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

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.

Figure 1

Haplotype homozygosity ( HAPH ), the integrated haplotype score ( |iHS| ) and F _ST near the POLLED locus. Breeds are Holstein (Hol, red), Jersey (Jer, purple), Angus (AA, black), Charolais (CC, yellow), Hereford (HH, green), Limousin (LL, blue), Murray Grey (MG, light blue) and Shorthorn (SS, grey). Points indicate windows with extreme (top 5%) values for HAPH, |iHS| or F _ST. F _ST of each breed with Holstein are highlighted in red (bottom panel). Trait units are multiples of an average window (HH, FST) or absolute standard deviations from the mean (|iHS|).

Figure 2

Haplotype homozygosity ( HAPH ), the integrated haplotype score ( |iHS| ) and mean F _ST near PLAG1 . Breeds are Holstein (Hol, red), Jersey (Jer, purple), Angus (AA, black), Charolais (CC, yellow), Limousin (LL, blue), Murray Grey (MG, light blue) and Shorthorn (SS, grey). Points indicate windows with extreme (top 5%) values for HAPH, |iHS| or F _ST. For simplicity, F _ST is presented as the mean for each breed with all other breeds. Trait units are multiples of an average window (HH, F _ST) or absolute standard deviations from the mean (|iHS|).