TABLE 2.
SNP markers associated with resistance to race 13 of P. effusa in spinach breeding populations. Progeny population was generated from a cross of resistant cultivars Swan, squirrel, Tonga, T-Bird with susceptible cultivars Whale and Polka.
| SNP markera | Allelesb | MAF | -log10
P-valuec |
R2 (%) MLMd | Nearest genese | Annotation | Kb away from the gene | |||
| TASSEL | GAPIT | PLINK | GENESIS | |||||||
| Association panel comprises seedlings from all genotyped population | ||||||||||
| S3_325976 | T:C | 0.39 | 4.85 | 4.83 | 7.05 | 8.23 | 13.87 | – | – | – |
| S3_325991 | A:C | 0.39 | 4.85 | 4.83 | 7.05 | 8.23 | 13.87 | – | – | – |
| S3_326104 | C:T | 0.38 | 2.79 | 3.67 | 6.36 | 7.00 | 7.75 | – | – | – |
| S3_395843 | A:C | 0.44 | 7.20 | 6.05 | 8.06 | 9.80 | 21.58 | Spo12719 | Receptor-like kinase | 5.98 Kb downstream |
| S3_396000 | C:A | 0.45 | 5.59 | 5.92 | 8.41 | 10.18 | 16.20 | Spo12719 | Receptor-like kinase | 6.13 Kb downstream |
| S3_396030 | G:A | 0.45 | 5.59 | 5.92 | 8.41 | 10.18 | 16.20 | Spo12719 | Receptor-like kinase | 6.16 Kb downstream |
| S3_473572 | C:T | 0.19 | 4.60 | 5.42 | 5.98 | 7.62 | 13.12 | – | – | – |
| S3_989568 | C:T | 0.20 | 5.11 | 5.68 | 5.63 | 6.57 | 14.64 | Spo12905 | NBS-LRR disease resistance protein | 6.88 Kb downstream |
| S3_1196085 | G:T | 0.16 | 6.28 | 7.39 | 7.33 | 9.65 | 18.32 | – | – | – |
| S3_1210582 | C:A | 0.20 | 9.00 | 8.31 | 3.91 | 12.13 | 27.30 | Spo12821 | CC-NBS-LRR disease resistance protein | 2.07 Kb upstream |
| S3_1210599 | A:G | 0.20 | 5.28 | 5.62 | 5.78 | 7.30 | 15.19 | Spo12821 | CC-NBS-LRR disease resistance protein | 2.06 Kb upstream |
| S3_1220905 | A:G | 0.20 | 7.46 | 7.26 | 4.02 | 10.81 | 23.22 | Spo12821 | CC-NBS-LRR disease resistance protein | 0.98 Kb downstream |
| S3_1220957 | T:C | 0.20 | 7.46 | 7.26 | 4.02 | 10.81 | 23.22 | Spo12821 | CC-NBS-LRR disease resistance protein | 1.03 Kb downstream |
| S3_1227676 | T:C | 0.18 | 6.55 | 6.11 | 3.53 | 9.43 | 19.48 | Spo12821 | CC-NBS-LRR disease resistance protein | 7.75 Kb downstream |
| S3_1257152 | A:C | 0.19 | 5.74 | 6.23 | 5.07 | 9.50 | 16.88 | – | – | – |
| S3_1257409 | A:G | 0.18 | 7.03 | 7.01 | 3.93 | 9.33 | 21.15 | – | – | – |
| S3_1269788 | T:A | 0.20 | 7.07 | 7.89 | 4.00 | 10.41 | 21.66 | – | – | – |
| S3_1269804 | T:C | 0.20 | 7.07 | 7.89 | 4.00 | 10.41 | 21.66 | – | – | – |
| S3_1269906 | A:C | 0.18 | 5.68 | 5.69 | 3.60 | 9.46 | 16.79 | – | – | – |
| Association panel comprises seedlings segregating only from a cross of Swan and Whale | ||||||||||
| S3_325976 | T:C | 0.49 | 6.54 | 3.37 | 3.36 | 3.65 | 0.34 | – | – | – |
| S3_325991 | A:C | 0.49 | 6.54 | 3.37 | 3.36 | 3.65 | 0.34 | – | – | – |
| S3_326104 | C:T | 0.48 | 5.29 | 3.69 | 3.43 | 5.11 | 0.34 | – | – | – |
| S3_692697f | A:T | 0.46 | 6.68 | 3.68 | 3.44 | 4.22 | 0.35 | Spo12784 | NB-ARC; leucine-rich repeat (LRR) | 2.69 Kb downstream |
| S3_948017f | C:T | 0.17 | 5.62 | 3.45 | – | 5.11 | 0.34 | Spo12903 | Leucine-rich repeat (LRR); NB-ARC | 18.00 Kb upstream |
| S3_954794f | T:A | 0.17 | 5.62 | 3.45 | – | 5.11 | 0.34 | Spo12903 | Leucine-rich repeat (LRR); NB-ARC | 11.23 Kb upstream |
| S3_1196085 | G:T | 0.19 | 5.32 | 3.51 | 2.89 | 2.39 | 0.32 | – | – | – |
| S3_1210582 | C:A | 0.18 | 5.39 | 3.37 | – | 4.87 | 0.33 | – | – | – |
| S3_1257152 | A:C | 0.19 | 5.25 | 3.47 | – | 4.73 | 0.32 | – | – | – |
| S3_1257409 | A:G | 0.19 | 5.19 | 3.12 | – | 4.41 | 0.33 | – | – | – |
aGenomic position of SNP marker on respective chromosomes. S3_325976 denotes the SNP marker on chromosome 3 positioned at 325976 bp. bBeneficial alleles in bold are SNP alleles with positive effects and contributing to providing disease resistance. cAssociation analysis was performed on four different programs. The principal components (PC) and kinship covariates were used in the TASSEL mixed linear model. Association analysis was conducted in GAPIT using the enriched compressed mixed linear model (EcMLM). The PC computed and used to run the logistic regression model in PLINK, and the genomic control (GC) association statistic was reported. Finally, a mixed model analysis in GENESIS was run using inbuilt PC-AiR and kinship matrices. dPhenotypic variance (%) explained by the marker from the TASSEL mixed linear model. eCandidate genes within the associated region were searched in the SpinachBase database (Collins et al., 2019; http://spinachbase.org/). The annotation and distance of the associated SNP from the candidate gene are reported in the table. fThese are uniquely associated SNPs only from the association panel comprising progeny population of Swan × Whale.