A molecular method for S-allele identification in apple based on allele-specific PCR

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Abstract
CDNA sequences corresponding to two self-incompatibility alleles (S-alleles) of the apple cv ‘Golden Delicious’ have previously been described, and now we report the identification of three additional S-allele cDNAs of apple, one of which was isolated from a pistil cDNA library of cv ‘Idared’ and two of which were obtained by reverse transcription-PCR (RT-PCR) on pistil RNA of cv ‘Queen's Cox’. A comparison of the deduced amino acid sequences of these five S-allele cDNAs revealed an average homology of 69%. Based on the nucleotide sequences of these S-allele cDNAs, we developed a molecular technique for the diagnostic identification of the five different S-alleles in apple cultivars. The method used consists of allele-specific PCR amplification of genomic DNA followed by digestion of the amplification product with an allele-specific restriction endonuclease. Analysis of a number of apple cultivars with known S-phenotype consistently showed coincidence of phenotypic and direct molecular data of the S-allele constitution of the cultivars. It is concluded that the S-allele identification approach reported here provides a rapid and useful method to determine the S-genotype of apple cultivars.