Table 3 Correspondence between diagnostic SSCP markers, cDNA alleles, and SNP alleles or haplotypes
LocusSSCP Marker (cDNA Allele)Corresponding SNP Allele or HaplotypeReference
PGSC0003DMG400013856Pain1-9a (Pain1-a) aPain1-A1544b(Draffehn et al. 2010)
PGSC0003DMG400013856Pain1-8c (Pain1-a) Pain1-C552A718b(Draffehn et al. 2010)
PGSC0003DMG400000735AGPsS-9a ↑AGPaseS-C1284T 1411C1457cThis paper
PGSC0003DMG400000735AGPsS-10a AGPaseS-C1259C1612cThis paper
Not annotatedStp23-8b, PHO1A-c (PHO1a-HA) PHO1a-T22A 322G824A2776bThis paper
PGSC0003DMG400028382StpL-3b, PHO1B-1b PHO1b-A158C159 A1250c(Li et al. 2013)
PGSC0003DMG400028382StpL-3e ↑PHO1b-G1305T1311c(Li et al. 2013)
PGSC0003DMG400028382StpL-3c PHO1b-C4404cThis paper
PGSC0003DMG400008942InvGE-6f (InvGE-a) InvGE-A1103b(Draffehn et al. 2010)
PGSC0003DMG402028252pCD141-3c (InvCD141-Sa) InvCD141-A280T288T339T543A630C1030G1031T1096b(Draffehn et al. 2010)
  • SSCP, single-strand conformation polymorphism; SNP, single-nucleotide polymorphism.

  • a The arrow indicates the direction of the allele effect on the traits, upwards for a positive (lower sugar content = greater chip quality, greater starch content) and downward for a negative effect (greater sugar content = lower chip quality, lower starch content).

  • b SNPs are numbered based on cDNA alleles, position 1 being A in the ATG start codon.

  • c SNPs are numbered based on the DM genomic sequence, position 1 being A in the ATG start codon.