Table 4.

Allele frequencies of significantly associated SNPs in the five major maize subpopulations and P -value of Fisher’s exact test of the null hypothesis of equal allele frequencies across subpopulations

		Resistance allele frequency (%) a						N b
Chromo-some	SNP physical position (bp)	SS c	NSS	TS	PC	SC	P- value	SS	NSS	TS	PC	SC
4	7,566,354	1.2	0.0	32.0	60.4	0.0	<2.2 × 10−16	164	171	222	48	51
4	7,618,125	0.6	0.0	30.7	47.9	0.0	<2.2 × 10−16	164	171	215	48	52
4	7,618,284	0.6	0.0	36.5	66.0	0.0	<2.2 × 10−16	159	168	211	47	51
4	9,353,851	0.6	0.6	31.9	0.0	0.0	<2.2 × 10−16	161	168	213	61	50
4	124,930,006	0.0	1.8	8.8	3.3	0.0	1.7 × 10−5	162	166	238	60	51
5	64,771,372	0.0	4.7	8.1	14.8	0.0	3.2 × 10−6	164	170	246	61	51
9	19,532,465	2.5	7.2	26.6	26.7	2.0	4.9 × 10−15	158	167	241	60	51
	Ear rot mean (%)d	39.6	39.6	43.0	41.3	61.1

^aAt all SNP loci the minor allele is associated with increased disease resistance.

^bN, total number of lines within each subpopulation with marker calls at a particular SNP locus.

^cSS, stiff stalk; NSS, non-stiff stalk; TS, tropical/subtropical; PC, popcorn; SC, sweet corn.

^dOverall phenotypic ear rot means are the average of least squares means across members of each subpopulation.