Li et al. Genetics Selection Evolution 2010, 42:32 http://www.gsejournal.org/content/42/1/32 R E S E A R C H G e n e t i c s Se l e c t i o n Ev o l u t i o n Open Access A microsatellite-based analysis for the detection of selection on BTA1 and BTA20 in northern Eurasian cattle (Bos taurus) populations Meng-Hua Li, Terhi Iso-Touru, Hannele Laurén, Juha Kantanen* Abstract Background: Microsatellites surrounding functionally important candidate genes or quantitative trait loci have received attention as proxy measures of polymorphism level at the candidate loci themselves. In cattle, selection for economically important traits is a long-term strategy and it has been reported that microsatellites are linked to these important loci. Methods: We have investigated the variation of seven microsatellites on BTA1 (Bos taurus autosome 1) and 16 on BTA20, using bovine populations of typical production types and horn status in northern Eurasia. Genetic variability of these loci and linkage disequilibrium among these loci were compared with those of 28 microsatellites on other bovine chromosomes. Four different tests were applied to detect molecular signatures of selection. Results: No marked difference in locus variability was found between microsatellites on BTA1, BTA20 and the other chromosomes in terms of different diversity indices. Average D′ values of pairwise syntenic markers (0.32 and 0.28 across BTA 1 and BTA20 respectively) were significantly (P < 0.05) higher than for non-syntenic markers (0.15). The Ewens-Watterson test, the Beaumont and Nichol’s modified frequentist test and the Bayesian FST-test indicated elevated or decreased genetic differentiation, at SOD1 and AGLA17 markers respectively, deviating significantly (P < 0.05) from neutral expectations. Furthermore, lnRV, lnRH and lnRθ’ statistics were used for the pairwise population comparison tests and were significantly less variable in one population relative to the other, providing additional evidence of selection signatures for two of the 51 loci. Moreover, the three Finnish native populations showed evidence of subpopulation divergence at SOD1 and AGLA17. Our data also indicate significant intergenic linkage disequilibrium around the candidate loci and suggest that hitchhiking selection has played a role in shaping the pattern of observed linkage disequilibrium. Conclusion: Hitchhiking due to tight linkage with alleles at candidate genes, e.g. the POLL gene, is a possible explanation for this pattern. The potential impact of selective breeding by man on cattle populations is discussed in the context of selection effects. Our results also suggest that a practical approach to detect loci under selection is to simultaneously apply multiple neutrality tests based on different assumptions and estimations. Background Expectation of neutrality regarding the mutation-drift equilibrium for microsatellite variation is not always valid due to demographic changes, including genetic bottlenecks and admixture (e.g. [1,2]), and selection at linked sites (e.g. [3,4]). In contrast to demographic pro- cesses, which affect the entire genome, selection * Correspondence: juha.kantanen@mtt.fi Biotechnology and Food Research, MTT Agrifood Research Finland, FI-31600 Jokioinen, Finland operates at specific sites associated with phenotypic traits, such as important quantitative trait loci (QTLs) and candidate genes. Selection leaves its signature in the chromosomal regions surrounding the sites, where sig- nificantly reduced or elevated levels of genetic variation can be maintained at linked neutral loci. Thus, selection not only affects the selected sites but also linked neutral loci and the footprints of selection acting on specific functional loci can be detected by genotyping poly- morphic microsatellites in the adjacent non-coding regions [5]. © 2010 Li et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.