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Powerful detection of polygenic selection and evidence of environmental adaptation in US beef cattle

Selection on complex traits can rapidly drive evolution, especially in stressful environments. This polygenic selection does not leave intense sweep signatures on the genome, rather many loci experience small allele frequency shifts, resulting in large cumulative phenotypic changes. Directional sele...

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Autores principales: Rowan, Troy N., Durbin, Harly J., Seabury, Christopher M., Schnabel, Robert D., Decker, Jared E.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8297814/
https://www.ncbi.nlm.nih.gov/pubmed/34292938
http://dx.doi.org/10.1371/journal.pgen.1009652
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author Rowan, Troy N.
Durbin, Harly J.
Seabury, Christopher M.
Schnabel, Robert D.
Decker, Jared E.
author_facet Rowan, Troy N.
Durbin, Harly J.
Seabury, Christopher M.
Schnabel, Robert D.
Decker, Jared E.
author_sort Rowan, Troy N.
collection PubMed
description Selection on complex traits can rapidly drive evolution, especially in stressful environments. This polygenic selection does not leave intense sweep signatures on the genome, rather many loci experience small allele frequency shifts, resulting in large cumulative phenotypic changes. Directional selection and local adaptation are changing populations; but, identifying loci underlying polygenic or environmental selection has been difficult. We use genomic data on tens of thousands of cattle from three populations, distributed over time and landscapes, in linear mixed models with novel dependent variables to map signatures of selection on complex traits and local adaptation. We identify 207 genomic loci associated with an animal’s birth date, representing ongoing selection for monogenic and polygenic traits. Additionally, hundreds of additional loci are associated with continuous and discrete environments, providing evidence for historical local adaptation. These candidate loci highlight the nervous system’s possible role in local adaptation. While advanced technologies have increased the rate of directional selection in cattle, it has likely been at the expense of historically generated local adaptation, which is especially problematic in changing climates. When applied to large, diverse cattle datasets, these selection mapping methods provide an insight into how selection on complex traits continually shapes the genome. Further, understanding the genomic loci implicated in adaptation may help us breed more adapted and efficient cattle, and begin to understand the basis for mammalian adaptation, especially in changing climates. These selection mapping approaches help clarify selective forces and loci in evolutionary, model, and agricultural contexts.
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spelling pubmed-82978142021-07-31 Powerful detection of polygenic selection and evidence of environmental adaptation in US beef cattle Rowan, Troy N. Durbin, Harly J. Seabury, Christopher M. Schnabel, Robert D. Decker, Jared E. PLoS Genet Research Article Selection on complex traits can rapidly drive evolution, especially in stressful environments. This polygenic selection does not leave intense sweep signatures on the genome, rather many loci experience small allele frequency shifts, resulting in large cumulative phenotypic changes. Directional selection and local adaptation are changing populations; but, identifying loci underlying polygenic or environmental selection has been difficult. We use genomic data on tens of thousands of cattle from three populations, distributed over time and landscapes, in linear mixed models with novel dependent variables to map signatures of selection on complex traits and local adaptation. We identify 207 genomic loci associated with an animal’s birth date, representing ongoing selection for monogenic and polygenic traits. Additionally, hundreds of additional loci are associated with continuous and discrete environments, providing evidence for historical local adaptation. These candidate loci highlight the nervous system’s possible role in local adaptation. While advanced technologies have increased the rate of directional selection in cattle, it has likely been at the expense of historically generated local adaptation, which is especially problematic in changing climates. When applied to large, diverse cattle datasets, these selection mapping methods provide an insight into how selection on complex traits continually shapes the genome. Further, understanding the genomic loci implicated in adaptation may help us breed more adapted and efficient cattle, and begin to understand the basis for mammalian adaptation, especially in changing climates. These selection mapping approaches help clarify selective forces and loci in evolutionary, model, and agricultural contexts. Public Library of Science 2021-07-22 /pmc/articles/PMC8297814/ /pubmed/34292938 http://dx.doi.org/10.1371/journal.pgen.1009652 Text en © 2021 Rowan et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Rowan, Troy N.
Durbin, Harly J.
Seabury, Christopher M.
Schnabel, Robert D.
Decker, Jared E.
Powerful detection of polygenic selection and evidence of environmental adaptation in US beef cattle
title Powerful detection of polygenic selection and evidence of environmental adaptation in US beef cattle
title_full Powerful detection of polygenic selection and evidence of environmental adaptation in US beef cattle
title_fullStr Powerful detection of polygenic selection and evidence of environmental adaptation in US beef cattle
title_full_unstemmed Powerful detection of polygenic selection and evidence of environmental adaptation in US beef cattle
title_short Powerful detection of polygenic selection and evidence of environmental adaptation in US beef cattle
title_sort powerful detection of polygenic selection and evidence of environmental adaptation in us beef cattle
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8297814/
https://www.ncbi.nlm.nih.gov/pubmed/34292938
http://dx.doi.org/10.1371/journal.pgen.1009652
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