Journal of Heredity Advance Access originally published online on January 24, 2008
Journal of Heredity 2008 99(2):112-124; doi:10.1093/jhered/esm104
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Utility of EST-Derived SSRs as Population Genetics Markers in a Beetle
From The USDA-ARS, Corn Insects and Crop Genetics Research Unit, Genetics Laboratory, Iowa State University, Ames, IA 50011; (Kim and Sappington); the University of Illinois, Department of Crop Science, S-316 Turner Hall, 1102 S. Goodwin Avenue, Urbana, IL 61801 (Ratcliffe); the USDA-ARS, North Central Agricultural Research Laboratory, 2923 Medary Avenue, Brookings, SD, 57006 (French); the University of Illinois, Biotechnology Center, 330 ERML, 1201 Gregory Drive, Urbana, IL 61801 (Liu)
Address correspondence to T. W. Sappington at the address above, or e-mail: tom.sappington{at}ars.usda.gov.
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, FIS, FST, 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.
Corresponding Editor: Lacey Knowles
Received November 7, 2006
Accepted October 11, 2007
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