Analysis of S-RNase alleles of almond (Prunus dulcis): characterization of new sequences, resolution of synonyms and evidence of intragenic recombination

Abstract

Cross-compatibility relationships in almond are controlled by a gametophytically expressed incompatibility system partly mediated by stylar RNases, of which 29 have been reported. To resolve possible synonyms and to provide data for phylogenetic analysis, 21 almond S-RNase alleles were cloned and sequenced from SP (signal peptide region) or C1 (first conserved region) to C5, except for the S 29 allele, which could be cloned only from SP to C1. Nineteen sequences (S 4 , S 6 , S 11 –S 22 , S 25 –S 29 ) were potentially new whereas S 10 and S 24 had previously been published but with different labels. The sequences for S 16 and S 17 were identical to that for S 1 , published previously; likewise, S 15 was identical to S 5 . In addition, S 4 and S 20 were identical, as were S 13 and S 19 . A revised version of the standard table of almond incompatibility genotypes is presented. Several alleles had AT or GA tandem repeats in their introns. Sequences of the 23 distinct newly cloned or already published alleles were aligned. Sliding windows analysis of Ka/Ks identified regions where positive selection may operate; in contrast to the Maloideae, most of the region from the beginning of C3 to the beginning of RC4 appeared not to be under positive selection. Phylogenetic analysis indicated four pairs of alleles had ‘bootstrap’ support > 80%: S 5 /S 10 , S 4 /S 8, S 11 /S 24 , and S 3 /S 6 . Various motifs up to 19 residues long occurred in at least two alleles, and their distributions were consistent with intragenic recombination, as were separate phylogenetic analyses of the 5′ and 3′ sections. Sequence comparison of phylogenetically related alleles indicated the significance of the region between RC4 and C5 in defining specificity.