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Artificial Selection Response due to Polygenic Adaptation from a Multilocus, Multiallelic Genetic Architecture.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. (Carlborg)
(Carlborg)
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. (Carlborg)ORCID iD: 0000-0001-8714-0812
(Carlborg)
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2017 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 34, no 10, p. 2678-2689Article in journal (Refereed) Published
Abstract [en]

The ability of a population to adapt to changes in their living conditions, whether in nature or captivity, often depends on polymorphisms in multiple genes across the genome. In-depth studies of such polygenic adaptations are difficult in natural populations, but can be approached using the resources provided by artificial selection experiments. Here, we dissect the genetic mechanisms involved in long-term selection responses of the Virginia chicken lines, populations that after 40 generations of divergent selection for 56-day body weight display a 9-fold difference in the selected trait. In the F15 generation of an intercross between the divergent lines, 20 loci explained >60% of the additive genetic variance for the selected trait. We focused particularly on fine-mapping seven major QTL that replicated in this population and found that only two fine-mapped to single, bi-allelic loci; the other five contained linked loci, multiple alleles or were epistatic. This detailed dissection of the polygenic adaptations in the Virginia lines provides a deeper understanding of the range of different genome-wide mechanisms that have been involved in these long-term selection responses. The results illustrate that the genetic architecture of a highly polygenic trait can involve a broad range of genetic mechanisms, and that this can be the case even in a small population bred from founders with limited genetic diversity.

Place, publisher, year, edition, pages
2017. Vol. 34, no 10, p. 2678-2689
Keywords [en]
epistasis, genetic architecture, genetic variation, multiallelic, multilocus, polygenic adaptation
National Category
Natural Sciences Genetics
Identifiers
URN: urn:nbn:se:uu:diva-332731DOI: 10.1093/molbev/msx194ISI: 000411814800019PubMedID: 28957504OAI: oai:DiVA.org:uu-332731DiVA, id: diva2:1153927
Funder
Swedish Research Council, 2012-4634Swedish Research Council Formas, 2010-643, 2013-450Available from: 2017-11-01 Created: 2017-11-01 Last updated: 2018-02-26
In thesis
1. Understanding the genetic basis of complex traits
Open this publication in new window or tab >>Understanding the genetic basis of complex traits
2018 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Recent advances in genetics and genomics have provided numerous opportunities to study the genetic basis of complex traits. Nevertheless, dissecting the genetic basis of complex traits is still challenged by the complex genetic architecture, in which many genes are involved, and many have small contributions to phenotypic variation, interactions with other genes or environmental factors. The aim of this thesis is to evaluate the genetic basis of the complex traits by exploring available genomic resources and analytical approaches. Four studies included in this thesis explore: the genetic basis of global transcriptome variation in natural population (Study I); the genetic basis of 8-week body weight in artificial selected chicken lines (Study II); the genetic basis of flowering time variation for Arabidopsis thaliana sampled from a wide range of ecological conditions (Study III and Study IV). Findings from this thesis show that the genetic architecture of complex traits involves many polymorphisms with variable effect sizes. Some of those polymorphisms are multi-allelic and have interactions with each other and environmental factors at the same time. The presence of many alleles with minor contributions to phenotypic variation in natural and artificially selected population demonstrates that response to natural and artificial selection has been achieved by polygenic adaptation. Furthermore, population-specific large-effect loci with long-range LD to QTL in functionally related pathways indicate that emergence and fixation of loci with large effects and co-evolution of loci in the related pathway is contributing to the local adaptation of Arabidopsis thaliana. Overall, this thesis shows the complexity of complex trait genetics and provides a few insights into study designs and analysis approaches for understanding the genetic basis of complex traits.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2018. p. 49
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine, ISSN 1651-6206 ; 1438
Keywords
genetic architecture, complex traits, epistasis, multi-allelic, genotype by environment interaction, polygenic adaptation
National Category
Medical and Health Sciences
Research subject
Biology with specialization in Evolutionary Genetics
Identifiers
urn:nbn:se:uu:diva-343174 (URN)978-91-513-0260-7 (ISBN)
Public defence
2018-04-27, C8:301, BMC, Husargatan 3, Uppsala, 09:15 (English)
Opponent
Supervisors
Available from: 2018-04-04 Created: 2018-02-26 Last updated: 2018-04-24

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Zan, YanjunLillie, MetteCarlborg, Örjan

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