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

BMC Genomics

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

SNP marker^a	Alleles	Reference allele^b	R allele	S allele	MAF	-log₁₀P Value^c						R² (%) SMR^d	Candidate gene ID^e	Functional annotation	Distance in Kb from the gene
SNP marker^a	Alleles	Reference allele^b	R allele	S allele	MAF	TASSEL SMR	TASSEL GLM	TASSEL MLM	PLINK (GC)	GENESIS	T-test	R² (%) SMR^d	Candidate gene ID^e	Functional annotation	Distance in Kb from the gene
S3_658,306	G/A	G	A	G	0.47	6.20	5.76	4.15^f	4.03^f	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	4.49^f	5.89	3.64^f	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	4.14^f	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	5.25^f	4.01^f	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	5.25^f	4.01^f	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

^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
^b Alleles on the Sp75 reference genome [22]
^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
^d Phenotypic variance (%) explained by the marker from the TASSEL single marker regression model
^e Candidate genes within the associated region were searched in the SpinachBase database (http://spinachbase.org/)
^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

ISSN: 1471-2164