Physical mapping of QTL for tuber yield, starch content and starch yield in tetraploid potato (Solanum tuberosum L.) by means of genome wide genotyping by sequencing and the 8.3 K SolCAP SNP array

Table 4 SNPs associated with TSC, TY and TSY in the QUEST population (n = 264)

SNP name	SNP alleles phu/tbr	Chromosome	Minor allele frequency^a	TSC (R²)^b	TY (R²)^b	TSY (R²)^b	SNP differential in case-control population for
ADXR_SNP5705 (5710) ^c	T/C	I	0.491 (C)	ns	* (2.0) ↑	** (3.5) ↑	TY, TSY, TSC
CP5_SNP3041	C/T	II	0.442 (C)	*** (5.1) ↑	ns	ns	TSC, TY
FBA_SNP_c2_11924	C/T	V	0.103 (T)	** (3.0) ↑	* (1.4) ↑	** (3.8) ↑	TSC
CP12.1_SNP_c2_54011	C/T	VI	0.082 (T)	ns	** (3.1) ↓	* (2.1) ↓	TY, TSY, TSC
MAK_SNP7832 (7475, 7634 7588)	T/C	VI	0.467 (T)	ns	*** (5.0) ↓	** (3.5) ↓	TY, TSY
MAK_SNP7576	G/A	VI	0.491 (A)	ns	*** (4.6) ↓	*** (5.9) ↓	TSC, TY, TSY
MAK_SNP7884	A/C	VI	0.113 (A)	ns	** (2.8) ↑	* (1.5) ↑	novel
QUA1_SNP_c2_9204	G/A	VI	0.452 (G)	ns	** (2.7) ↓	* (1.8) -	novel
QUA1_SNP9502	G/A	VI	0.070 (G)	ns	** (3.3) ↑	* (1.8) -	novel
QUA1_SNP_c2_9203	C/G	VI	0.453 (C)	ns	** (3.0) ↓	* (2.2) -	TY, TSY
PPR_SNP7181	T/C	IX	0.495 (C)	*** (4.8) ↑	ns	ns	TSC, TY
PPR_SNP7037 (7077)	C/T	IX	0.440 (T)	** (3.1) ↑	ns	ns	TSC, TY
PPR_SNP7083	A/G	IX	0.318 (G)	** (2.2) -	ns	ns	TSC, TY
RP60S_SNP_c2_3063	T/C	IX	0.157 (T)	* (1.3) ↑	* (2.0) ↑	** (3.9) ↑	TY, TSY
CIS_SNP4479	C/G	XII	0.438 (C)	*** (4.2) ↓	ns	ns	novel

Associations of SNPs with a minimum minor allele frequency of 1% and at least one association at p < 0.01 are shown
^aThe minor frequency allele is shown in parenthesis
^bns = not significant at α =0.05; * significant at α = 0.05, ** significant at α = 0.01, *** significant at α = 0.001; Arrows indicate the effect of the minor frequency SNP allele on the trait compared to the population mean: ↑ increasing, ↓ decreasing, − ambiguous
^cNumbers in parenthesis identify SNPs in nearly complete LD that showed similar associations

ISSN: 1471-2164