Dynamics of Adaptive Alleles in Divergently Selected Body Weight Lines of Chickens
Open Access
- 1 December 2013
- journal article
- research article
- Published by Oxford University Press (OUP) in G3 Genes|Genomes|Genetics
- Vol. 3 (12), 2305-2312
- https://doi.org/10.1534/g3.113.008375
Abstract
By studying genomic changes over time in populations subjected to strong artificial directional selection, we can gain insights to the dynamics of beneficial alleles originating from the founder population or emerging as novel mutations undergoing ongoing selection. The Virginia lines are a chicken resource population generated by long-term bi-directional, single-trait selection for juvenile body weight. We studied genome-wide allele frequency changes from generation 40 to 53 using genome-wide genotypes from directional and relaxed selection lines. Overall, there were small changes in allele frequencies at individual loci over the studied time period; but, on average, the changes were greater in lines with larger phenotypic changes. This is consistent with previous findings that much of the response to selection over the first 40 years of selection was attributable to utilization of standing genetic variation at many loci in the genome, indicating a mostly polygenic architecture for body weight. Over the course of the selection experiment, the largest phenotypic response to selection was observed in the high-weight selected line, and in this line we detected a single locus where the allele frequency changed rapidly during a late stage of the experiment. This locus likely contains a novel, beneficial mutation that appeared between generations 40 and 45 and was driven to fixation in 5 to 10 generations. This result illustrates the dependence of continued long-term selection response on standing genetic variation at many loci as well as strong, novel, beneficial mutations.Keywords
This publication has 26 references indexed in Scilit:
- How does adaptation sweep through the genome? Insights from long-term selection experimentsProceedings Of The Royal Society B-Biological Sciences, 2012
- Hundreds of variants clustered in genomic loci and biological pathways affect human heightNature, 2010
- The population genetics of beneficial mutationsPhilosophical Transactions Of The Royal Society B-Biological Sciences, 2010
- Genetic analysis of an F2 intercross between two chicken lines divergently selected for body-weightBMC Genomics, 2009
- A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rateGenome Research, 2008
- Phenotypic evolution from genetic polymorphisms in a radial network architectureBMC Biology, 2007
- A Single IGF1 Allele Is a Major Determinant of Small Size in DogsScience, 2007
- AnimalQTLdb: a livestock QTL database tool set for positional QTL information mining and beyondNucleic Acids Research, 2006
- Epistasis and the release of genetic variation during long-term selectionNature Genetics, 2006
- Haploview: analysis and visualization of LD and haplotype mapsBioinformatics, 2004