Genetic and epigenetic differentiation in response to genomic selection for avian lay date

Melanie Lindner; Irene Verhagen; A. Christa Mateman; Kees van Oers; Veronika N. Laine; Marcel E. Visser

doi:10.1111/eva.13703

journal article Open Access Jun 28, 2024

Genetic and epigenetic differentiation in response to genomic selection for avian lay date

Melanie Lindner

Irene Verhagen A. Christa Mateman Kees van Oers Veronika N. Laine

Marcel E. Visser

Evolutionary Applications Vol. 17 No. 7 · Wiley

View at Publisher Save 10.1111/eva.13703

Abstract

AbstractAnthropogenic climate change has led to globally increasing temperatures at an unprecedented pace and, to persist, wild species have to adapt to their changing world. We, however, often fail to derive reliable predictions of species' adaptive potential. Genomic selection represents a powerful tool to investigate the adaptive potential of a species, but constitutes a ‘blind process’ with regard to the underlying genomic architecture of the relevant phenotypes. Here, we used great tit (Parus major) females from a genomic selection experiment for avian lay date to zoom into this blind process. We aimed to identify the genetic variants that responded to genomic selection and epigenetic variants that accompanied this response and, this way, might reflect heritable genetic variation at the epigenetic level. We applied whole genome bisulfite sequencing to blood samples of individual great tit females from the third generation of bidirectional genomic selection lines for early and late lay date. Genomic selection resulted in differences at both the genetic and epigenetic level. Genetic variants that showed signatures of selection were located within genes mostly linked to brain development and functioning, including LOC107203824 (SOX3‐like). SOX3 is a transcription factor that is required for normal hypothalamo‐pituitary axis development and functioning, an essential part of the reproductive axis. As for epigenetic differentiation, the early selection line showed hypomethylation relative to the late selection line. Sites with differential DNA methylation were located in genes important for various biological processes, including gonadal functioning (e.g., MSTN and PIK3CB). Overall, genomic selection for avian lay date provided insights into where within the genome the heritable genetic variation for lay date, on which selection can operate, resides and indicates that some of this variation might be reflected by epigenetic variants.

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Details

Published: Jun 28, 2024
Vol/Issue: 17(7)
License: View

Authors

M

Melanie Lindner

Department of Animal Ecology Netherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands; Chronobiology Unit, Groningen Institute for Evolutionary Life Sciences (GELIFES) University of Groningen Groningen The Netherlands

I

Irene Verhagen

Wageningen University & Research (WUR) Wageningen The Netherlands

A

A. Christa Mateman

Department of Animal Ecology Netherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands

K

Kees van Oers

Department of Animal Ecology Netherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands; Behavioural Ecology Group Wageningen University & Research (WUR) Wageningen The Netherlands

V

Veronika N. Laine

Finnish Museum of Natural History University of Helsinki Helsinki Finland

M

Marcel E. Visser

Department of Animal Ecology Netherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands; Chronobiology Unit, Groningen Institute for Evolutionary Life Sciences (GELIFES) University of Groningen Groningen The Netherlands

Funding

European Research Council Award: ERC‐2013‐AdG 339092

Cite This Article

Melanie Lindner, Irene Verhagen, A. Christa Mateman, et al. (2024). Genetic and epigenetic differentiation in response to genomic selection for avian lay date. Evolutionary Applications, 17(7). https://doi.org/10.1111/eva.13703

Genetic and epigenetic differentiation in response to genomic selection for avian lay date

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