Abstract：Interspecies distant hybridization is one of the methods to create new germplasm of fruit trees, but how to detect the true interspecies hybrids has always lacked efficient and reliable technical means. This research was based on genomic research and the comparative analysis of the whole genome sequence of apple(Malus) and pear (Pyrus). Based on the indels from the 2 genomes, the InDel specific molecular marker was designed. This study combined PCR detection, and screened out 6 pairs of specific molecular markers with high specificity, good repeatability and clear amplification bands. Among them, 3 pairs of specific sequences from pear genome and 3 pairs of specific sequences from apple genome could effectively detect the differences between them. The above 6 pairs of specific molecular markers were used to identify 311 individuals from the progeny of the cross between the 3 groups of pear and apple. The results showed that the progeny of 7 strains could simultaneously amplify specific bands of apple and pear, which were identified as inter-genus hybrids that accounting for 2.3% of the total hybrid progeny. Among them, 1 was Malus domestica cv. 'Starking'×'Comice', 3 were 'Golden Delicious'×'Dangshansuli', 3 were 'Fuji''×'Comice'. Therefore, 6 pairs of inter-generic specific primers for pear and apple can be used for identification of distant hybrids at seedling stage. The technical method developed in this research to use gene-specific molecular markers to identify the intergeneric hybridization of 'Rosaceae' Pyrus and Malus would not only provide efficient and accurate detection markers for the distant hybridization of apples and pears, but also provides a valuable example for identification of inter-genus hybrids of other fruit trees.
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