Utility of EST-Derived SSRs as Population Genetics Markers in a Beetle

Abstract

Microsatellite, or simple sequence repeat (SSR), loci can be identified by mining expressed sequence tag (EST) databases, and where these are available, marker development time and expense can be decreased considerably over conventional strategies of probing the entire genome. However, it is unclear whether they provide information on population structure similar to that generated by anonymous genomic SSRs. We performed comparative population genetic analyses between EST-derived SSRs (EST-SSRs) and anonymous SSRs developed from genomic DNA for the same set of populations of the insect Diabrotica virgifera, a beetle in the family Chrysomelidae. Compared with noncoding, nontranscribed regions, EST-SSRs were generally less polymorphic but had reduced occurrence of null alleles and greater cross-species amplification. Neutrality tests suggested the loci were not under positive selection. Across all populations and all loci, the genomic and EST-SSRs performed similarly in estimating genetic diversity, F(IS), F(ST), population assignment and exclusion tests, and detection of distinct populations. These findings, therefore, indicate that the EST-SSRs examined can be used with confidence in future genetic studies of Diabrotica populations and suggest that EST libraries can be added as a valuable source of markers for population genetics studies in insects and other animals.

Characterization of novel genic SSR markers in Linum usitatissimum (L.) and their transferability across eleven Linum species

“…When they are amplified across different species not necessarily are compared the same genomic regions which can conduct to erroneous conclusions (Pashley et al 2006). Although, Genomic Simple Sequence Repeats (G-SSRs) have been developed in cultivated flax (Roose-Amsaleg et al 2006;Deng et al 2010;SotoCerda et al 2010) their transferability to related species is generally low because they commonly occur in noncoding regions of the genome which are not highly conserved (Kim et al 2008). Moreover, homoplasy is another limitation of G-SSRs in evolutionary studies where identical band sizes may not be identical by descent (Thiel et al 2003).…”

SSR data mined from expressed sequence tags of phytoparasitic nematodes

“…Moreover, EST-SSRs have been found to be significantly more transferable across taxonomic boundaries than traditional SSRs (Sim et al, 2009;Ellis & Burke, 2007) and the levels of polymorphism of transcribed EST-SSR regions appear to be similar to those of genomic-SSR regions (Tehrani et al, 2009). As EST-SSRs generally have fewer null alleles, greater cross-species amplification, and less allelic variability than genomic SSRs, EST-SSRs have been used widely in plant genetic studies (Aggarwal et al, 2007;Park et al, 2005;Wang et al, 2007) and population genetic studies (Ellis & Burke, HELMINTHOLOGIA, 47, 1: 8 -19, 2010 SSR data mined from expressed sequence tags of phytoparasitic nematodes al., 2007;Wang et al, 2006;Kim et al, 2008). Furthermore, as EST-SSRs are derived from coding sequences, they could be involved in regulating gene expression (Kunzler et al, 1995;Moxon &Wills, 1999), and the varieties of repeat units might reflect gene expression (Wells & Warren, 1998).…”

A Core Set of Microsatellite Markers for Western Corn Rootworm (Coleoptera: Chrysomelidae) Population Genetics Studies

“…For example, a potentially large number of microsatellites could be developed inexpensively through mining D. v. virgifera expressed sequence tag (EST) databases (Kim et al 2008). Although EST-derived microsatellites loci are part of an expressed gene and thus may be subject to direct selection, background selection, or genetic hitchhiking (Li et al 2002), polymorphisms in EST-derived microsatellites often behave as effectively neutral markers and can provide valid information about the genetic structure of natural populations (Woodhead et al 2005, Kim et al 2008.…”

“…The presence of null alleles in the population thus biases estimates of population genetics parameters through overestimation of homozygosity, so it is important to exclude markers harboring such alleles from the core set. To screen for null alleles, controlled single-pair crosses of D. v. virgifera were made as described by Kim et al (2008). Genomic DNA was extracted from the parents and Ϸ50 of the F 1 offspring from each cross.…”

“…Diabrotica microsatellite markers have been developed by three collaborating laboratories (Kim and Sappington 2005b, Kim et al 2008, Waits and Stolz 2008. Several of these markers have been successfully used to assess genetic structure of both natural populations (Kim and Sappington 2005a, Miller et al 2006, 2007, Kim et al 2008) and laboratory colonies (Kim et al 2007) of D. v. virgifera, and to identify routes of invasion in Europe (Miller et al 2005).…”