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Submitted to: Acta Horticulturae
Publication Type: Peer Reviewed Journal Publication Acceptance Date: 3/12/2019 Publication Date: 2/26/2021 Citation: Chen, C. 2021. Genotyping variability of computationally categorized peach microsatellite markers. Acta Horticulturae. 1304/107-112. https://doi.org/10.17660/ActaHortic.2021.1304.17. DOI: https://doi.org/10.17660/ActaHortic.2021.1304.17 Interpretive Summary: DNA markers have been widely used in genetics mapping, variety authentication, phylogenetic analysis, and other studies. The obstacle to develop them into usable markers is how to optimally select downsized subsets of the primers for genotyping, which accordingly reduces amplification failure and monomorphism often occurring in randomly chosen primers of unknown distribution, reliability, and polymorphism. It is essential to computationally align the numerous primer sequences onto a quality reference genome, and to categorize them into subgroups by calculated genomic and expressed amplicon size differences (ASD). A look into genotyping variability of computationally categorized peach microsatellite markers can provide helpful guidance on selection of primers with better successful rate and improvement polymorphism.
Technical Abstract: Numerous expressed sequence tag (EST) simple sequence repeat (SSR) primers can be easily mined out. The obstacle to develop them into usable markers is how to optimally select downsized subsets of the primers for genotyping, which accordingly reduces amplification failure and monomorphism often occurring in randomly chosen primers of unknown distribution, reliability, and polymorphism. It is essential to computationally align the numerous primer sequences onto a quality reference genome, and to categorize them into subgroups by calculated genomic and expressed amplicon size differences (ASD). In this study, 288 optimally selected peach EST-SSR primers with known chromosomal distribution, SSR types and ASD subgroups were evaluated using representative peach cultivars and Prunus species. The 288 primers were spread on peach genome main scaffolds 1 to 8 (64, 34, 33, 36, 25, 29, 29, and 32 primers, respectively) and minor scaffolds 9 to 12 (1, 2, 2, and 1, respectively). The primers were also categorized by the SSR motif unit lengths into six types: 82 bi-type, 80 tri-type, 37 tetra-type, 16 penta-type, 15 hexa-type, and 58 compound-type; and by the ASD into five subgroups: 110 “deletion” (ASD<0), 50 “same-size” (ASD=0), 45 “insertion” (0 |
