Genome-Wide Association Studies and QTL Mapping Reveal a New Locus Associated with Resistance to Bacterial Pustule Caused by Xanthomonas citri pv. glycines in Soybean
Abstract
:1. Introduction
2. Results
2.1. Phenotypic Evaluation of Bacterial Pustule Resistance in Soybean Accessions
2.2. Genome-Wide Association Study for Bacterial Pustule Resistance
2.3. Haplotype Analysis
2.4. Investigation of LD Blocks Based on WGS Data and Additional Allelic Variation
2.5. QTL Mapping
3. Discussion
3.1. Xanthomonas citri Reactions in the GWAS Panel
3.2. GWAS Highlights Two Genomic Regions Associated with BP Resistance in Soybean
3.3. New Resistance Locus to BP Confer Resistance to Tropical Adapted Soybean Cultivars and Their Ancestors
3.4. Exploring the Regions Identified by GWAS
4. Materials and Methods
4.1. GWAS Plant Materials and QTL Mapping Population
4.2. Phenotypic Evaluation for Bacterial Pustule
4.3. DNA Extraction, GBS Library Preparation, and SNP Calling for GWAS
4.4. Panels Composition and SoySNP50K Analysis
4.5. Population Structure and Association Mapping
4.6. Linkage Disequilibrium Detection, Haplotype Analysis, and Candidate Gene Annotations
4.7. Inheritance Analysis and QTL MAPPING
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Disease Score | Class | IBS 333 | IBS 327 | ||
---|---|---|---|---|---|
Number of Accessions | % | Number of Accessions | % | ||
0 | I | 0 | 0 | 34 | 18.8 |
1 | R | 64 | 35.2 | 30 | 16.6 |
2 | MR | 28 | 15.4 | 35 | 19.3 |
3 | MS | 17 | 9.3 | 25 | 13.8 |
4 | S | 35 | 19.2 | 56 | 30.9 |
5 | HS | 38 | 20.9 | 1 | 0.6 |
Total | - | 182 | 100% | 181 | 100% |
ISOLATE | SNP | MLM | CMLM | FarmCPU | BLINK | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Chr | Position | Trait | p | FDR | Effect | MAF | p | FDR | Effect | MAF | p | FDR | Effect | MAF | p | FDR | Effect | MAF | |
IBS 327 | 6 | 7,549,194 | DS | - | - | - | - | - | - | - | - | 2 × 10−7 | 1.2 × 10−3 | −0.39 | 0.35 | - | - | - | - |
11 | 1,564,029 | DS | - | - | - | - | - | - | - | - | 2 × 10−7 | 1.2 × 10−3 | −0.49 | 0.18 | - | - | - | - | |
13 | 42,076,334 | DS | - | - | - | - | - | - | - | - | 4 × 10−8 | 5.6 × 10−4 | 0.43 | 0.50 | - | - | - | - | |
14 | 5,884,688 | DS | - | - | - | - | - | - | - | - | 1 × 10−7 | 1.1 × 10−3 | 0.51 | 0.20 | - | - | - | - | |
18 | 1,872,108 | DS | 2 × 10−6 | 1.3 × 10−2 | 0.66 | 0.43 | 2 × 10−6 | 1.3 × 10−2 | 0.66 | 0.43 | - | - | - | - | - | - | - | - | |
1,872,252 | DS | 3 × 10−7 | 6.8 × 10−3 | −0.70 | 0.44 | 3 × 10−7 | 6.8 × 10−3 | −0.70 | 0.44 | 2 × 10−12 | 4.5 × 10−8 | −0.57 | 0.44 | 1 × 10−11 | 2.6 × 10−7 | −0.69 | 0.44 | ||
IBS 333 | 2 | 40,793,724 | %NLA | - | - | - | - | - | - | - | - | - | - | - | - | 4 × 10−7 | 2.9 × 10−3 | 3.49 | 0.04 |
3 | 39,054,333 | %NLA | - | - | - | - | - | - | - | - | 5 × 10−8 | 6.5 × 10−4 | −3.17 | 0.05 | - | - | - | - | |
5 | 32,140,407 | %NLA | - | - | - | - | - | - | - | - | 1 × 10−6 | 7.6 × 10−3 | −2.30 | 0.08 | 5 × 10−10 | 1.3 × 10−5 | −3.70 | 0.08 | |
6 | 49,886,965 | DS | 2 × 10−9 | 4.4 × 10−5 | −0.82 | 0.44 | 2 × 10−9 | 4.4 × 10−5 | −0.82 | 0.44 | 2 × 10−7 | 3.3 × 10−3 | −0.44 | 0.44 | 6 × 10−20 | 1.7 × 10−15 | −0.93 | 0.44 | |
%NLA | - | - | - | - | - | - | - | - | - | - | - | - | 7 × 10−8 | 8.8 × 10−4 | −1.60 | 0.44 | |||
%YLA | - | - | - | - | - | - | - | - | - | - | - | - | 7 × 10−11 | 1.8 × 10−6 | −2.20 | 0.44 | |||
6 | 50,029,391 | DS | - | - | - | - | - | - | - | - | 9 × 10−7 | 7.7 × 10−3 | −0.47 | 0.19 | - | - | - | - | |
6 | 50,048,102 | DS | - | - | - | - | - | - | - | - | - | - | - | - | 3 × 10−10 | 4.2 × 10−6 | 0.86 | 0.13 | |
7 | 25,379,321 | %YLA | - | - | - | - | - | - | - | - | 2 × 10−6 | 2.4 × 10−2 | −1.18 | 0.18 | − | - | - | - | |
11 | 6,791,972 | DS | - | - | - | - | - | - | - | - | 2 × 10−7 | 3.3 × 10−3 | 0.37 | 0.41 | - | - | - | - | |
7,274,359 | %NLA | - | - | - | - | - | - | - | - | 6 × 10−11 | 1.5 × 10−6 | −3.89 | 0.06 | 4 × 10−7 | 2.9 × 10−3 | −3.60 | 0.06 | ||
%YLA | - | - | - | - | - | - | - | - | - | - | - | - | 1 × 10−7 | 1.8 × 10−3 | −4.14 | 0.06 | |||
13 | 41,078,868 | %NLA | - | - | - | - | - | - | - | - | 2 × 10−7 | 1.8 × 10−3 | 2.27 | 0.07 | - | - | - | - | |
17 | 37,084,674 | %NLA | - | - | - | - | - | - | - | - | 1 × 10−6 | 6.7 × 10−3 | 1.15 | 0.27 | - | - | - | - | |
18 | 16,111,543 | %NLA | - | - | - | - | - | - | - | - | - | - | - | - | 9 × 10−7 | 5.0 × 10−3 | 1.50 | 0.22 | |
16,926,588 | %YLA | - | - | - | - | - | - | - | - | 9 × 10−8 | 2.5 × 10−3 | −1.78 | 0.24 | - | - | - | - | ||
37,488,371 | DS | - | - | - | - | - | - | - | - | 1 × 10−6 | 7.7 × 10−3 | 0.48 | 0.18 | - | - | - | - |
Haplotype ID | Positions in the Soybean Genome | I/R/MR | MS/S/HS | N | GF |
---|---|---|---|---|---|
Chr06:49,886,965 (T/C) | IBS 333 | 173 | |||
Hap-resistant | T | 65 | 11 | 76 | 86% |
Hap-susceptible | C | 21 | 76 | 97 | 78% |
Chr11:6,791,972 (A/G) | 173 | ||||
Hap-resistant | A | 48 | 23 | 71 | 68% |
Hap-susceptible | G | 37 | 65 | 102 | 64% |
Chr13:42,076,334 (A/G) | IBS 327 | 165 | |||
Hap-resistant | A | 59 | 24 | 83 | 71% |
Hap-susceptible | G | 30 | 52 | 82 | 63% |
Chr18:1,872,108 (A/G) | 164 | ||||
Hap-resistant | A | 69 | 25 | 94 | 73% |
Hap-susceptible | G | 23 | 47 | 70 | 67% |
Chr18:1,872,252 (T/G) | 163 | ||||
Hap-resistant | T | 71 | 22 | 93 | 76% |
Hap-susceptible | G | 20 | 50 | 70 | 71% |
Observed | Expected | |||||
---|---|---|---|---|---|---|
Plant Material | R | S | R | S | χ2 | p-Value |
Williams 82 | 2 | - | ||||
PI 416937 | - | 2 | ||||
F2 | 63 | 163 | 56.5 | 169.5 | 0.9971 | 0.318 ns |
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Cardoso-Sichieri, R.; Oliveira, L.S.; Lopes-Caitar, V.S.; Silva, D.C.G.d.; Lopes, I.d.O.N.; Oliveira, M.F.d.; Arias, C.A.; Abdelnoor, R.V.; Marcelino-Guimarães, F.C. Genome-Wide Association Studies and QTL Mapping Reveal a New Locus Associated with Resistance to Bacterial Pustule Caused by Xanthomonas citri pv. glycines in Soybean. Plants 2024, 13, 2484. https://doi.org/10.3390/plants13172484
Cardoso-Sichieri R, Oliveira LS, Lopes-Caitar VS, Silva DCGd, Lopes IdON, Oliveira MFd, Arias CA, Abdelnoor RV, Marcelino-Guimarães FC. Genome-Wide Association Studies and QTL Mapping Reveal a New Locus Associated with Resistance to Bacterial Pustule Caused by Xanthomonas citri pv. glycines in Soybean. Plants. 2024; 13(17):2484. https://doi.org/10.3390/plants13172484
Chicago/Turabian StyleCardoso-Sichieri, Rafaella, Liliane Santana Oliveira, Valéria Stefania Lopes-Caitar, Danielle Cristina Gregório da Silva, Ivani de O. N. Lopes, Marcelo Fernandes de Oliveira, Carlos Arrabal Arias, Ricardo Vilela Abdelnoor, and Francismar Corrêa Marcelino-Guimarães. 2024. "Genome-Wide Association Studies and QTL Mapping Reveal a New Locus Associated with Resistance to Bacterial Pustule Caused by Xanthomonas citri pv. glycines in Soybean" Plants 13, no. 17: 2484. https://doi.org/10.3390/plants13172484