Genomic and Genotyping Characterization of Haplotype-Based Polymorphic Microsatellites in Prunus

Abstract

Efficient utilization of microsatellites in genetic studies remains impeded largely due to the unknown status of their primer reliability, chromosomal location, and allele polymorphism. Discovery and characterization of microsatellite polymorphisms in a taxon will disclose the unknowns and gain new insights into the polymorphic alleles. In this study, we revealed the polymorphism status, primer categorization, chromosomal distribution, gene function, and genotyping performance of 319 haplotype-based polymorphic microsatellites (HPM) in expressed sequence tags (EST) of Prunus species, including peach, apricot, almond, plums, and cherries. Of the HPM, 262 are between two EST haplotypes and 57 are among three and more EST. In terms of species, 127 microsatellite polymorphisms are from different EST of peach, 108 from different EST between peach and other species, and 84fromdifferent EST between non-peach species. Based on the primer sequence alignments on the peach genome, there was one HPM per 678 kb and the 319 HPM were grouped into seven categories. The primers from the “deletion” category tended to yield higher allele numbers and polymorphism information content (PIC) values. Statistical analysis revealed the mean allele number, heterozygosity, PIC, and gene diversity value were all significantly higher in the HPM than in the haplotype-based non-polymorphic microsatellites (HNM), suggesting utilization of HPM markers could substantially increase the likelihood of allele polymorphism. Of the 234 unigenes annotated, 99 (42.3%) were categorized into binding function and 84 (35.9%) into catalytic activity, implying that these polymorphic alleles might have evolved primarily to play regulatory roles or catalyze enzymatic reactions.