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Cited by 8Genetic and phenotypic traits in livestockAnimal Behavior and ReproductionEpigenetics and DNA Methylation

Genetic and Epigenetic Differentiation in Response to Genomic Selection for Avian Lay Date

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Lindner, Melanie, Verhagen, Irene, Mateman, A. Christa, van Oers, Kees, Laine, Veronika N., Visser, Marcel E.·2024·Evolutionary Applications
DOI 10.1111/eva.13703PMC PMC11211926
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Abstract

Anthropogenic 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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  • Genetic variation remains stable throughout the sexual cycle or repeated asexual propagation, whereas epigenetic variation may be unstable even during asexual propagation.

    “Genetic variation remains stable throughout the sexual cycle or repeated asexual propagation, whereas epigenetic variation may be unstable even during asexual propagation [29].”

    From Somaclonal Variation and Clonal Fidelity in Commercial Micropropagation: Challenges and Perspectives (2025) · cites this paper as [29]

    The Discussion (page unavailable) says there is limited evidence for stable inheritance of spontaneous epigenetic mutations in vertebrates and describes DNA-methylation reprogramming during fertilization. It does not establish that genetic variation remains stable across sexual cycles or repeated asexual propagation, or that epigenetic variation is unstable during asexual propagation. (LLM, conf=0.78)

    Experimental — accuracy not yet measured

  • In plant tissue culture, stress conditions can influence epigenetic stability and genetic makeup, often triggering epigenetic modifications that regulate plant responses to environmental cues.

    “In plant tissue culture, stress conditions can influence the epigenetic stability and genetic makeup of plant materials, often triggering epigenetic modifications that regulate plant responses to environmental cues [29,50].”

    From Somaclonal Variation and Clonal Fidelity in Commercial Micropropagation: Challenges and Perspectives (2025) · cites this paper as [29]

    The Introduction (page not specified) discusses environmentally induced epigenetic modifications and describes epigenetic processes as responsive to the environment in maize. It does not address plant tissue culture or show that culture-related stress changes the epigenetic stability or genetic makeup of plant materials. (LLM, conf=0.85)

    Experimental — accuracy not yet measured

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Cited by

Sorted by citations

Authors
Lindner, M., Verhagen, I., Mateman, A. C., van Oers, K., Laine, V. N., & Visser, M. E.
Affiliations
  • University of Groningen (NL)
  • Wageningen University & Research (NL)
  • Netherlands Institute of Ecology (NL)
  • Department of Animal Ecology Netherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
  • University of Helsinki (FI)
Corresponding author
Lindner, Melanie
ORCID
Venue
Evolutionary Applications
Publisher
Wiley
Published
2024-06-28
Volume
17
Issue
7
Pages
e13703-e13703
ISSN
  • 1752-4563 (ISSN-L)
  • 1752-4571
DOI
10.1111/eva.13703
PMC
PMC11211926
OpenAlex
W4400123532
Cited by
8
References
1
Citations by year
2026: 4 · 2025: 3 · 2024: 1
FWCI
2.12
Type
journal article
Language
en
Open access
Licence
Locations
  • Evolutionary Applications (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • KNAW Research Portal (The Royal Netherlands Academy of Arts and Sciences) (publishedVersion, cc-by)
  • White Rose Research Online (University of Leeds, The University of Sheffield, University of York) (submittedVersion)
  • Socio-Environmental Systems Modeling (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
  • Työväentutkimus Vuosikirja (submittedVersion)
  • University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion, cc-by)
Funders
European Research Council (ERC‐2013‐AdG 339092)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
  • Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Animal Behavior and Reproduction
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
Keywords
genomic selection, Parus major, DNA methylation, adaptive potential, climate change, hypothalamic-pituitary axis, SOX3, brain development, breeding phenology, myostatin, PIK3CB

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