Identification of a new self-incompatibility allele (S31) in a Hungarian almond cultivar and its reliable detection

Self-incompatibility of almond Prunus dulcis (Mill.) D.A. Webb] is controlled by the S-locus with 30 described allelic variants. In this study, PCR amplification, cloning and DNA sequence analysis revealed a new S-RNase allele in a Hungarian cultivar, ‘Tétényi bőtermő’. This new allele was labelled as S₃₁. Since S₃₁ is characterized by almost identical intron sizes as S₉, consensus PCR was not successful in discrimination of the alleles, even if fluorescently labelled fragments were sized on an automated sequencer. Therefore, an allele-specific forward primer (PdS31-F) was designed to anneal selectively within the second intron of the S₃₁-RNase gene and used in combination with the EM-PC3consRD consensus primer. This allowed for the successful discrimination of S₃₁ from S₉. The PdS31-F primer and allele-specific PCR in general might be useful in the identification of different alleles with matching intron sizes that might occur during screening for S-alleles in a more diverse population, e.g. local cultivars from Central Europe to Asia.