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Bidirectional Selection for Body Weight on Standing Genetic Variation in a Chicken Model

Journal article
Authors Mette Lillie
C. F. Honaker
P. B. Siegel
O. Carlborg
Published in G3-Genes Genomes Genetics
Volume 9
Issue 4
Pages 1165-1173
ISSN 2160-1836
Publication year 2019
Published at
Pages 1165-1173
Language en
Links dx.doi.org/10.1534/g3.119.400038
Keywords Chicken, White Plymouth Rock, selective sweeps, body weight, quantitative trait, genome-wide association, term divergent selection, long-term, soft, sweeps, adaptation, diversity, traits, lines, framework, responses, Genetics & Heredity, ephan w, 1992, theoretical population biology, v41, p237
Subject categories Genetics

Abstract

Experimental populations of model organisms provide valuable opportunities to unravel the genomic impact of selection in a controlled system. The Virginia body weight chicken lines represent a unique resource to investigate signatures of selection in a system where long-term, single-trait, bidirectional selection has been carried out for more than 60 generations. At 55 generations of divergent selection, earlier analyses of pooled genome resequencing data from these lines revealed that 14.2% of the genome showed extreme differentiation between the selected lines, contained within 395 genomic regions. Here, we report more detailed analyses of these data exploring the regions displaying within- and between-line genomic signatures of the bidirectional selection applied in these lines. Despite the strict selection regime for opposite extremes in body weight, this did not result in opposite genomic signatures between the lines. The lines often displayed a duality of the sweep signatures, where an extended region of homozygosity in one line, in contrast to mosaic pattern of heterozygosity in the other line. These haplotype mosaics consisted of short, distinct haploblocks of variable between-line divergence, likely the results of a complex demographic history involving bottlenecks, introgressions and moderate inbreeding. We demonstrate this using the example of complex haplotype mosaicism in the growth1 QTL. These mosaics represent the standing genetic variation available at the onset of selection in the founder population. Selection on standing genetic variation can thus result in different signatures depending on the intensity and direction of selection.

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