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United States Department of Agriculture

Agricultural Research Service

Research Project: ECOLOGICALLY-BASED MANAGEMENT OF INSECT PESTS OF CORN Title: The application and performance of single nucleotide polymorphism markers for population genetic analyses of Lepidoptera

Authors
item Coates, Brad
item Bayles, Darrell
item Wanner, Kevin -
item Robertson, Hugh -
item Hellmich, Richard
item Sappington, Thomas

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: June 10, 2011
Publication Date: June 29, 2011
Citation: Coates, B.S., Bayles, D.O., Wanner, K.W., Robertson, H.M., Hellmich II, R.L., Sappington, T.W. 2011. The application and performance of single nucleotide polymorphism markers for population genetic analyses of Lepidoptera. Frontiers in Genetics. 2(38):1-10.

Interpretive Summary: The European corn borer and several other moth species feed upon and cause damage to crop plants resulting in significant economic loss to producers, growers, and farmers. Populations of these insect pests can change over time as a result of adaptations to their local environment and in response to management practices employed by stakeholders to control feeding damage to crop plants. Random mutations are routinely used by scientists as genetic markers for reconstructing the ancestry of individuals and estimating the relatedness of populations and movement of individuals between them. To assist in these efforts, we developed a large number of genetic markers that detect mutations at many single nucleotide positions within the genome of the European corn borer. We then applied these markers to estimate the level of genetic differences between populations. These results will be useful to all scientists interested in the population genetics of moths and butterflies.

Technical Abstract: Single nucleotide polymorphisms (SNPs) are nucleotide substitution mutations that tend to be at high densities within eukaryotic genomes. The development of assays that detect allelic variation at SNP loci is attractive for genome mapping, population genetics, and phylogeographic applications. A pipeline for the development and analysis of single locus markers from a total of 2742 putative SNPs within 7414 expressed sequence tags (ESTs) from the non-model species Ostrinia nubilalis (Lepidoptera: Crambidae) is described. Assays to detect variation at 763 SNP loci were designed to amplify within 24 multiplex polymerase chain reactions, of which 5 multiplex reactions (178 loci) were performed for SNP detection on the SEQUENOM MassARRAY [R]. Validation criteria of lack of significant deviation from Mendelian inheritance and Hardy-Weinberg equilibrium were met by 84 SNP marker loci. Genotyping data were used to estimate O. nubilalis population-level variation, linkage, and genealogical relationships. We also investigated the effects of ascertainment bias on heterozygosity and FST estimates due to sampling design. Results indicate that SNPs are an abundant source of mutation data that can be screened and analyzed for use in the study of non-model species, but several factors should be considered when SNP data is used to infer population structure, evolutionary history, and genetic diversity.

Last Modified: 11/27/2014
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