TABLE 3.

Haplotype-based association analysis at the race 13 of P. effusa resistance loci in spinach association panel comprising breeding populations from a cross of race 13 resistant cultivars Swan, squirrel, Tonga, T-Bird with susceptible cultivars Whale and Polka.

Haplotypesa			Allele frequencyb		−log10 P-valuec
SNPsd	Allelee	Frequencyf	Susceptible	Resistant	Logistic model	Linear model
S3_325976, S3_325991	CC	0.385	0.218	0.545	6.66	9.45
S3_396000, S3_396030	AA	0.454	0.253	0.648	8.84	12.78
S3_948017, S3_954794	TA	0.072	0.006	0.135	2.75	5.49
S3_1209978, S3_1209990	CG	0.140	0.018	0.259	4.52	9.83
S3_1220905, S3_1220957	GC	0.189	0.006	0.373	4.72	17.04
S3_1227442, S3_1227482, S3_1227676	TGC	0.169	0.007	0.324	5.19	14.82
S3_1269788, S3_1269804	AC	0.188	0.006	0.371	4.75	17.11

^aHaplotype blocks were identified using SNPs in the 0.3–1.3 Mb region of chromosome 3 in the Haploview program (Barrett et al., 2005) and the Plink v 1.70 (Purcell et al., 2007). ^bFrequency of haplotype alleles among the resistant and susceptible groups. ^cHaplotype association analysis was performed using logistic and linear regression models as implemented in Plink v1.70 (Purcell et al., 2007). ^dThe SNPs are named for chromosome and position. S3_325976 means SNP loci are located on chromosome 3 at 325976 bp. The SNPs in bold were also associated with a single marker association test, as listed in Table 2. ^eResistant haplotypes alleles in the population. Only beneficial haplotypes associated with the resistance were presented. ^fFrequency of haplotype alleles in the population under study.