, Method S2. GBS library preparation, Method S3. Lipid extraction and UPLC-MS.

Published
2021
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14. Additional file 12 of Genotyping and lipid profiling of 601 cultivated sunflower lines reveals novel genetic determinants of oil fatty acid content

Author

Chernova, Alina I., Gubaev, Rim F., Singh, Anupam, Sherbina, Katrina, Goryunova, Svetlana V., Martynova, Elena U., Goryunov, Denis V., Boldyrev, Stepan V., Vanyushkina, Anna A., Anikanov, Nikolay A., Stekolshchikova, Elena A., Yushina, Ekaterina A., Demurin, Yakov N., Mukhina, Zhanna M., Gavrilova, Vera A., Anisimova, Irina N., Karabitsina, Yulia I., Alpatieva, Natalia V., Chang, Peter L., Khaitovich, Philipp, Mazin, Pavel V., and Nuzhdin, Sergey V.

Abstract

Additional file 12: FigureS12. Data clean up using blank samples. Top panels show dependence of average log2 seed sample intensity of FAs and TAGs (two dilutions) on average log2 intensity of same lipids in blank samples (see Methods). Straight and dashed lines correspond to equal intensities in both types of sample and to two-fold higher concentration in seed samples compared to blanks, respectively. Bottom panels show the same lipids as top panels in coordinates of total FA (TAG) chain length (x-axis), and number of double bounds (y-axis), point size is proportional to log2 average intensity in seed samples. Only lipids with log2(sample/blank) > 1 were used in analysis, remaining FAs and TAGs (shown in red) were filtered out.

Published
2021
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15. Additional file 11 of Genotyping and lipid profiling of 601 cultivated sunflower lines reveals novel genetic determinants of oil fatty acid content

Author

Chernova, Alina I., Gubaev, Rim F., Singh, Anupam, Sherbina, Katrina, Goryunova, Svetlana V., Martynova, Elena U., Goryunov, Denis V., Boldyrev, Stepan V., Vanyushkina, Anna A., Anikanov, Nikolay A., Stekolshchikova, Elena A., Yushina, Ekaterina A., Demurin, Yakov N., Mukhina, Zhanna M., Gavrilova, Vera A., Anisimova, Irina N., Karabitsina, Yulia I., Alpatieva, Natalia V., Chang, Peter L., Khaitovich, Philipp, Mazin, Pavel V., and Nuzhdin, Sergey V.

Abstract

Additional file 11: FigureS11. LD blocks containing significant SNPs. Each panel represents one significant association, traits and chromosome names where significant loci is located are shown in panel titles. Each panel schematically shows associated loci with all detected SNPs. LD-blocks detected by Haploview software are shown by heatmaps, r2 (%) for each SNP pair is shown by color and numbers.

Published
2021
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16. Additional file 23 of Genotyping and lipid profiling of 601 cultivated sunflower lines reveals novel genetic determinants of oil fatty acid content

Author

Chernova, Alina I., Gubaev, Rim F., Singh, Anupam, Sherbina, Katrina, Goryunova, Svetlana V., Martynova, Elena U., Goryunov, Denis V., Boldyrev, Stepan V., Vanyushkina, Anna A., Anikanov, Nikolay A., Stekolshchikova, Elena A., Yushina, Ekaterina A., Demurin, Yakov N., Mukhina, Zhanna M., Gavrilova, Vera A., Anisimova, Irina N., Karabitsina, Yulia I., Alpatieva, Natalia V., Chang, Peter L., Khaitovich, Philipp, Mazin, Pavel V., and Nuzhdin, Sergey V.

Abstract

Additional file 23: AppendixS1. Description of the lines used in the study.

Published
2021
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17. Additional file 7 of Genotyping and lipid profiling of 601 cultivated sunflower lines reveals novel genetic determinants of oil fatty acid content

Author

Chernova, Alina I., Gubaev, Rim F., Singh, Anupam, Sherbina, Katrina, Goryunova, Svetlana V., Martynova, Elena U., Goryunov, Denis V., Boldyrev, Stepan V., Vanyushkina, Anna A., Anikanov, Nikolay A., Stekolshchikova, Elena A., Yushina, Ekaterina A., Demurin, Yakov N., Mukhina, Zhanna M., Gavrilova, Vera A., Anisimova, Irina N., Karabitsina, Yulia I., Alpatieva, Natalia V., Chang, Peter L., Khaitovich, Philipp, Mazin, Pavel V., and Nuzhdin, Sergey V.

Abstract

Additional file 7: FigureS7. Replication experiment on 6 genotypes: relative abundances of all TAGs detected by LC-MS with dilution 1:3 with significant (FDR

Published
2021
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