Genome-wide association study of Fusarium ear rot disease in the U.S.A. maize inbred line collection

BMC Plant Biology

Table 3 Chromosome locations (AGP v2 coordinates), allele effect estimates, genes containing SNP, and other summary statistics for the seven SNPs significantly associated with Fusarium ear rot resistance from the two inbred association panel analyses

Chromosome	SNP physical position (bp)	p -value	FDR adjusted P-value	Minor allele frequency	Allele effect (%) ^a	( R ²) ^b	Gene containing SNP	SNP effect	RMIP
		Full inbred panel (1689 lines) analysis
5	64,771,372	8.83 × 10⁻⁷	0.089	0.07	−0.170	1.3	GRMZM2G060659	mis-sense (A/T)	0.38
9	19,532,465	8.44 × 10⁻⁸	0.017	0.15	−0.134	1.5	GRMZM2G035665	mis-sense (V/A)	0.94
		Filtered inbred panel (737 lines tested in three years) analysis
4	7,566,354	7.34 × 10⁻⁷	0.074	0.10	−0.230	2.9	GRMZM2G372364	intron variant
4	7,618,125	2.67 × 10⁻⁶	0.175	0.10	−0.225	2.6	GRMZM2G012821	mis-sense (N/D)
4	7,618,284	3.96 × 10⁻⁶	0.175	0.11	−0.205	2.5	GRMZM2G012821	mis-sense (D/N)
4	9,353,851	6.14 × 10⁻⁷	0.074	0.07	−0.254	3.0	GRMZM2G419836	3′ UTR variant
4	124,930,006	4.36 × 10⁻⁶	0.175	0.04	−0.271	2.5	GRMZM2G106752	mis-sense (L/S)

^aAllele effects are reported back-transformed to the original 0-100% disease severity scale. Effects are in reference to the minor allele.
^bR ², proportion of total entry mean variance associated with a SNP after accounting for background polygenic variance.

ISSN: 1471-2229