Dataset Information

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 Results:We 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. Conclusions:The 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.

SUBMITTER: Nichols J

PROVIDER: S-EPMC6240448 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature

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In silico detection of polymorphic microsatellites in the endangered Isis tamarind, <i>Alectryon ramiflorus</i> (Sapindaceae).

Nichols Joel J Conroy Gabriel C GC Kasinadhuni Naga N Lamont Robert W RW Ogbourne Steven M SM

Applications in plant sciences 20181115 11

<h4>Premise of the study</h4><i>Alectryon ramiflorus</i> (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.<h4>Methods and results</h4>We used next-generation sequencing and bioinformatics to detect polymorphic mi ...[more]

PMID: 30473942

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Project description:BACKGROUND: Simple Sequence Repeat (SSR) or microsatellite markers are valuable for genetic research. Experimental methods to develop SSR markers are laborious, time consuming and expensive. In silico approaches have become a practicable and relatively inexpensive alternative during the last decade, although testing putative SSR markers still is time consuming and expensive. In many species only a relatively small percentage of SSR markers turn out to be polymorphic. This is particularly true for markers derived from expressed sequence tags (ESTs). In EST databases a large redundancy of sequences is present, which may contain information on length-polymorphisms in the SSR they contain, and whether they have been derived from heterozygotes or from different genotypes. Up to now, although a number of programs have been developed to identify SSRs in EST sequences, no software can detect putatively polymorphic SSRs. RESULTS: We have developed PolySSR, a new pipeline to identify polymorphic SSRs rather than just SSRs. Sequence information is obtained from public EST databases derived from heterozygous individuals and/or at least two different genotypes. The pipeline includes PCR-primer design for the putatively polymorphic SSR markers, taking into account Single Nucleotide Polymorphisms (SNPs) in the flanking regions, thereby improving the success rate of the potential markers. A large number of polymorphic SSRs were identified using publicly available EST sequences of potato, tomato, rice, Arabidopsis, Brassica and chicken.The SSRs obtained were divided into long and short based on the number of times the motif was repeated. Surprisingly, the frequency of polymorphic SSRs was much higher in the short SSRs. CONCLUSION: PolySSR is a very effective tool to identify polymorphic SSRs. Using PolySSR, several hundred putative markers were developed and stored in a searchable database. Validation experiments showed that almost all markers that were indicated as putatively polymorphic by polySSR were indeed polymorphic. This greatly improves the efficiency of marker development, especially in species where there are low levels of polymorphism, like tomato. When combined with the new sequencing technologies PolySSR will have a big impact on the development of polymorphic SSRs in any species.PolySSR and the polymorphic SSR marker database are available from http://www.bioinformatics.nl/tools/polyssr/.

Dataset Information

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

Publications

In silico detection of polymorphic microsatellites in the endangered Isis tamarind, <i>Alectryon ramiflorus</i> (Sapindaceae).

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