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Table 2 Haplotype association analysis at the P. effusa race 16 resistance locus in population segregating from cultivar Whale

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

SNP haplotypesa Haplotypes Ratiosb -log10P valuec Candidate genesd
Alleles Frequency Susceptible Resistant
S3_658,306, S3_692697 GA 0.5 0.75 0.4 8.5 Spo12736, Spo12784
AT 0.29 0.1 0.37 6.2
S3_1227787, S3_1227802, S3_1231197 CGT 0.45 0.24 0.54 6.4 Spo12821
AAC 0.39 0.67 0.28 11
  1. a The SNPs are named for chromosome and position. Here S3_658,306 means SNP loci are located on chromosome 3 and positioned at 658306 bp
  2. b Ratio of haplotype alleles among the resistant and susceptible panels
  3. c Haplotype blocks were identified, and association analysis performed in Haploview 4.2 software [38]
  4. d Candidate genes were searched in the spinach genome [22] available at Disease resistance genes within the haplotype block or nearby the haplotype blocks that contain the associated SNPs were reported. The Spo12736 and the Spo12784 gene, both annotated as NB-ARC; leucine-rich repeat (LRR) is 8.92 Kb downstream and 2.69 Kb upstream of the Pfs16 associated SNP S3_658,306 and S3_692697. The second haplotype block does not harbor the disease resistance gene, but the SNP S3_122787 is only 7.86 Kb downstream of the Spo12821 gene annotated as CC-NBS-LRR disease resistance protein