648 AJCS 4(8):648-659 (2010) ISSN:1835-2707 Genetic variation of S-alleles in wild almonds and their related Prunus species Alireza Rahemi* 1 , Reza Fatahi 2 , Ali Ebadi 2 , Toktam Taghavi 2 , Darab Hassani 3 , Thomas Gradziel 4 and José Chaparro 5 1 Department of Horticultural Science, Science and Research Branch, Islamic Azad University, Tehran, Iran 2 Department of Horticultural Science, University of Tehran, Karaj, Iran 3 Department of Horticulture, Seed and Plant Improvement Institute, Karaj, Iran 4 Department of Plant Science, University of California, Davis, CA, USA 5 Department of Horticultural Science, University of Florida, Gainesville, FL. USA * Corresponding author: a.rahemi@srbiau.ac.ir; a_rahemi@yahoo.com Abstract Wild almond genotypes are a rich source of desirable characteristics which can be useful to almond breeding programs. However, almonds express self-incompatibility which affects breeding parent selection. Self-incompatibility is controlled by a multi-allelic, single gene (S-locus). Here, the S-alleles were studied in 96 wild almonds and related Prunus species from 10 taxonomic groups. Polymerase chain reactions (PCR) were carried out using six sets of primers including: three degenerate primer pairs (PaConsI-F(FAM)/EM- PC1consRD, PaConsI-F(FAM)/EM-PC3consRD, EM-PC2consFD/EM-PC3consRD), one general primer pair AS1II/AmyC5R, one allele specific primer pair (CEBASf/AmyC5R), and one set of multiplex primers (AS1II/CEBASf/AmyC5R). The number of amplified bands (155) and their size ranges were higher than in previous reports. The primers, including the allele specific (CEBASf/AmyC5R), did not amplify any self-compatibility allele (Sf) among samples evaluated. Sizes of amplified alleles were compared with previous reports in almond and labeled accordingly. Alleles S9, S2, S13, and S25 had the highest frequencies (12.26, 8.39, 7.74, and 7.74 percent respectively). Alleles S16, S17, S18, S19, S22, and S28 were not observed in examined samples and alleles S15 and S26 had a low frequency (0.65). Presumably, the geographical distribution of these species had influenced their S-allele frequencies. The taxonomic groups were clustered by using amplified allele sizes from the first degenerate primers (PaConsI-F(FAM)/EM-PC1consRD). The dendrogram revealed that S-alleles were more similar within a taxonomic group than among groups. Keywords: Geographical distribution, S-allele, Self-compatibility, Self-incompatibility, S-RNase, Taxonomic groups Introduction Almonds are primarily self-incompatible (SI) (Tufts, 1919; Gregory, 2004). The self-incompatibility prevents self- fertilization (Socias i Company and Felipe, 1992) which can be an advantage in evolution as it increases out-crossing (Ortega and Dicenta, 2003) and prevents inbreeding depression (de Nettancourt, 1977; Halasz et al., 2005). The out-crossings increase almond diversity, distribution and adaptation to different geographical locations (Kester and Gradziel, 1996; Woolley et al., 2000). This high diversity and rich genetic pool is useful in almond breeding, as valuable characteristics can be found in almond germplasm (Popov et al., 1929). Knowledge of self-incompatibility status of almonds and their related species is very important in breeding programs (Vezvaei, 1994). S-alleles identity is particularly important for designing crosses and choosing parents for breeding self-compatible cultivars suitable for monoculture orchards with reduced need for honeybee pollinators (Batlle et al., 1997; Channuntapipat et al., 2003; Martinez-Gomez et al., 2003; Lopez et al., 2006; Ortega et al., 2006). These studies can also help determine the origin of cultivated and wild almonds (Martinez-Gomez et al., 2003; Zeinalabedini et al., 2007a). In almond, incompatibility is controlled by a single multi- allelic S-locus (Gagnard, 1954; Channuntapipat et al., 2001; Halasz et al., 2008). Incompatibility loci have five conserved regions (C1-C5), a hypervariable region (RHV) and two introns (Ushijima et al., 1998). While S-alleles of almond can be determined by several approaches, molecular methods can determine S-alleles faster, and more precisely. This technique is being routinely used for the identification of cross- incompatibility groupings for current almond cultivars (Gradziel et al., 2001a; Ortega and Dicenta, 2003; Sanchez- Perez et al., 2004). To date, 44 S-alleles have been detected in cultivated almonds (Kodad et al., 2008 and Ortega et al., 2009). Tamura et al. (2000) initially used the general primers (AS1II and AmyC5R) for amplification of S-alleles in almond. Ma and Oliviera (2001) and Channuntapipat et al. (2001, 2002, 2003) subsequently designed other primers for amplification of new S- alleles. Sanchez-Perez et al. (2004) introduced the allele