Genome-wide association analysis for fumonisin content in maize kernels

Samayoa, L. F.; Cao, A.; Santiago, R.; Malvar, R. A.; Butrón, A.

doi:10.1186/s12870-019-1759-1

BMC Plant Biology

Table 2 Summary of Genome-wide association study (GWAS) for kernel resistance to fumonisin contamination using a maize inbred panel evaluated under inoculation with Fusarium verticillioides in two years

From: Genome-wide association analysis for fumonisin content in maize kernels

QTL	Bin¹	Allele⁺	R²	QTL SI	SNP position²	p-value	RMIP	containing-SNP gene_v2³	containing-SNP gene_v4
1	1.07	0.95	0.11	220,709,603–222,205,493	220,941,497	9.04*10⁻⁹	0.80	GRMZM2G078401	Zm00001d032372
2	1.09	0.93	0.08	256,662,974–256,798,243	256,669,820	7.85*10⁻⁷	0.56	GRMZM2G149028	Zm00001d033386
					256,692,784	2.56*10⁻⁷	0.63	GRMZM2G100448	Zm00001d033388
					256,692,818	2.54*10⁻⁷	0.63
					256,693,243	2.56*10⁻⁷	0.63
3	2.08	0.93	0.07	213,583,622–213,815,822	213,588,927	3.84*10⁻⁷	0.51	GRMZM2G422576	Zm00001d007029
					213,588,940	3.72*10⁻⁷	0.51
4	3.02	0.94	0.09	6,970,377–7,206,031	7,119,636	1.25*10^− 8	0.58	GRMZM2G104176	Zm00001d039513
5	3.04	0.91	0.10	15,040,634–15,127,310	15,056,252	1.85*10⁻⁷	0.70	GRMZM2G165044	Zm00001d039769
					15,057,326	5.40*10⁻⁹	0.74
					15,057,331	2.59*10⁻⁸	0.64
					15,057,578	2.25*10⁻⁸	0.73
6	3.05	0.93	0.09	147,969,891–148,289,200	147,971,443	4.11*10⁻⁹	0.69	GRMZM2G701801	Zm00001d042061
7	3.06	0.94	0.11	169,052,376–169,117,125	169,073,710	1.04*10⁻¹⁰	0.60	GRMZM2G026855	Zm00001d042555
					169,073,715	1.04*10⁻¹⁰	0.60
					169,073,720	1.05*10⁻¹⁰	0.60
					169,078,446	4.77*10⁻⁹	0.56
8	3.06	0.93	0.08	173,006,714–173,381,106	173,283,279	5.89*10⁻⁷	0.53	GRMZM2G060255	Zm00001d042658
9	3.08	0.91	0.10	206,261,823–207,246,656	206,605,245	1.22*10⁻⁶	0.56	GRMZM2G169654	Zm00001d043782
						4.68*10⁻⁸	0.62	GRMZM2G028467	Zm00001d043801
10	3.09	0.89	0.09	217,324,678–217,572,395	217,558,124	2.46*10⁻⁸	0.53	GRMZM2G042421	Zm00001d044173
11	4.02	0.93	0.08	5,405,928–5,466,378	5,406,694	2.03*10⁻⁷	0.57	GRMZM2G154414	Zm00001d048837
					5,410,388	2.09*10⁻⁷	0.55
12	4.05	0.87	0.12	centromere	82,892,426	3.60*10⁻⁸	0.58
					82,892,436	3.60*10⁻⁸	0.58
					82,892,557	3.60*10⁻⁸	0.58	GRMZM2G111117	Zm00001d050400
					83,027,805	3.60*10⁻⁸	0.58	GRMZM2G178169	Zm00001d050401
					83,033,318	3.60*10⁻⁸	0.58
					83,572,578	2.10*10⁻⁸	0.74	AC198937.4_FG005	Zm00001d050410
					83,738,156	2.11*10⁻⁸	0.77
					84,453,345	3.44*10⁻⁸	0.73	GRMZM2G123362	Zm00001d050434
					88,069,675	2.54*10⁻⁸	0.56
					88,098,841	2.50*10⁻⁸	0.52
					96,545,683	1.17*10⁻⁷	0.54	GRMZM2G140095	Zm00001d050575
13	5.02	0.95	0.08	14,815,481–14,839,860	14,839,828	6.99*10⁻⁹	0.58	GRMZM2G066449	Zm00001d013611
14	6.07	0.90	0.10	164,365,931–164,378,580	164,369,763	3.76*10⁻⁹	0.61	GRMZM2G038183	Zm00001d038998
15	7.05	0.93	0.10	171,058,866–171,182,450	171,182,417	2.89*10⁻⁹	0.64	GRMZM2G009021	Zm00001d022400
16	8.07	0.85	0.10	167,189,708–167,286,546	167,284,361	3.19*10⁻⁹	0.54	GRMZM2G177324	Zm00001d012329
17	9.03	0.91	0.09	centromere	87,360,835	1.88*10⁻⁸	0.50	GRMZM2G159641	Zm00001d046455

¹Bin in which QTLs are located; Allele⁺ stands up for the frequency of favorable allele; R² for the proportion of the phenotypic variance explained by the QTL; QTL SI for the supporting interval of the QTL on the RefGenB73_v2, region in which appreciable linkage disequilibrium is observed between SNPs (r² > 0.4), SI could not be visualized using LD plots from TASSEL when SNP were localized in centromeric regions where LD is extremely high
²SNP position for the position in bp of the significant SNP on the RefGenB73_v2; p-value for the association between polymorphic variation at the SNP and phenotypic variation for fumonisin content; RMIP for resample model inclusion probability
³Filtered genes in the RefGenB73_v2 and RefGenB73_v4 versions of the B73 sequence that contain the significant SNP (or the closest filtered gene in bold)

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ISSN: 1471-2229

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