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Background  Fruits from several species of the Rosaceae family are reported to cause allergic reactions in certain populations. The allergens identified belong to mainly four protein families: pathogenesis related 10 proteins, thaumatin-like proteins, lipid transfer proteins and profilins. These families of putative allergen genes in apple ( Mal d 1  to  4 ) have been mapped on linkage maps and subsequent genetic study on allelic diversity and hypoallergenic traits has been carried out recently. In peach ( Prunus persica ), these allergen gene families are denoted as  Pru p 1  to  4  and for almond ( Prunus dulcis ) Pru du 1  to  4 . Genetic analysis using current molecular tools may be helpful to establish the cause of allergenicity differences observed among different peach cultivars. This study was to characterize putative peach allergen genes for their genomic sequences and linkage map positions, and to compare them with previously characterized homologous genes in apple ( Malus domestica ).    Results  Eight  Pru p/du 1  genes were identified, four of which were new. All the  Pru p/du 1  genes were mapped in a single bin on the top of linkage group 1 (G1). Five  Pru p/du 2  genes were mapped on four different linkage groups, two very similar  Pru p/du 2.01  genes ( A  and  B ) were on G3,  Pru p/du 2.02  on G7, Pru p/du 2.03  on G8 and  Pru p/du 2.04  on G1. There were differences in the intron and exon structure in these  Pru p/du 2  genes and in their amino acid composition. Three  Pru p/du 3  genes (3.01–3.03) containing an intron and a mini exon of 10 nt were mapped in a cluster on G6. Two  Pru p/du 4  genes ( Pru p/du 4.01  and  4.02 ) were located on G1 and G7, respectively. The  Pru p/du 1  cluster on G1 aligned to the  Mal d 1  clusters on LG16;  Pru p/du 2.01A  and  B  on G3 to  Mal d 2.01A  and  B  on LG9; the  Pru p/du 3  cluster on G6 to  Mal d 3.01  on LG12;  Pru p/du 4.01  on G1 to  Mal d 4.03  on LG2; and  Pru p/du 4.02  on G7 to  Mal d 4.02  on LG2.    Conclusion  A total of 18 putative peach/almond allergen genes have been mapped on five linkage groups. Their positions confirm the high macro-synteny between peach/almond and apple. The insight gained will help to identify key genes causing differences in allergenicity among different cultivars of peach and other  Prunus  species.

Genomic characterization of putative allergen genes in peach/almond and their synteny with apple