Table 1. Overview of significant associations detected with EMMAX and MLMM.
| Rank | B. oleracea | A. thaliana | Variance explained | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Trait | Chr | Pos | Method | RR | BayesB | Gene ID | Ortholog | Description | Phenotypic | Genetic | MAF |
| Apical Length | 2 | 26,787,029 | MLMMI | 30,559 | 29,378 | Bol035969 | AtSec6 | Cell growth | 4.1 | 37.3 | 0.05 |
| Apical Length | 3 | 20,986,662 | MLMMI | 2397 | 1712 | Bol035507 | AT1G53730 | Protein coding | 11.6 | 105.3 | 0.03 |
| Apical Length | 6 | 4,914,166 | MLMMI | 4902 | 1785 | Bol032997 | — | Protein kinase | 10.6 | 96.0 | 0.08 |
| Apical Length | 6 | 34,494,415 | MLMMU | 2111 | 1194 | Bol040102 | AT1G71780 | Biological processes | 2.2 | 20.3 | 0.13 |
| Cluster Width | 2 | 5,063,181 | EMMAXU | 8 | 4 | Bol007138 | AT1G03220 | Proteolysis | 19.1 | 34.1 | 0.22 |
| Curd Width | 2 | 3,528,844 | EMMAXU | 1 | 1 | Bol021232 | AT5G19110 | Heat stress | 14.4 | 32.6 | 0.44 |
| Curd Width | 2 | 5,063,181 | EMMAXU | 6 | 4 | Bol007138 | AT1G03220 | Proteolysis | 12.1 | 27.4 | 0.22 |
| Length of Nearest Branch | 9 | 25,012,587 | MLMMU | 2 | 2 | Bol012235 | — | unknown | 7.9 | 158.7 | 0.06 |
| Number of Branches | 6 | 2,323,306 | EMMAXU | 2 | 2 | Bol035509 | AT1G75310 | Protein binding | 6.2 | 23.7 | 0.06 |
| Number of Branches | 6 | 2,323,306 | MLMMU | 2 | 2 | Bol035509 | AT1G75310 | Protein binding | 6.2 | 23.7 | 0.06 |
| Number of Branches | 7 | 41.524,584 | EMMAXU | 1 | 1 | Bol024369 | AT2G17050 | NBS gene family | 8.5 | 32.6 | 0.21 |
| Number of Branches | 7 | 41,524,584 | MLMMU | 1 | 1 | Bol024369 | AT2G17050 | NBS gene family | 8.5 | 32.6 | 0.21 |
| Number of Days to Budding | 1 | 37,688,065 | EMMAXU | 1 | 1 | Bol023068 | AT3G09240 | Signaling pathway | 13.5 | 14.4 | 0.2 |
| Number of Days to Budding | 1 | 37,688,065 | MLMMU | 1 | 1 | Bol023068 | AT3G09240 | Signaling pathway | 13.5 | 14.4 | 0.2 |
| Number of Days to Budding | 2 | 2,708,156 | MLMMU | 5 | 6 | Bol024638 | AT5G10090 | Flowering related | 16.4 | 17.4 | 0.57 |
| Number of Days to Budding | 2 | 2,708,163 | MLMMU | 6 | 5 | Bol024638 | AT5G65160 | Flowering related | 16.4 | 17.4 | 0.57 |
| Number of Days to Budding | 2 | 2,708,182 | MLMMU | 7 | 4 | Bol024638 | AT5G65180 | Flowering related | 16.4 | 17.4 | 0.57 |
| Number of Days to Budding | 6 | 2,949,314 | EMMAXI | 1861 | 572 | Bol026132 | AT1G75010 | Flowering | 25.2 | 26.8 | 0.05 |
| Number of Days to Budding | 6 | 2,949,314 | MLMMI | 1861 | 572 | Bol026132 | AT1G75010 | Flowering | 25.2 | 26.8 | 0.05 |
| Number of Days to Budding | 7 | 936,738 | EMMAXI | 2 | 5 | Bol027177 | — | unknown | 4.2 | 4.5 | 0.36 |
| Number of Days to Budding | 7 | 936,738 | MLMMI | 2 | 5 | Bol027177 | — | unknown | 4.2 | 4.5 | 0.36 |
| Number of Days to Budding | 7 | 936,770 | EMMAXI | 1 | 1 | Bol027177 | — | unknown | 6.4 | 6.8 | 0.23 |
| Number of Days to Budding | 7 | 936,770 | MLMMI | 1 | 1 | Bol027177 | — | unknown | 6.4 | 6.8 | 0.23 |
| Number of Days to Budding | 7 | 41,524,584 | MLMMU | 2 | 3 | Bol024369 | AT2G17050 | NBS gene family | 4.1 | 4.4 | 0.21 |
The Rank column indicates which rank the significant association had among marker effects in the genomic prediction with ridge regression (RR) or BayesB methods. The last letter in the Method column indicates in which data set the QTL was discovered (U, unimputed, I, imputed). Phenotypic and genotypic variance indicate the percentage of variance explained by the respective SNP. Chr, chromosome; MAF, minor allele frequency; Pos, position.