Genome-Wide Association Study Reveals Marker–Trait Associations with Resistance to Pythium irregulare from Soybean Germplasm
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Material
2.2. Inoculum Preparation
2.3. Resistance Evaluation and Assessment
2.4. Statistical Analysis
2.5. Genome-Wide Association Study
3. Results
3.1. Phenotypic Evaluation of Soybean Germplasm for P. irregulare Resistance
3.2. Genome-Wide Association Study and Candidate Gene Analysis of Pythium irregulare Resistance
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Isolate Br 2-3-5 | Isolate SE21_0607_01 | Pooled | ||||||
---|---|---|---|---|---|---|---|---|
Estimator | Effect | p-Value a | Estimator | Effect | p-Value a | Estimator | Effect | p-Value a |
Intercept | 0.126 | 3.16 × 10−1 | Intercept | 0.176 | 5.74 × 10−3 | Intercept | 0.114 | 2.89 × 10−1 |
PI 490766 | 0.521 | 4.54 × 10−4 * | PI 548520 | 0.256 | 1.08 × 10−3 * | PI 548520 | 0.358 | 4.02 × 10−3 * |
PI 547459 | 0.488 | 1.00 × 10−3 * | PI 578503 | 0.253 | 1.28 × 10−3 * | FC 29333 | 0.373 | 9.14 × 10−3 * |
PI 591511 | 0.401 | 6.82 × 10−3 * | PI 84987 A | 0.139 | 6.96 × 10−2 | PI 84946-2 | 0.321 | 2.49 × 10−2 * |
PI 547460 | 0.390 | 8.51 × 10−3 * | PI 632418 | 0.135 | 7.75 × 10−2 | PI 490766 | 0.273 | 2.81 × 10−2 * |
PI 548520 | 0.385 | 9.33 × 10−3 * | PI 548521 | 0.131 | 8.80 × 10−2 | PI 547459 | 0.271 | 2.94 × 10−2 * |
FC 29333 | 0.381 | 1.01 × 10−2 * | PI 603549 | 0.108 | 1.58 × 10−1 | PI 548362 | 0.310 | 3.00 × 10−2 * |
PI 548360 | 0.331 | 2.52 × 10−2 * | PI 567258 | 0.104 | 1.74 × 10−1 | PI 548360 | 0.245 | 4.82 × 10−2 * |
PI 84946-2 | 0.329 | 2.63 × 10−2 * | PI 438239 B | 0.088 | 2.46 × 10−1 | PI 591511 | 0.242 | 5.14 × 10−2 |
PI 548362 | 0.318 | 3.15 × 10−2 * | PI 88468 | 0.085 | 2.63 × 10−1 | PI 547460 | 0.237 | 5.64 × 10−2 |
PI 639559 B | 0.268 | 6.97 × 10−2 | PI 548360 | 0.085 | 2.66 × 10−1 | PI 639559 B | 0.260 | 6.86 × 10−2 |
Isolate | Predictor | SS | MS | NDF | DDF | F-Value | p-Value a |
---|---|---|---|---|---|---|---|
Br 2-3-5 | Accession | 10.089 | 0.04874 | 207 | 414 | 1.4958 | 3.120 × 10−4 * |
SE21_0607_01 | Accession | 1.083 | 0.0258 | 42 | 84 | 2.9961 | 9.530 × 10−6 * |
Pooled | Accession | 9.057 | 0.0438 | 207 | 539 | 1.4333 | 6.728 × 10−4 * |
Marker Name | Chromosome | Position (bp) a | Major/Minor Allele | MAF b | p-Value c | RRW Effect d |
---|---|---|---|---|---|---|
ss715621416 | 15 | 26,089,343 | C/A | 0.087 | 3.56 × 10−15 | 0.172 |
ss715606444 | 10 | 36,778,506 | C/T | 0.082 | 1.53 × 10−6 | 0.093 |
SNP Marker | Major/Minor Allele | Effect | PI 548520 | FC 29333 | PI 84946-2 | PI 490766 | PI 547459 | PI 548362 | PI 548360 |
---|---|---|---|---|---|---|---|---|---|
ss715621416 | C/A | 0.172 | C | A | C | A | A | C | C |
ss715606444 | C/T | 0.093 | T | C | C | T | T | T | C |
Sum of allelic effects: | 0.265 | 0.093 | 0.172 | 0 | 0.265 | 0.265 | 0.093 | 0 | |
Pooled mean RRW: | 0.472 ± 0.12 | 0.507 ± 0.35 | 0.455 ± 0.37 | 0.386 ± 0.16 | 0.384 ± 0.16 | 0.444 ± 0.30 | 0.359 ± 0.06 | ||
Pooled mean adjusted stand count: | 0.794 ± 0.15 | 0.467 ± 0.24 | 0.222 ± 0.18 | 0.597 ± 0.10 | 0.594 ± 0.17 | 0.444 ± 0.24 | 0.581 ± 0.09 |
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Detranaltes, C.; Ma, J.; Cai, G. Genome-Wide Association Study Reveals Marker–Trait Associations with Resistance to Pythium irregulare from Soybean Germplasm. Int. J. Plant Biol. 2024, 15, 769-782. https://doi.org/10.3390/ijpb15030056
Detranaltes C, Ma J, Cai G. Genome-Wide Association Study Reveals Marker–Trait Associations with Resistance to Pythium irregulare from Soybean Germplasm. International Journal of Plant Biology. 2024; 15(3):769-782. https://doi.org/10.3390/ijpb15030056
Chicago/Turabian StyleDetranaltes, Christopher, Jianxin Ma, and Guohong Cai. 2024. "Genome-Wide Association Study Reveals Marker–Trait Associations with Resistance to Pythium irregulare from Soybean Germplasm" International Journal of Plant Biology 15, no. 3: 769-782. https://doi.org/10.3390/ijpb15030056
APA StyleDetranaltes, C., Ma, J., & Cai, G. (2024). Genome-Wide Association Study Reveals Marker–Trait Associations with Resistance to Pythium irregulare from Soybean Germplasm. International Journal of Plant Biology, 15(3), 769-782. https://doi.org/10.3390/ijpb15030056