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Open Access Research article

A novel analytical method, Birth Date Selection Mapping, detects response of the Angus (Bos taurus) genome to selection on complex traits

Jared E Decker1, Daniel A Vasco12, Stephanie D McKay13, Matthew C McClure14, Megan M Rolf15, JaeWoo Kim1, Sally L Northcutt6, Stewart Bauck7, Brent W Woodward8, Robert D Schnabel1 and Jeremy F Taylor1*

Author affiliations

1 Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA

2 Department of Biology, Duke University, Durham, NC, 27708, USA

3 Department of Animal Science, University of Vermont, Burlington, VT, 05405, USA

4 Bovine Functional Genomics Laboratory, ARS, USDA, Beltsville, MD, 20705, USA

5 Department of Animal Science, Oklahoma State University, Stillwater, OK, 74078, USA

6 American Angus Association, 3201 Frederick Ave, Saint Joseph, MO, 64506, USA

7 GeneSeek, 4665 Innovation Drive, Suite 120, Lincoln, NE, 68521, USA

8 NextGen, Duluth, GA, 30096, USA

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Citation and License

BMC Genomics 2012, 13:606  doi:10.1186/1471-2164-13-606

Published: 9 November 2012

Abstract

Background

Several methods have recently been developed to identify regions of the genome that have been exposed to strong selection. However, recent theoretical and empirical work suggests that polygenic models are required to identify the genomic regions that are more moderately responding to ongoing selection on complex traits. We examine the effects of multi-trait selection on the genome of a population of US registered Angus beef cattle born over a 50-year period representing approximately 10 generations of selection. We present results from the application of a quantitative genetic model, called Birth Date Selection Mapping, to identify signatures of recent ongoing selection.

Results

We show that US Angus cattle have been systematically selected to alter their mean additive genetic merit for most of the 16 production traits routinely recorded by breeders. Using Birth Date Selection Mapping, we estimate the time-dependency of allele frequency for 44,817 SNP loci using genomic best linear unbiased prediction, generalized least squares, and BayesCĎ€ analyses. Finally, we reconstruct the primary phenotypes that have historically been exposed to selection from a genome-wide analysis of the 16 production traits and gene ontology enrichment analysis.

Conclusions

We demonstrate that Birth Date Selection Mapping utilizing mixed models corrects for time-dependent pedigree sampling effects that lead to spurious SNP associations and reveals genomic signatures of ongoing selection on complex traits. Because multiple traits have historically been selected in concert and most quantitative trait loci have small effects, selection has incrementally altered allele frequencies throughout the genome. Two quantitative trait loci of large effect were not the most strongly selected of the loci due to their antagonistic pleiotropic effects on strongly selected phenotypes. Birth Date Selection Mapping may readily be extended to temporally-stratified human or model organism populations.

Keywords:
Selective sweep; Selection mapping; Polygenic model; Pleiotropy; Cattle; Phenotype; Genotype; GWAS; SNP