Primers design strategy. A) Part of the coding sequence alignment of the 31 Mal d 1 isoallergen genes was retrieved from the ‘Golden Delicious’ genome sequence (Additional file 2). The sequences were named according to their related Mal d 1 genes and the accession numbers retrieved from the Apple GBrowse - Malus x domestica v1.0 . The white marked nucleotides highlight the mismatched residues in the consensus sequence. The SNPs specific for the loci Mal d 1.01 and -1.02 are indicated with red circles. B) Part of the alignment on all allelic gDNA sequences for Mal d 1.01 and -1.02 was obtained from the literature . The sequences of the two reverse primers for Mal d 1 .01 and -1.02 are also included in the alignment. The sequences were named according to their related Mal d 1 genes, ID numbers from the database and genotypic origins: FS: Fiesta; RD: Red Delicious; DS: Discovery; PM: Prima; GD: Golden Delicious; JO: Jonagold; FJ: Fuji; IM: Ingrid Marie; SC: Suncrisp; RG: Royal Gala. The SNP positions are indicated with successive numbers from 1 to 11. The red boxes indicate the two locus-differentiating SNPs exploited for primer design; the green box highlights an allele-differentiating SNP.
Pagliarani et al. BMC Plant Biology 2013 13:51 doi:10.1186/1471-2229-13-51