Validation of SNP markers associated with late leaf spot resistance in groundnut

Figures & data

Table 1. KASP SNP markers linked to LLS resistance QTL (qLLSA02) in groundnut.

SNP ID	Position	Resistance allele	Susceptible allele	Donor source
GKAMA02GL582	1271582	G	C	A.cardenasii
GKAMA02GL975	1156975	G	C	A.cardenasii
GKAMA02GL829	435829	C	A	A.cardenasii
GKAMA02GL779	436779	C	T	A.cardenasii

Pandey et al., 2017.

Figure 1. Genotypic clustering of F₂ lines after screening with SNP marker GKAMA02GL582.

Table 2. Summary statistics for molecular data.

SNP ID	Plate No	Allele count	Hom Res	Het	Hom Susc	Uncallable	Unused	Well count
GKAMA02GL582	Plate 1	94	30	45	19	0	0	94
	Plate 2	94	34	41	19	0	0	94
	Sum	188	64	86	38	0	0	188
GKAMA02GL975	Plate 1	92	18	44	30	1	1	94
	Plate 2	93	19	40	34	1	0	94
	Sum	185	37	84	64	2	1	188
GKAMA02GL829	Plate 1	79	38	14	27	8	7	94
	Plate 2	88	37	10	41	6	0	94
	Sum	167	75	24	68	14	7	188
GKAMA02GL779	Plate 1	91	32	52	7	0	3	94
	Plate 2	93	28	58	7	0	1	94
	Sum	184	60	110	14	0	4	188
	Total	724	236	304	184	16	12	752

Table 3. Genotype of parents at four loci linked to LLS resistance.

	GKAMA02GL582	GKAMA02GL975	GKAMA02GL829	GKAMA02GL779
CS 16	G:G	G:G	C:C	C:C
Shitouqi	C:C	C:C	A:A	C:C

Table 4. Phenotype of genotypic groups.

GKAMA02GL582
Genotype	G:G	G:C	C:C	LSD 5%	CV%	S.E	F pr.
Mean LLS score	1.494a	5.375b	8.909c	0.2988	25.8	0.4929	<0.001
Phenotype	Resistant	Moderate	Susceptible
GKAMA02GL975
Genotype	G:G	G:C	C:C	LSD 5%	CV%	S.E	F pr.
Mean LLS score	1.098a	5.812b	8.829c	0.2616	20.1	0.384	<0.001
Phenotype	Resistant	Moderate	Susceptible
GKAMA02GL829
Genotype	C:C	C:A	A:A	LSD 5%	CV%	S.E	F pr.
Mean LLS score	1.125a	4.78b	7.85c	0.2668	20.8	0.3974	<0.001
Phenotype	Resistant	Moderate	Susceptible

Figure 2. Regression of three SNP markers on LLS scores. (a) SNP GKAMA02GL829, (b) SNP GKAMA02GL975 (c) SNP GKAMA02GL582.

Table 5. Goodness of fit statistics.

SNP	GKAMA02GL829	GKAMA02GL975	GKAMA02GL582
Observations	130	130	130
df	128	128	128
St. Error	0.493	0.389	0.405
R²	0.615	0.781	0.780
Adjusted R²	0.613	0.758	0.729

Pandey, M. K., Khan, A. W., Singh, V. K., Vishwakarma, M. K., Shasidhar, Y., Kumar, V., Garg, V., Bhat, R. S., Chitikineni, A., Janila, P., Guo, B., & Varshney, R. K. (2017). QTL-seq approach identified genomic regions and diagnostic markers for rust and late leaf spot resistance in groundnut (Arachis hypogaea L.). Plant Biotechnology Journal, 15(8), 927–941. https://doi.org/10.1111/pbi.12686

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Data availability statement

Data will be made available upon reasonable request.