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

Kemper, Kathryn E., Saxton, Sarah J., Bolormaa, Sunduimijid, Hayes, Benjamin J. and Goddard, Michael E. (2014) Selection for complex traits leaves little or no classic signatures of selection. BMC Genomics, 15 . doi:10.1186/1471-2164-15-246


Author Kemper, Kathryn E.
Saxton, Sarah J.
Bolormaa, Sunduimijid
Hayes, Benjamin J.
Goddard, Michael E.
Title Selection for complex traits leaves little or no classic signatures of selection
Journal name BMC Genomics   Check publisher's open access policy
ISSN 1471-2164
Publication date 2014-03-28
Year available 2014
Sub-type Article (original research)
DOI 10.1186/1471-2164-15-246
Open Access Status DOI
Volume 15
Total pages 14
Place of publication London, United Kingdom
Publisher BioMed Central
Language eng
Formatted abstract
Background: 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.

Results: 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.

Conclusions: 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.
Keyword Complex traits
Selection signatures
Genomic regions
Bos taurus cattle
Quantitative trait loci (QTL)
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Queensland Alliance for Agriculture and Food Innovation
 
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