Genomic architecture of potato resistance to Synchytrium endobioticum disentangled using SSR markers and the 8.3k SolCAP SNP genotyping array

Obidiegwu, Jude Eijkeme; Sanetomo, Rena; Flath, Kerstin; Tacke, Eckhard; Hofferbert, Hans-Reinhard; Hofmann, Andrea; Walkemeier, Birgit; Gebhardt, Christiane

doi:10.1186/s12863-015-0195-y

Table 2 Markers linked with resistance to S. endobioticum pathotypes 1, 2, 6 and 18 in the BNA2 family

From: Genomic architecture of potato resistance to Synchytrium endobioticum disentangled using SSR markers and the 8.3k SolCAP SNP genotyping array

Marker	Chr. no.	Alleles ^e	Parental genotype Ps-354	Parental genotype Pr-355	P1, χ ^2g	P2, χ ²	P6, χ ²	P18, χ ²
Solcap_c2_2505	I	A↑/G	GAAA	GGGA	16.27**^f	ns^f	ns	ns
GP194_snp7^b	I	A/T↑	AATT	AAAT	ns	ns	ns	8.09*
Solcap_c1_6853	III	T/G↑	TTTT	TTTG	ns	7.75*	8.91*	ns
STM1002-224^a	IV	1↑/0	0	1	7.93**	8.03**	8.99**	8.20**
Solcap_c2_35942	IV	A↑/G	GGGG	AGGG	14.99***	11.28**	12.78 ***	10.62**
Solcap_c1_15965	V	T/G	TTTG	TGGG	ns	ns	ns	ns
StI004-96^a	VI	1↑/0	0	1	9.25**	ns	ns	11.04**
Solcap_c1_9224	VI	T/C↑	TCCC	CCCC	ns	ns	ns	8.28*
Solcap_c2_25250	VII	T/C	TTTC	TTTC	ns	ns	ns	ns
Solcap_c2_28588	VIII	T/G	TTTT	TTTG	ns	ns	ns	ns
Solcap_c2_1106	X	G↑/C	CCCC	GCCC	15.26***	13.34***	8.45 **	13.76***
Solcap_c1_4319^c	XI	A↑/G	AGGG	AGGG	23.25***	32.77***	38.70***	21.16***
Solcap_c1_4319_2	XI	G/A	GGAA	AAAA	ns	ns	ns	ns
Solcap_c1_4319_3	XI	T/C	TCCC	CCCC	ns	ns	ns	ns
Solcap_c1_4322^c	XI	T↑/C	TCCC	TCCC	18.40***	34.55***	40.20***	18.86***
Y1delATT	XI	1↑/0	0	1	32.70***	51.05***	46.59***	46.11***
Solcap_c2_12276	XI	A/C	ACCC	ACCC	ns	ns	ns	ns
GP125_snp10^b	XI	C↑/A	CCCC	CCCA	7.58**	5.48*	6.16*	ns
GP259_snp7^b	XI	A/G↑	AAAG	AAAG	10.18*	18.58***	13.17**	20.72***
GP259_snp2^b	XI	G↑/A	GGGG	GGAA	6.84*	ns	ns	7.94*
GP259_snp16/17^b	XI	AC/GA↑	AAAG/CCCA	AAAA/CCCC	ns	7.57 **	15.31***	ns
St_At5g16710_snp4^b	XI	G/C↑	GGGC	GGGG	ns	14.26**	17.21**	8.16*
St_At5g16710_snp5^b	XI	A↑/G	AAGG	AAAA	ns	7.04*	ns	ns
St_At5g16710_snp1^b,d	XI	T/A↑	TTAA	TAAA	ns	14.21**	13.61**	9.46*
St_At5g16710_snp3^b,d	XI	C/A↑	CCAA	CAAA	ns	14.47**	14.82**	10.42*
St_At5g16710_snp6^b,d	XI	A/T↑	AATT	ATTT	ns	15.73**	12.76**	9.01*
St_At5g16710_snp10^b	XI	A/G↑	AGGG	AAAG	10.40*	ns	ns	ns
St_At5g16710_snp11^b	XI	C↑/T	CCCT	CCTT	14.75**	8.50*	11.84**	10.10*
Solcap_c1_7770	XII	T/C↑	TTTC	TTCC	ns	12.20**	8.15*	18.64***
Solcap_c2_33630	XII	T/C↑	TTCC	TTCC	ns	17.75**	18.41**	15.81**
Solcap_c2_33630_1 (~Solcap_c2_41100)	XII	A/G↑	AAGG	?	ns	17.76**	17.64**	21.41**
Solcap_c2_33630_2	XII	G/A↑	GGAA	GGAA	9.74*	21.72***	19.27**	23.03***

^aMarker was genotyped in 94 BNA2 individuals.
^bMarker was genotyped in 90 BNA2 individuals.
^cSNPs c1_4319 and c1_4322 co-segregated in the BNA2 family.
^dSNPs St_At5g16710_snp1, St_At5g16710_snp3 and St_At5g16710_snp6 co-segregated in the BNA2 family.
^eThe allele linked to greater resistance is indicated by ↑.
^fns: p > 0.05, *0.05 > p > 0.01, **0.01 > p > 0.001, ***p < 0.001.
^gChi-square values were obtained with the Kruskal-Wallis test for a phenotypic difference between genotypic classes.

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