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Open Access Highly Accessed Research article

Selection for complex traits leaves little or no classic signatures of selection

Kathryn E Kemper1*, Sarah J Saxton12, Sunduimijid Bolormaa3, Benjamin J Hayes345 and Michael E Goddard13

Author Affiliations

1 Department of Agriculture and Food Systems, University of Melbourne, Parkville 3052, Australia

2 Australian Dairy Herd Improvement Scheme, 22 William Street, Melbourne 3000, Australia

3 Department of Environment and Primary Industries, AgriBio, Bundoora 3086, Australia

4 La Trobe University, Bundoora 3086, Australia

5 Dairy Futures Co-operative Research Centre, Bundoora 3086, Australia

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BMC Genomics 2014, 15:246  doi:10.1186/1471-2164-15-246

Published: 28 March 2014



Selection signatures aim to identify genomic regions underlying recent adaptations in populations. However, the effects of selection in the genome are difficult to distinguish from random processes, such as genetic drift. Often associations between selection signatures and selected variants for complex traits is assumed even though this is rarely (if ever) tested. In this paper, we use 8 breeds of domestic cattle under strong artificial selection to investigate if selection signatures are co-located in genomic regions which are likely to be under selection.


Our approaches to identify selection signatures (haplotype heterozygosity, integrated haplotype score and FST) identified strong and recent selection near many loci with mutations affecting simple traits under strong selection, such as coat colour. However, there was little evidence for a genome-wide association between strong selection signatures and regions affecting complex traits under selection, such as milk yield in dairy cattle. Even identifying selection signatures near some major loci was hindered by factors including allelic heterogeneity, selection for ancestral alleles and interactions with nearby selected loci.


Selection signatures detect loci with large effects under strong selection. However, the methodology is often assumed to also detect loci affecting complex traits where the selection pressure at an individual locus is weak. We present empirical evidence to suggests little discernible ‘selection signature’ for complex traits in the genome of dairy cattle despite very strong and recent artificial selection.