Genome-Wide Association Study for Powdery Mildew and Rusts Adult Plant Resistance in European Spring Barley from Polish Gene Bank
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Material
2.2. Field Experiments and Phenotypic Evaluation
2.3. Weather Conditions
2.4. Statistical Analysis
2.5. Genotyping
2.6. Data Filtering Process
2.7. Genome-Wide Association Study (GWAS)
3. Results
3.1. Phenotypic Assessment of PM, SR, and BBR
3.1.1. Powdery Mildew
3.1.2. Barley Stem Rust
3.1.3. Barley Brown Rust
3.1.4. Relationship between PM, BBR, and SR
3.2. GWAS Analysis for Marker Trait Associations
3.2.1. Powdery Mildew GWAS
3.2.2. Barley Brown Rust GWAS
3.2.3. Stem Rust GWAS
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Sub-Collection | Country of Origin | Group | Germplasm Numbers (n) | |
---|---|---|---|---|
Polish | POL | I | A | 51 |
B | 49 | |||
C | 37 | |||
West-Central European | CSK, DEU, DNK, AUT | II | A | 91 |
B | 59 | |||
French | FRA | III | A | 14 |
B | 21 | |||
Great British | GBR, IRL | IV | A | 22 |
B | 8 | |||
Other European countries | NLD, FIN, NOR | V | A | 16 |
B | 15 | |||
Swedish | SWE | VI | A | 12 |
B | 26 | |||
Other non-European countries | VII | 10 | ||
Total | 431 |
Chromosome | Powdery Mildew (PM) | Stem Rust (SR) | Barley Brown Rust (BBR) | ||||||
---|---|---|---|---|---|---|---|---|---|
2019 | Maximum Scores Across All Replicates 2018–2019 | 2019 | Maximum Scores Across All Replicates 2018–2019 | 2019 | Maximum Scores Across All Replicates 2018–2019 | ||||
Heading Stage (HA) | Milky-Waxy Stage (MW) | Heading Stage (HA) | Milky-Waxy Stage (MW) | Heading Stage (HA) | Milky-Waxy Stage (MW) | ||||
1H | 2 | 0 | 0 | 2 | 6 | 0 | 2 | 0 | 0 |
2H | 0 | 0 | 2 | 5 | 4 | 0 | 1 | 0 | 1 |
3H | 1 | 0 | 1 | 2 | 0 | 0 | 0 | 0 | 3 |
4H | 1 | 0 | 1 | 4 | 1 | 0 | 0 | 0 | 0 |
5H | 1 | 0 | 0 | 3 | 3 | 0 | 2 | 0 | 1 |
6H | 0 | 0 | 1 | 3 | 3 | 0 | 0 | 1 | 0 |
7H | 0 | 0 | 0 | 3 | 9 | 1 | 1 | 0 | 2 |
Total | 5 | 0 | 5 | 22 | 26 | 1 | 6 | 1 | 7 |
Disease | Year | Growth Stage | Powdery Mildew (PM) | Barley Brown Rust (BBR) | Stem Rust (SR) | |||||
---|---|---|---|---|---|---|---|---|---|---|
2019 | 2018 | 2019 | 2018 | 2019 | ||||||
HA | MW | MW | HA | MW | MW | HA | MW | |||
Powdery mildew (PM) | 2019 | HA | 1.000 | |||||||
MW | 0.771 *** | 1.000 | ||||||||
2018 | MW | 0.315 ** | 0.186 * | 1.000 | ||||||
Barley brown rust (BBR) | 2019 | HA | 0.309 ** | 0.194 * | 0.149 * | 1.000 | ||||
MW | 0.215 ** | 0.123 * | 0.089 | 0.695 *** | 1.000 | |||||
2018 | MW | 0.144 * | 0.050 | 0.488 *** | 0.329 ** | 0.122 * | 1.000 | |||
Stem rust (SR) | 2019 | HA | 0.174* | 0.126 * | 0.022 | 0.166 * | 0.133 * | 0.054 | 1.000 | |
MW | 0.174 * | 0.092 | −0.012 | 0.277 ** | 0.231 ** | −0.012 | 0.074 | 1.000 | ||
2018 | MW | 0.100 * | 0.036 | 0.347 *** | 0.227 ** | 0.174 * | 0.383 *** | 0.062 | −0.019 |
Trait | SNP ID | Chromosome | Alleles | SNP Physical Localization | p-Value | FDR_Adjusted_p-Values |
---|---|---|---|---|---|---|
PM-HA | 3911365-45 | 1H | G/A | 368985776 | <0.0001 | 0.0698 |
PM-HA | 3262583-22 | 1H | A/C | 519071852 | 0.7863 | 0.9757 |
PM-HA | 3259998-68 | 3H | G/C | 17670801 | 0.0114 | 0.6563 |
PM-HA | 3432490-28 | 4H | T/C | 627441392 | 0.3438 | 0.8421 |
PM-HA | 4169584-26 | 5H | G/T | 650318560 | 0.0362 | 0.6563 |
PM | 6278248-38 | 2H | T/C | 706966122 | <0.0001 | <0.0001 |
PM | 3255391-29 | 3H | G/A | 611444890 | <0.0001 | <0.0001 |
PM | 3432490-28 | 4H | T/C | 627441392 | <0.0001 | <0.0001 |
PM | 6270346-59 | 6H | C/G | 352566440 | 0.0826 | 0.7632 |
PM | 3254946-37 | 2H | C/T | 69199631 | 0.2554 | 0.9025 |
Trait | SNP ID | Chromosome | Alleles | SNP Physical Localization | p-Value | FDR_Adjusted_p-Value |
---|---|---|---|---|---|---|
BBR-MW | 3432368-45 | 6H | A/G | 541093516 | <0.0001 | <0.0001 |
BBR | 3254780-21 | 2H | C/T | 745071336 | 0.2754 | 0.7942 |
BBR | 3255391-29 | 3H | G/A | 611444890 | 0.5133 | 0.9340 |
BBR | 3398205-7 | 3H | A/G | 611554417 | 0.5133 | 0.9340 |
BBR | 3432906-23 | 3H | T/G | 173445890 | 0.1095 | 0.7760 |
BBR | 3256738-34 | 5H | A/G | 371708131 | 0.4108 | 0.8968 |
BBR | 3919209-42 | 7H | G/C | 632737838 | 0.3551 | 0.8500 |
BBR | 5260969-17 | 7H | T/G | 638276193 | 0.6841 | 0.9699 |
Trait | SNP ID | Chromosome | Alleles | SNP Physical Localization | p-Value | FDR_Adjusted_p-Value |
---|---|---|---|---|---|---|
SR-HA | 3916722-6 | 1H | G/A | 443692735 | <0.0001 | <0.0001 |
SR-HA | 7242068-56 | 1H | C/G | 54281150 | <0.0001 | <0.0001 |
SR-HA | 3257827-54 | 2H | A/G | 612548328 | <0.0001 | <0.0001 |
SR-HA | 3254861-28 | 2H | T/G | 672603288 | <0.0001 | <0.0001 |
SR-HA | 3920041-34 | 3H | G/A | 553941251 | <0.0001 | <0.0001 |
SR-HA | 3920041-34 | 3H | G/A | 553941251 | <0.0001 | <0.0001 |
SR-HA | 100017008-29 | 3H | T/G | 236509272 | <0.0001 | <0.0001 |
SR-HA | 3260326-22 | 5H | C/T | 584321761 | <0.0001 | <0.0001 |
SR-HA | 3911523-28 | 5H | G/A | 582296115 | <0.0001 | <0.0001 |
SR-HA | 3926286-9 | 6H | T/C | 582688589 | <0.0001 | <0.0001 |
SR-HA | 8658544-48 | 6H | C/A | 19549390 | <0.0001 | <0.0001 |
SR-HA | 3665999-27 | 6H | G/A | 89415341 | 0.0018 | 0.2114 |
SR-HA | 6437148-27 | 7H | G/C | 625898188 | 0.9998 | 1.0000 |
SR-HA | 7242117-49 | 7H | G/T | 576216690 | <0.0001 | 0.0086 |
SR-MW | 3911365-45 | 1H | G/A | 368985776 | <0.0001 | 0.0059 |
SR-MW | 3924215-36 | 1H | C/T | 368983947 | 0.0001 | 0.0157 |
SR-MW | 3255467-46 | 1H | A/G | 361648993 | 0.0001 | 0.0200 |
SR-MW | 6429360-14 | 1H | C/T | 361649059 | 0.0001 | 0.0200 |
SR-MW | 4007106-27 | 1H | T/A | 87353500 | 0.0001 | 0.0269 |
SR-MW | 7242068-56 | 1H | C/G | 54281150 | 0.0003 | 0.0462 |
SR-MW | 3256098-57 | 2H | A/G | 724576571 | 0.0002 | 0.0300 |
SR-MW | 4329845-19 | 2H | G/C | 724652573 | 0.0002 | 0.0344 |
SR-MW | 3256445-31 | 2H | G/T | 651160368 | 0.0002 | 0.0398 |
SR-MW | 3255089-30 | 2H | G/C | 760930749 | 0.0003 | 0.0462 |
SR-MW | 3924288-41 | 4H | A/G | 36945544 | 0.0001 | 0.0160 |
SR-MW | 14350408-63 | 5H | T/C | 453639849 | 0.0001 | 0.0183 |
SR-MW | 3254700-12 | 5H | C/G | 622959955 | 0.0002 | 0.0360 |
SR-MW | 3398368-6 | 5H | C/G | 623060574 | 0.0003 | 0.0398 |
SR-MW | 7244989-23 | 6H | G/A | 56338324 | <0.0001 | 0.0115 |
SR-MW | 3261100-7 | 6H | G/A | 549171429 | 0.0001 | 0.0200 |
SR-MW | 4790439-14 | 6H | C/G | 548288936 | 0.0002 | 0.0360 |
SR-MW | 3925588-20 | 7H | T/G | 472163680 | <0.0001 | 0.0049 |
SR-MW | 4792770-43 | 7H | A/G | 384858359 | <0.0001 | 0.0049 |
SR-MW | 3918497-64 | 7H | A/G | 552832603 | <0.0001 | 0.0049 |
SR-MW | 3920255-11 | 7H | G/A | 553641369 | <0.0001 | 0.0049 |
SR-MW | 6277097-23 | 7H | C/G | 555109356 | <0.0001 | 0.0049 |
SR-MW | 3432458-59 | 7H | T/C | 357545360 | <0.0001 | 0.0049 |
SR-MW | 5258884-14 | 7H | G/T | 372119583 | <0.0001 | 0.0049 |
SR-MW | 13142583-10 | 7H | G/A | 556433100 | <0.0001 | 0.0049 |
SR-MW | 3258004-51 | 7H | T/C | 606094789 | 0.0003 | 0.0445 |
SR | 3918497-64 | 7H | A/G | 552832603 | <0.0001 | 0.0049 |
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Czembor, J.H.; Czembor, E.; Suchecki, R.; Watson-Haigh, N.S. Genome-Wide Association Study for Powdery Mildew and Rusts Adult Plant Resistance in European Spring Barley from Polish Gene Bank. Agronomy 2022, 12, 7. https://doi.org/10.3390/agronomy12010007
Czembor JH, Czembor E, Suchecki R, Watson-Haigh NS. Genome-Wide Association Study for Powdery Mildew and Rusts Adult Plant Resistance in European Spring Barley from Polish Gene Bank. Agronomy. 2022; 12(1):7. https://doi.org/10.3390/agronomy12010007
Chicago/Turabian StyleCzembor, Jerzy H., Elzbieta Czembor, Radoslaw Suchecki, and Nathan S. Watson-Haigh. 2022. "Genome-Wide Association Study for Powdery Mildew and Rusts Adult Plant Resistance in European Spring Barley from Polish Gene Bank" Agronomy 12, no. 1: 7. https://doi.org/10.3390/agronomy12010007
APA StyleCzembor, J. H., Czembor, E., Suchecki, R., & Watson-Haigh, N. S. (2022). Genome-Wide Association Study for Powdery Mildew and Rusts Adult Plant Resistance in European Spring Barley from Polish Gene Bank. Agronomy, 12(1), 7. https://doi.org/10.3390/agronomy12010007