Limits on the reproducibility of marker associations with southern leaf blight resistance in the maize nested association mapping population

Table 5 Concordance of variants associated with SLB resistance at resample model inclusion probabilities (RMIPs) of 0.05 and 0.25 from five GWAS analyses

Comparisons	GWAS models^a	RMIP ≥ 0.05				RMIP ≥ 0.25
		No. of all significant SNPs^b	Proportion of overlapped SNPs (%)^c			No. of all significant SNPs	Proportion of overlapped SNPs (%)^c
		No. of all significant SNPs^b	10-kb window	100-kb window	200-kb window	No. of all significant SNPs	10-kb window	100-kb window	200-kb window
GWAS marker density	B vs. C	326 (151,175)	26	36	38	45 (25,20)	13	13	13
GWAS marker density	D vs. E	393 (201,192)	22	34	39	54 (28,26)	11	11	15
Genetic map density	C vs. E	367 (175,192)	14	21	23	46 (20,26)	9	9	9
Genetic map density	B vs. D	352 (151,201)	25	29	35	53 (25,28)	26	28	28
GWAS and genetic marker density	C vs. D	376 (175,201)	13	21	22	48 (20,28)	4	8	8
GWAS and genetic marker density	B vs. E	343 (151,192)	7	13	15	51 (25,26)	4	4	4
GWAS and genetic marker density and P-value	A vs. E	437 (245,192)	6	12	15	52 (26,26)	4	4	4

^aSee Table 1 for details of each GWAS model.
^bTotal number of all the significant SNPs from a pair of analyses is shown outside of parentheses and numbers of significant SNPs from each analysis considered separately are inside the parenthesis.
^cProportion of overlapped SNPs was estimated as the total number of overlapped SNPs from a pair of analyses/total number of all the significant SNPs from the two analyses.
Comparisons show the input(s) that differed in each pair of GWAS comparisons.

ISSN: 1471-2164