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

BMC Genomics

Table 3 Selection accuracy and efficiency of the significantly associated SNP markers for association panel of spinach population generated by crossing Whale and Lazio. The association panel comprises 172 spinach lines, of which 123 and 49 were resistant and susceptible to race 16 of the P. effusa race. For each SNP, the number of lines under each genotypic class was counted for the full panel, the resistant, and susceptible groups to calculate selection accuracy and efficiency

SNP marker	SNP type	Genotype	Number of lines and percentage						Selection Accuracy (%)^a	Selection efficiency (%)^b
			All (172)	Percent	Susceptible (49)	Percent	Resistant (123)	Percent
S3_658,306	G/A	GG	56	39.2	30	71.4	26	25.7	86.2	52.4
		AG	41	28.7	7	16.7	34	33.7
		AA	46	32.2	5	11.9	41	40.6
		NN	29		7		22
S3_692697	A/T	AA	82	50.0	42	87.5	40	34.5	92.7	46.3
		AT	58	35.4	2	4.2	56	48.3
		TT	24	14.6	4	8.3	20	17.2
		NN	8		1		7
S3_1050601	T/A	TT	49	28.7	9	18.4	40	32.8	84.6	60.8
		AT	74	43.3	10	20.4	64	52.5
		AA	48	28.1	30	61.2	18	14.8
		NN	1		0		1
S3_1227787	C/A	CC	58	38.2	9	20.0	49	45.8	84.3	56.6
		AC	44	28.9	7	15.6	37	34.6
		AA	50	32.9	29	64.4	21	19.6
		NN	20		4		16
S3_1227802	G/A	GG	58	38.2	9	20.0	49	45.8	84.3	56.6
		AG	44	28.9	7	15.6	37	34.6
		AA	50	32.9	29	64.4	21	19.6
		NN	20		4		16
S3_1231197	T/C	TT	58	34.3	7	14.3	51	42.5	83.9	61.5
		CT	66	39.1	13	26.5	53	44.2
		CC	45	26.6	29	59.2	16	13.3
		NN	3		0		3

^a Selection accuracy (%) is the ratio of resistant lines with beneficial SNPs divided by the sum of resistant and susceptible lines with beneficial SNPs
^b Selection efficiency (%) is the ratio of resistant lines with beneficial SNPs divided by the total number of genotyped lines

ISSN: 1471-2164