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Table 1 SNP markers significantly associated with P. effusa race 16 resistance in population segregating from cultivar Whale

From: High resolution mapping and candidate gene identification of downy mildew race 16 resistance in spinach

SNP markera Alleles Reference alleleb R allele S allele MAF -log10P Valuec R2 (%) SMRd Candidate gene IDe Functional annotation Distance in Kb from the gene
TASSEL SMR TASSEL GLM TASSEL MLM PLINK (GC) GENESIS T-test
S3_658,306 G/A G A G 0.47 6.20 5.76 4.15f 4.03f 5.47 6.32 18.5 Spo12736 NB-ARC; leucine-rich repeat (LRR) 8.92 upstream
S3_692697 A/T A T A 0.32 9.66 7.98 5.92 4.49f 5.89 3.64f 24.1 Spo12784 NB-ARC; leucine-rich repeat (LRR) 2.69 downstream
S3_1050601 T/A T T A 0.5 9.09 9.22 7.20 4.14f 5.51 5.71 22.1 Spo12908 CC-NBS-LRR disease resistance protein 10.83 downstream
S3_1227787 C/A C C A 0.47 6.80 6.42 5.25f 4.01f 5.37 5.91 19.0 Spo12821 CC-NBS-LRR disease resistance protein 7.86 downstream
S3_1227802 G/A G G A 0.47 6.80 6.42 5.25f 4.01f 5.37 5.91 19.0 7.88 downstream
S3_1231197 C/T C T C 0.46 9.27 9.61 6.96 5.39 7.35 8.26 22.7 11.27 downstream
  1. a Position of SNP marker on respective chromosome in basepairs. The SNP marker S3_658,306 is located on chromosome 3 and positioned at 658306 bp
  2. b Alleles on the Sp75 reference genome [22]
  3. c Four different association models were performed on three different programs. The principal components (PC) were used in TASSEL general linear model, and the PC and kinship covariates were used in the TASSEL mixed linear model. PC was used to conduct the logistic regression in PLINK, and the genomic control (GC) statistic was reported. Mixed model analysis in GENESIS was run using inbuilt PC-AiR and kinship matrices
  4. d Phenotypic variance (%) explained by the marker from the TASSEL single marker regression model
  5. e Candidate genes within the associated region were searched in the SpinachBase database (http://spinachbase.org/)
  6. f The SNP association signals were below the Bonferroni threshold in this model. However, the association signals on other models support the SNP as of a high-confidence association, and the result was presented based on association reports obtained from multiple models