TABLE 3.
List of SNPs significantly associated with pitch canker resistance (α < 0.05) and their effects on genotypic (clonal) and phenotypic (lesion length) variation
| SNP_ID | Allele A | Allele B | Mean (log mm) | 95% confidence interval (log mm) | % phenotypic standard deviation | % diff in clonal variance | % σ2Phenotypic due to SNP effect in clonal variance |
|---|---|---|---|---|---|---|---|
| 0_15227_01_160 | T | C | 0.040 | [0.002, 0.078] | 4.775 | 0.924 | 0.236 |
| 0_15382_01_104 | G | A | 0.061 | [0.007, 0.115] | 7.210 | 3.832 | 0.980 |
| 0_2234_01_128 | G | T | 0.048 | [0.009, 0.087] | 5.697 | 1.745 | 0.446 |
| 0_6323_01_248 | G | C | 0.045 | [0.002, 0.088] | 5.307 | 0.889 | 0.227 |
| 0_9288_01_372 | A | G | 0.048 | [0.011, 0.085] | 5.662 | 0.288 | 0.074 |
| 1_3327_01_116 | A | G | 0.054 | [0.005, 0.103] | 6.383 | 2.187 | 0.559 |
| 2_4484_02_622 | T | C | 0.057 | [0.004, 0.110] | 6.738 | 1.101 | 0.282 |
| 2_6181_02_400 | T | G | 0.057 | [0.005, 0.110] | 6.761 | 1.129 | 0.289 |
| 2_8946_02_437 | G | C | 0.056 | [0.003, 0.107] | 6.560 | 1.031 | 0.264 |
| CL4336Contig1_01_180 | T | C | 0.053 | [0.001, 0.106] | 6.277 | 1.519 | 0.389 |
Mean SNP effects on the phenotype were estimated from the last 20,000 iterations in the BAMD program, along with the corresponding 95% confidence intervals. The contribution of the SNP to the phenotype is shown as the percentage of the phenotypic standard deviation, whereas genotypic effects are indicated as the percentage of difference in the clonal variance. The percentage of the phenotypic variance due to the SNP effect in clonal variance is an indicator of the genetic contribution of the SNP to the phenotype.