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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 http://www.spianchbase.org. 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