Abstract
Microsatellites play an important role when investigating population and ecological genetics, although high effort in development and genotyping constitute a technical constraint and remains a major bottleneck. Here we use a microsatellite genotyping approach utilizing sequences of amplicons for allele calling (SSR-GBS) based on Illumina that requires less effort and time. The approach consist of development of highly polymorphic loci, sequencing of multiplexed PCR amplified microsatellites on an Illumina Miseq PE 300 platform and bioinformatic treatment of the sequenced data using custom scripts. The procedure allows automation in allele calling, which can be more reliably replicated and thereby removes biases that might prevent concatenation of datasets from different analyses. Additionally, the methodology enhances information content in the sequenced data beyond the traditional amplicon length (AL) approaches. Using 26 newly developed microsatellite markers and SSR-GBS we investigate the population genetic assessment of anthropogenically altered populations of East African Nile tilapia to show the potential of this genotyping approach. More precisely, we compare genotypic data generated considering AL and whole amplicon information (WAI). We found that genotypes based on WAI are not only able to recover a higher number of alleles but also a more detailed genetic structure pattern. We discuss the capability and importance of WAI allele calling and show perspectives for implementation in the future conservation genetic studies. More specifically, we demonstrate how the current markers and techniques might contribute useful information for studies concerning resources sustainable exploitation and conservation using the East African Nile tilapia.
Highlights
Microsatellites/simple sequence repeats (SSR) or short tandem repeats (STRs) have proved reliable as ideal genetic markers in population genetic studies (Guichoux et al 2011; Selkoe and Toonen 2006; Schlotterer et al 1991)
The use of these markers is further rendered reliable following the genesis of next-generation sequencing (NGS) technologies and the identification of numerous loci in non-model species accompanied by reduced costs (Guichoux et al 2011; Curto et al 2013)
This study is a proof of concept testing the ability of SSR-GBS in producing genotype data with a higher statistical power than the traditional SSR amplicon length genotyping due to its potential in recovering SNPs associated with SSR motif variation. This provides a higher number of alleles and reduces the length homoplasy effect that is characteristic to this marker system. We demonstrate this by comparing the importance and strengths of the two allele calling methods (WAI and the AL, similar to the traditional electropherogram methods)
Summary
Microsatellites/simple sequence repeats (SSR) or short tandem repeats (STRs) have proved reliable as ideal genetic markers in population genetic studies (Guichoux et al 2011; Selkoe and Toonen 2006; Schlotterer et al 1991). This is due to their important attributes including, but not limited. Many of the previous genetic studies on Nile Tilapia, have utilised finger print methods (Mwanja et al 1996, 2008; Agnèse et al 1997; Seyoum and Kornfield 1992) Developed SSR had been employed, but frequently with low number of loci investigated and the resulting low amount of statistical power, (e.g. Bezault et al 2012; Lee and Kocher 1996; Hassanien and Gilbey 2005; Tariq Ezaz et al 2004)
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