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Bidirectional Selection for Body Weight on Standing Genetic Variation in a Chicken Model
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Univ Gothenburg, Dept Biol & Environm Sci, Gothenburg, Sweden.ORCID iD: 0000-0001-8714-0812
Virginia Polytech Inst & State Univ, Dept Anim & Poultry Sci, Blacksburg, VA USA.
Virginia Polytech Inst & State Univ, Dept Anim & Poultry Sci, Blacksburg, VA USA.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.ORCID iD: 0000-0002-2722-5264
2019 (English)In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 9, no 4, p. 1165-1173Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2019. Vol. 9, no 4, p. 1165-1173
Keywords [en]
Chicken, White Plymouth Rock, selective sweeps, body weight, quantitative trait
National Category
Genetics
Identifiers
URN: urn:nbn:se:uu:diva-382651DOI: 10.1534/g3.119.400038ISI: 000463929500018PubMedID: 30737239OAI: oai:DiVA.org:uu-382651DiVA, id: diva2:1307791
Funder
Swedish Research CouncilKnut and Alice Wallenberg FoundationSwedish National Infrastructure for Computing (SNIC), b2015010Swedish Research Council Formas, DNR 221-2013-450Available from: 2019-04-29 Created: 2019-04-29 Last updated: 2019-04-29Bibliographically approved

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