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Table 2 Differential RADseq SNPs causing amino acid changes with unidirectional allele effect on TSC, TY and TSY in QUEST case-control populations

From: 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

SNP position (v2.1.11) Amino acid change Locus PGSC0003 Locus position [Mbp] (v4.03) Annotation Function category
chr01:37,823,297 G/R DMG400036984 chr01: 42.92 Gene of unknown function Unknown
chr01:63,201,542 M/K DMG400025974 chr01: 70.21 EF hand family protein Calcium binding (IPR002048)a
chr01:63,201,571 K/N DMG400025974 chr01: 70.21 EF hand family protein dito
chr01:63,201,582 V/F DMG400025974 chr01: 70.21 EF hand family protein dito
chr01:76,804,110 G/R DMG400025760 chr01: 83.89 Homeobox protein HAT3.1 Transcription regulation (uniprot/Q04996)b
chr01:78,272,215 H/Y DMG400025931 chr01: 85.36 GTP-binding protein alpha subunit, gna Signalling [59]
chr01:78,272,224 Y/D DMG400025931 chr01: 85.36 GTP-binding protein alpha subunit, gna dito
chr02:46,113,238 R/G DMG400012646 chr02: 47.66 Conserved gene of unknown function Unknown
chr05:4,555,061 D/G DMG400018440 chr05: 4.78 Conserved gene of unknown function Unknown
chr05:5,636,330 S/F DMG400017641 chr05: 5.99 Conserved gene of unknown function Unknown
chr06:47,805,636 C/G DMG402027033 chr06: 53.48 Zinc finger family protein Multiple regulatory functions [60]
chr07:872,052 I/L DMG400011219 chr07: 1.53 Tetratricopeptide repeat protein Protein-protein interactions, complex assembly (IPR013026)
chr07:872,053 I/N DMG400011219 chr07: 1.53 Tetratricopeptide repeat protein dito
chr08:5,319,820 L/F DMG400005778 chr08: 4.84 NADPH-dependent thioredoxin reductase B Defense to stress [61]
chr10:1,920,325 A/S DMG400025036 chr10: 1.91 Nucleic acid binding protein Unknown
chr11:3,818,033 T/I DMG400016135 chr11: 2.31 Tyrosine phosphatase Posttranlational regulation [62]
chr11:9,422,323 V/L DMG400044200 chr11: 9.48 Gene of unknown function Unknown
chr11:36,440,960 I/L DMG400000457 chr11: 39.25 Lethal leaf spot 1 Chlorophyll catabolism, cell death [63]
chr11:36,440,962 S/N DMG400000457 chr11: 39.25 Lethal leaf spot 1 dito
chr12:50,607,969 M/V DMG400041652 chr12: 52.23 Microsomal oleic acid desaturase Lipid metabolism
chr12:50,608,022 Q/H DMG400041652 chr12: 52.23 Microsomal oleic acid desaturase dito
chr12:50,526,275 D/N DMG400011613 chr12: 52.32 ABC transporter family protein Transport [64]
chr12:51,537,813 E/G DMG400004984 chr12: 53.87 Conserved gene of unknown function Unknown
chr12:58,658,881 P/S DMG400023861 chr12: 60.72 Extensin Ext1 Cell wall [57]
chr12:58,658,917 E/K DMG400023861 chr12: 60.72 Extensin Ext1 dito
chr12:58,658,927 S/L DMG400023861 chr12: 60.72 Extensin Ext1 dito
  1. aEntry in the InterPro database (http://www.ebi.ac.uk/interpro/)
  2. bEntry in the uniprot database (http://www.uniprot.org/)