Identification of self-incompatibility alleles in Iranian almond cultivars by PCR using consensus and allele-specific primers

The S-genotypes of sixteen Iranian cultivars of almond [Prunus dulcis Miller (D.A. Webb)] were determined using a PCR approach with different sets of consensus and allele-specific primers. Using the primers AS1II and AmyC5R (single PCR), or AS1II, AmyC5R, and CEBASf (multiplex PCR), eight PCR products corresponding to known alleles, as well as four bands not corresponding to previously reported sizes, were amplified. PCR with the second intron primers EM-PC2consFD and EM-PC3consRD, and the first intron primers PaConsI-F and EM-PC1consRD, resulted in the amplification of 12 alleles S-1, S-2, S-3, S-7, S-8, S-9, S-10, S-12, S-13, S-23, S-27, and S-29. A putative new allele was detected in the cultivar 'Mamaei', which corresponded to PCR products of 1,780 bp, 1,400 bp, and 370 by using AS1II and AmyC5R, EM-PC2consFD and EM-PC3consRD, and PaConsI-F and EM-PC1consRD, respectively. Products of 850 bp, 520 bp, and 195 6p, were observed in 'Shirbadam' using these primers, indicating another new allele. Some of these results were confirmed using allele-specific primers. The alleles S-2, S-7, and S-13 were most common, as each was found in four of the cultivars assayed. Three new cross-incompatibility groups (CIGs) are proposed on the basis of the genotypes obtained. Employing a combination of consensus and allele-specific primers resulted in complete and more precise genotyping. Identification of S-alleles in all the cultivars assayed, despite their unknown parentages, showed that these PCR techniques provide an efficient and rapid method to genotype almond cultivars.