In silico detection of polymorphic microsatellites in the endangered Isis tamarind, Alectryon ramiflorus (Sapindaceae)

Abstract

Premise of the Study Alectryon ramiflorus (Sapindaceae) is an endangered rainforest tree known from only two populations. In this study, we identified polymorphic microsatellites, in silico, improving the effectiveness and efficiency of microsatellite development of nonmodel species. The development of genetic markers will support future conservation management of the species.Methods and ResultsWe used next‐generation sequencing and bioinformatics to detect polymorphic microsatellites, in silico, reducing both the time and cost of marker development. A panel of 15 microsatellites, 12 of which were polymorphic, were subsequently characterized in 64 adult trees representing the entire species range. Mean observed heterozygosity and expected heterozygosity were 0.471 and 0.425, respectively. The polymorphism information content across loci ranged from 0.152 to 0.875.ConclusionsThe microsatellite markers developed in this study will be useful in gaining an understanding of A. ramiflorus’ genetic diversity, level of inbreeding, and population structure and for guiding future restoration and management efforts.

Multi‐individual microsatellite identification: A multiple genome approach to microsatellite design (MiMi)

“…The application of a microsatellite‐picking tool such as pal_finder typically results in tens of thousands of potential loci, and therefore it makes logical sense to attempt to apply in silico marker optimisation methods over laboratory optimisation, to increase the efficiency in identifying informative loci. MiMi is the first tool, to our knowledge, that allows this range of important characteristics to be observed at the marker design stage (but see Nichols, Conroy, Kasinadhuni, Lamont, & Ogbourne, ). In a direct comparison between the traditional and MiMi methods, we show that the application of MiMi resulted in a 58% increase in the rate of identification of informative microsatellite markers, facilitating a 16% reduction in costs associated with the development of a microsatellite marker panel.…”