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.