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ARS Home » Southeast Area » Byron, Georgia » Fruit and Tree Nut Research » Research » Publications at this Location » Publication #316560

Research Project: Breeding Stone Fruit Adapted to the Production Environment of the Southeastern United States

Location: Fruit and Tree Nut Research

Title: Genomic and genotyping characterization of haplotype-based polymorphic microsatellites in Prunus

Author
item Chen, Chunxian
item Bock, Clive
item Beckman, Thomas - Tom
item Wood, Bruce
item Okie, William - Retired ARS Employee

Submitted to: Journal of Genetics and Genome Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/27/2015
Publication Date: 5/30/2015
Citation: Chen, C., Bock, C.H., Beckman, T.G., Wood, B.W., Okie, W.R. 2015. Genomic and genotyping characterization of haplotype-based polymorphic microsatellites in Prunus. Journal of Genetics and Genome Research. 2:014.

Interpretive Summary: Expressed sequence tag (EST) simple sequence repeat (SSR) markers have been widely used in linkage analysis, gene mapping, variety authentication and other genetic studies. However, 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. Identification of and investigation into polymorphic microsatellites could substantially improve the polymorphism rate.

Technical 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 84 from different 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.