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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

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

Gene Alleles 1 Minor allele frequency CQA 2R2[%] CQS R2[%] TSC R2[%] TSY R2[%]
Putative Kunitz-type tuber invertase inhibitor (KT-InvInh) A/G261GATGAT114, 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*** ↑
T/C3117 0.16 (C3117) ns 4.3* ↑ 7.4** ↑ 6.1** ↑
  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.
  2. 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.