Table 2.
Summary of the number of independent SNPs/number of SNPs associated with the seven traits
| Method | Genetic cluster | Trait | ||||||
|---|---|---|---|---|---|---|---|---|
| BB | Height | DBH | FD | WD | MFA | WS | ||
| CMLM | Whole pop. | 10/16 (0.68–6.70) | 0 | 2/3 (1.15–1.51) | 3/6 (2.22–5.19) | 3/3 (0.68–0.82) | 0 | 0 |
| ALP | 7/12 | 0 | 0 | NA | 0 | 0 | 0 | |
| CEU | 2/5 | 0 | 0 | NA | 0 | 0 | 1/2 | |
| CSE | 2/4 | 0 | 0 | NA | 0 | 0 | 0 | |
| NPL | 2/4 | 0 | 0 | NA | 0 | 0 | 0 | |
| Rus_Bal | 0 | 0 | 0 | NA | 0 | 0 | 2/2 | |
| ROM | NA | NA | NA | NA | NA | NA | NA | |
| NFE | 0 | 0 | NA | NA | 0 | 0 | 0 | |
| BLINK | Whole pop. | 24/24 (0.13–6.70) | 3/3 (0.33–0.48) | 2/2 (0.57–0.62) | 1/1 (5.19) | 3/3 (0.07–0.82) | 0 | 0 |
| ALP | 1/1 | 0 | 0 | NA | 2/2 | 0 | 0 | |
| CEU | 2/2 | 0 | 0 | NA | 0 | 0 | 1/2 | |
| CSE | 2/2 | 0 | 0 | NA | 0 | 0 | 0 | |
| NPL | 1/1 | 0 | 0 | NA | 0 | 0 | 0 | |
| Rus_Bal | 0 | 0 | 0 | NA | 0 | 0 | 3/3 | |
| ROM | NA | NA | NA | NA | NA | NA | NA | |
| NFE | 6/6 | 0 | NA | NA | 0 | 1/2 | 0 | |
| Total SNPs | 40/47 (0.13–6.70) | 3/3 (0.33–0.48) | 4/5 (0.57–1.51) | 3/6 (2.22–5.19) | 6/6 (0.07–0.82) | 1/2 (0.14) | 4/5 (0.06–0.21) | |
| R2* | 15.7 | 1.5 | 2.6 | 4.9 | 2.4 | 0.1 | 0.5 | |
| R2** | 4.7 | 1.7 | NA | NA | 0 | 0 | 0 | |
In this study, we performed GWAS in the whole elite tree population and seven genetic clusters by two methods (CMLM and BLINK), phenotypic variance explained (PVE2) by a single SNP shown in parenthesis, and cumulative phenotypic variance explained by all associated SNPs (R2*) for each trait in the whole elite tree population and the validation population (R2**) in the two full-sib progeny field plantations in Northern Sweden. BB budburst stage, DBH diameter at breast height, FD frost damage, WD wood density, MFA microfibril angle, WS wood stiffness. NA: represents that we did not perform CMLM for each genetic cluster because of small cluster size in several clusters, such as NFE and ROM in Table 1