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

BMC Genomics

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

SNP haplotypes^a	Haplotypes		Ratios^b		-log₁₀P value^c	Candidate genes^d
SNP haplotypes^a	Alleles	Frequency	Susceptible	Resistant	-log₁₀P value^c	Candidate genes^d
S3_658,306, S3_692697	GA	0.5	0.75	0.4	8.5	Spo12736, Spo12784
S3_658,306, S3_692697	AT	0.29	0.1	0.37	6.2	Spo12736, Spo12784
S3_1227787, S3_1227802, S3_1231197	CGT	0.45	0.24	0.54	6.4	Spo12821
S3_1227787, S3_1227802, S3_1231197	AAC	0.39	0.67	0.28	11	Spo12821

^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
^b Ratio of haplotype alleles among the resistant and susceptible panels
^c Haplotype blocks were identified, and association analysis performed in Haploview 4.2 software [38]
^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

ISSN: 1471-2164