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United States Department of Agriculture

Agricultural Research Service

Title: Utility of EST-derived SSRs as Population Genetics Markers in a Beetle

item Kim, Kyung
item Ratcliffe, Susan - UNIVERSITY OF ILLINOIS
item French, Bryan
item Sappington, Thomas

Submitted to: Journal of Heredity
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 11, 2007
Publication Date: February 1, 2008
Citation: Kim, K.S., Ratcliffe, S.T., French, B.W., Liu, L., Sappington, T.W. 2008. Utility of EST-derived SSRs as Population Genetics Markers in a Beetle. Journal of Heredity. 99(2):112-124.

Interpretive Summary: Microsatellites are a type of DNA marker that is very useful in studying insects and other organisms, but they are time-consuming and expensive to develop. An alternative, faster method of identifying microsatellites involves screening DNA sequences in expressed sequence tag (EST) databases that exist for many species. We compared the results of using EST-derived microsatellites with conventional microsatellites to characterize the genetics of several populations of the western corn rootworm, a major insect pest of corn. The analysis indicated a few minor differences in the results generated by the two types of markers, but on the whole the results show that EST-derived microsatellites are reliable for use in population studies. Although our study was on a particular insect pest, the results are likely applicable to other animals of all kinds. The results will allow faster and less-expensive development of microsatellite markers for many animal species by scientists who otherwise might be unable to afford to develop this extremely useful kind of marker.

Technical Abstract: Microsatellites are extremely useful DNA markers in population genetics studies of animals, but they are time-consuming and expensive to develop. Microsatellite loci can be identified by mining expressed sequence tag (EST) databases, and if these could be used, marker development time would be decreased considerably over current strategies of probing the entire genome. However, because EST-derived microsatellites are nested in expressed genes that are presumably under selective constraints, it is unknown whether they would provide information on population structure similar to that given by anonymous genomic microsatellites that are more likely to be selectively neutral. To address this question, we performed comparative population genetic analyses between EST-derived microsatellites and anonymous microsatellites developed from genomic DNA for the same set of populations of the insect Diabrotica virgifera, a beetle in the family Chrysomelidae. Seventeen loci of each derivation were analyzed for general genetic characteristics, polymorphism, occurrence of null alleles, and interspecific transferability. Seven of these microsatellites were further used for estimating population genetic parameters of six geographic populations of corn rootworm (five D. v. virgifera and one D. v. zeae). Compared to non-coding, nontranscribed regions, EST-derived microsatellites were generally less polymorphic, but had reduced occurrence of null alleles, and greater cross-species amplification. Estimates of population genetic structure and genetic distances generated by the EST-derived microsatellites were generally congruent with the results from the genomic microsatellites. Across all populations and all loci, the genomic and EST-derived microsatellites showed very similar estimates of genetic diversity, Fis, and Fst. The two types of microsatellites were significantly correlated in the rank order of pairwise Fst's and genetic distance estimates, and there were no significant differences among the central values of these measures. Similar power in population clustering, in assigning individuals to their source population, and an identical number of distinct populations were detected between genomic and EST-derived microsatellites. These findings, therefore, indicate that EST-derived microsatellites can be added as a useful marker source for population genetics study of Diabrotica populations. The potential utility of EST-derived microsatellites for population genetic studies of insects and other animals is discussed.

Last Modified: 12/1/2015
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