Bioinformatic Analysis of Self-Incompatibility Locus in Pear Species, Pyrus communis L. and Evaluation of the Related Alleles in Some Commercial and Native Cultivars

New identified alleles of self-incompatibility locus in Pyrus communis and renumbering of these alleles caused some confusion in their evaluation and categorization. Therefore, this research was performed for a comprehensive bioinformatics review on all 27 S-alleles of this species, and identification of S-alleles in some native Iranian pear cultivars. The results demonstrated that 21 S-alleles, out of 27 identified S-alleles are completely sequenced, that subsequently all 13 parts of them, including promoter, signal region, conserved C1 to C5, intron region and 6 intermediate region were aligned. Bioinformatic analysis revealed considerable conservation also in promoter, signal and terminal parts of locus and their appropriateness for primer design, also showed presence of two CAAT and two coherent TAAT boxes in most promoter regions of S-alleles. Cluster analysis of various parts of alleles showed the complete similarity of polypeptide sequence of S119 and S121 alleles, but in intron region they were moderately different, this high similarity level causes some mistakes in S-alleling of some cultivars such as Dargazi. Comparison of the results also demonstrated that due to sequence similarities and gene flow of other species, the specific primer method is not a trustable method for S-alleling in pear. Finally, S-alleling of some cultivars confirmed S104 in two control cultivars, Coscia and Beurre Diel, also in central Asian cultivar, Krus Siehan, also S108 in Krusalun and S107 in Shekkari and Shahmiveh cultivars, while S119 in Esfarayeni and Dargazi. Interestingly, S35 from P. ussuriensis in Shirin Torkan, Konjuni and Kaftarbache cultivars and S19 from P.×bretschneideri as the second allele of Shekkari cultivar were detected that reconfirming the previously reported gene flow of other Pyrus species in the native Iranian pear cultivars.