Identification of molecular markers linked to Fusarium ear rot genes in maize plants Zea mays L

Figures & data

Table 1. List of the seven SSR-marker-generated polymorphism between the parents.

Marker	Primer sequences	Annual temperature (°C)	Product size (bp)	No. of amplification products	No. of polymorphic products
SSR85	GGATCTTCGTTGCAGTTCTT CATCAGTGATCCTCCACCAT	55	135–160	2	2
bnlg1063	GGAGACAACCCCGACGAC GGTACCAGAGCCACAGATCC	55	105–120	2	2
bnlg1740	TTTTCTCCTTGAGTTCGTTCG ACAGGCAGAGCTCTCACACA	55	125–160	2	2
umc2082	TAGCTGCCCCTCTTCCGTCT GTCGTGGCGTAGAGACTAGGGAT	55	100–130	2	2
bnlg1621	CTCTTCGATCTTTAAGAGAGAGAGAG ACACGAGGCACTGGTACTAACG	55	170–200	2	2
umc2059	GGAAAAGGAGGAACAGTGTAAGCA AGCGTGATCAGACGTACAATGCTA	55	110–130	2	2
umc2013	GGGACGAGAGTCTGTTGTTGTTG GTTGATGCATGTGACTCTGGAAAC	55	110–125	2	2

Figure 1. Experimental validation of bn1g1063 SSR marker in 20 lanes in F₂ cross individuals.

Figure 2. Experimental validation of bn1gumc2082 SSR marker in 20 lanes in F₂ crosses individuals.

Figure 3. Experimental validation of bn1g1621 SSR marker in 20 lanes in F₂ crosses individuals.

Figure 4. Experimental validation of umc2013 SSR marker in 20 lanes in F₂ crosses individuals.

Figure 5. Experimental validation of bn1g1740 SSR marker in 20 lanes in F₂ crosses individuals.

Figure 6. Experimental validation of umc2059 SSR marker in 20 lanes in F₂ crosses individuals.

Figure 7. Experimental validation of SSR85 SSR marker in 20 lanes in F₂ crosses individuals.

Table 2. Significant association between Fusarium ear rot resistance and markers (SSR and STS) in the 280 F₂ plant population using Chi square (χ²) and simple regression (r²) analysis.

Tool	Marker	No. of tested plants	S	H	R	Expected ratio	χ^2	r^2
SSR	bnlg1063	280	64	142	74	1:2:1	0.77^ns	0.46
	umc2082	280	71	145	64	1:2:1	0.71^ns	0.41
	bnlg1621	280	68	141	71	1:2:1	0.08^ns	0.42
	umc2013	280	64	137	79	1:2:1	1.74^ns	0.36
	bnlg1740	280	66	143	71	1:2:1	0.31^ns	0.42
	umc2059	280	65	137	78	1:2:1	1.34^ns	0.34
	SSR85	280	60	151	69	1:2:1	2.31^ns	0.28
STS	STS06	280	60	154	66	1:2:1	3.06^ns	0.30

Note: S, susceptible plants; R, resistant plants; H, heterozygous.

ns: non-significant at 0.05 level of probability.

Figure 8. STS fragments produced by STS06.

Table 3. Genetic characteristics of QTL related to Fusarium ear rot resistance genes in the 280 F₂ plants population.

Marker	Chromosome bin	Map (cM)	LOD	R^2 (%)	P value	Additive effect
bnlg1063	3.06	16.8	36.4	24	0.00000	−1.01
umc2082	4.03	20.7	26.7	23	0.00000	−1.00
bnlg1621	4.06	17.1	33.7	26	0.00000	−1.02
umc2013	5.07	26.7	18.9	17	0.00000	−0.84
bnlg1740	6.07	17.6	33.2	32	0.00000	−1.16
umc2059	6.08	26.9	18.1	16	0.00000	−0.81
SSR85	10.03/04	29.4	13.5	17	0.00000	−0.88
STS06	10.03/04	26.4	16.5	13	0.00000	−0.78

Figure 9. SSR markers (bnlg1063, umc2082, bnlg1621, umc2013, bnlg1740, umc2059 and SSR85), STS marker (STS06) and QTL for Fusarium ear rot resistance genes were located through the MAPMAKER QTL analysis. All distances are given in centi-Morgan, using Kosambi's mapping function.

Table 4. Analysis of variance of Fusarium ear rot resistance of F₂ progeny on seven SSR and STS markers.

Marker	Source	DF	SS	MS	F	P value
	Model	2	62,602.18	31,301.09	38.16	0.00001
bnlg1063	Error	277	227,223.9	820.30
	Total	279	289,826.1
	Model	2	47796.74	2389.37	27.35	0.0001
umc2082	Error	277	242,029.3	873.75
	Total	279	289,826.1
	Model	2	55245.32	27622.66	32.62	0.0001
bnlg1621	Error	277	234,580.8	846.86
	Total	279	289,826.1
	Model	2	38,782.18	19,391.09	21.39	0.0001
umc2013	Error	277	251,043.9	906.29
	Total	279	289,826.1
	Model	2	52,942.72	26,471.36	30.95	0.0001
bnlg1740	Error	277	236,883.4	855.17
	Total	279	289,826.1
	Model	2	34481.64	17240.82	18.70	0.0001
umc2059	Error	277	255,344.4	921.82
	Total	279	289,826.1
	Model	2	24532.54	12266.27	12.81	0.0001
SSR85	Error	277	265,293.5	957.738
	Total	279	289,826.1
	Model	2	26781.67	13390.84	14.10	0.0001
STS06	Error	277	263,044.4	949.62
	Total	279	289,826.1

Table 5. Genetic characteristics of QTL related to agronomic traits of the 280 F₂ plants derived from NC300 × GM1002 population using SSR and STS markers.

Trait	Marker	Chromosome bin	QTL (cM)	LOD	R^2 (%)	P value	Additional effect
100 KW	bnlg1063	3.06	38.0	8.3	15	0.00000	3.83
	umc2082	4.03	39.0	7.4	12	0.00000	3.44
	bnlg1621	4.06	36.6	8.7	13	0.00000	3.56
	umc2013	5.07	46.7	4.7	8	0.00000	2.77
	bnlg1740	6.07	40.6	7.2	18	0.00000	4.20
	umc2059	6.08	50.1	3.7	6	0.00000	2.35
	ssr85	10.03/04	49.4	3.3	5	0.00011	2.30
GYME	bnlg1063	3.06	53.0	2.9	6	0.00003	13.24
	bnlg1740	6.07	52.7	2.9	9	0.00000	16.59
GYP	bnlg1063	3.06	53.1	2.9	3	0.00200	12.85
	bnlg1740	6.07	52.7	2.9	4	0.00024	15.49