Table 2.
SNPs significantly associated with resistance to bacterial pustule, caused by Xanthomonas citri, in isolates IBS 327 and IBS 333, tested using statistical models for qualitative (DS) and quantitative (%NLA and %YLA) phenotypes (traits). SNP = single polymorphism nucleotide; Chr = chromosome; MLM, CMLM, FarmCPU and Blink are the models applied in GWAS analysis (see Section 4); DS = disease score; %NLA = percentage of necrotic leaf area; %YLA = percentage of yellowish leaf area; FDR = false discovery rate adjusted by the H and B method; p = p-value; effect = marker effect for the model; MAF = minor allele frequency.
| 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 | - | - | - | - | ||