Table 3.
Studies of genome‐wide selection in Brassica napus
| Populations | Traits | Marker | Model | Prediction ability | Reference |
|---|---|---|---|---|---|
| 391 winter type DH lines | SY, PH, FT, PC, OC, GLU | 253 SNP | RR‐BLUP | 0.41–0.84 (GLU to PH) | Wurschum et al. (2014) |
| BayesB | 0.34–0.81 (SY to PH) | ||||
| TN DH population | FT | 1248 SNP | RR‐BLUP, RKHS, Bayesian LASSO, BayesA, Bayes B, Random Forest, SVM (linear kernel), SVM (Gaussian kernel) | 0.638, 0.639, 0.639, 0.645, 0.644, 0.611, 0.593, 0.651 | Li et al. (2015) |
| 477 parents and 950 hybrids | SY, OY, OC, GLU, FT, SE, LS | 24 403 SNP | RR‐BLUP | 0.45, 0.75, 0.81, 0.61, 0.56, 0.29, 0.39 | Jan et al. (2016) |
| TN DH population | OC, PC, EAC, LEN, SAC, GLU | 60K DNA array | RR‐BLUP, BayesCπ, EG‐BLUP, GBLUP, MAS | 0.76, 0.66, 0.89, 0.76, 0.81, 0.79 | Zou et al. (2016b) |
| TN DH population and 318 hybrids | SY | 60K DNA array | GBLUP (A) | 0.49 (A), | Liu et al. (2017) |
| GBLUP (A + D) | 0.65 (A + D), | ||||
| GBLUP (A + D + E) | 0.72 (A + D + E) | ||||
| 225 parents and 448 hybrids | SY, TSW, SE, FT, OC, PC, GLU | 60K DNA array | GCA RR‐BLUP | 0.35–0.82 (SY to GLU) | Werner et al. (2018) |
| GCA + SCA RR‐BULP | |||||
| RR‐BULP + de novo GWAS | |||||
| GCA BayesB | |||||
| GCA + SCA BayesB | |||||
| GCA BBR + SCA BayesB | |||||
| 67 parents and 363 hybrids | SY, FT, SN, TSW, GLU, EAC, OC, OLE, LEI, LEN | 43 106 (SNPT) + 5496 (SNPS) | GBLUP (SNPT + A + D) | 0.73, 0.97, 0.77, 0.65, 0.97, 0.99, 0.70, 0.99, 0.91, 0.83 | Hu et al. (2020) |
| GBLUP (SNPS + A + D) | |||||
| GBLUP (SNPT+S + A + D) | |||||
| GBLUP (SNPT + SNPS + A + D) | |||||
| GBLUP (SNPT+S + A + D + E) | |||||
| A DH population with 148 lines | SY, FT, MAT, FD, TSW, OC, PC, GLU, SAT | 368 SNP | GBLUP | 0.14, 0.54, 0.58, 0.53, 0.66, 0.42, 0.55, 0.56, 0.47 | Koscielny et al. (2020) |
| 377 parents and 750 hybrids | SY, OY, SE, PC, FT, OC, GLU, LA, Biovolume, PH, MPH‐LA, MPH‐PH, MPH‐Biovolume | 13 201 SNP + 19 479 transcripts + 154 primary metabolites | GBLUP, RKHS | 0.32, 0.53, 0.27, 0.53, 0.64, 0.70, 0.61, 0.61, 0.59, 0.46, 0.42, 0.37 | Knoch et al. (2021) |
| 218 plants | Sclerotinia stem rot resistance | 24 634 SNP | LMM (A), LMM (A + AA), Bayes A, Bayes B, Bayes C, LASSO, BRR | 0.74, 0.76, 0.56, 0.69, 0.68, 0.63, 0.70 | Derbyshire et al. (2021) |
SY, seed yield; PH, plant height; LA, leaf area; FT, flowering time; FD, flowering duration; MAT, number of days to maturity; PC, protein content; OC, Oil content; GLU, glucosinolate content; OY, oil yield; SE, seedling emergence; LS, lodging resistance; EAC, erucic acid content; SAT, saturated fatty acid content; LEN, linolenic acid content; SAC, stearic acid content; SN, seed number per pod; TSW, thousand seeds weight; OLE, oleic acid content; LEI, linoleic acid content. BLUP, best linear unbiased prediction; RR‑BLUP, ridge regression BLUP; BBR, Bayesian Ridge Regression; GBLUP, genomic best linear unbiased prediction; EG‐BLUP, extended GBLUP; LMM, linear mixed models; RKHS, reproducing kernel Hilbert space regression based on Gaussian kernels; MAS, marker‐assisted selection; MPH, middle parent heterosis; GCA, general combining ability; SCA, specific combining ability; A, additive effects; D, dominance effects; E, epistatic interaction effects; SNPT, SNP markers identified with traditional B. napus reference genome; SNPS, species specific introgression SNP markers.