Novel candidate genes influencing natural variation in potato tuber cold sweetening identified by comparative proteomics and association mapping

Table 3 SNPs/Indels associated with tuber starch content (TSC), starch yield (TSY), chip quality after harvest (without cold storage, CQA) and 3 months cold storage (CQS) in the CHIPS-ALL population

Gene	Alleles ¹	Minor allele frequency	CQA ²R²[%]	CQS R²[%]	TSC R²[%]	TSY R²[%]
Putative Kunitz-type tuber invertase inhibitor (KT-InvInh)	A/G₂₆₁ (±GATGAT₁₁₄, G/T₃₃₄)	0.20 (G₂₆₁)	ns	ns	11.2*** ↑	11.6*** ↑
	C/G₂₀₆ (C/G₃₅₂, C/G₃₆₂, A/T₃₉₁, A/G/C₄₃₀)	0.13 (G₂₀₆)	ns	ns	6.5** ↑	8.7*** ↑
	A/G₃₉₅ (G/A₃₉₆)	0.02 (G₃₉₅)	ns	ns	7.2*** ↑	9.4*** ↑
Leucine aminopeptidase, neutral (LapN)	G/A₂₇₄₆	0.11 (A₂₇₄₆)	4.1** ↑	10.5*** ↑	17.5*** ↑	14.1*** ↑
Leucine aminopeptidase, neutral (LapN)	T/C₃₁₁₇	0.16 (C₃₁₁₇)	ns	4.3* ↑	7.4** ↑	6.1** ↑

¹Alleles with highly similar distribution in the CHIPS-ALL population and similar associations are shown in parentheses. SNP alleles forming the minor frequency haplotype are italics.
²ns: not significant. The level of significance is indicated by * for 0.05 > p >0.01, ** for 0.01 > p >0.001 and *** for p <0.001. Arrows indicate the direction of effect of the minor frequency allele, which increased average tuber starch content, starch yield and chip quality in all cases.

ISSN: 1471-2229