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

IF 3.5 2区 生物学 Q1 EVOLUTIONARY BIOLOGY
Melanie Lindner, Irene Verhagen, A. Christa Mateman, Kees van Oers, Veronika N. Laine, Marcel E. Visser
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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.

Abstract Image

针对禽类产蛋期基因组选择的遗传和表观遗传分化。
人为气候变化导致全球气温以前所未有的速度上升,野生物种要想生存下去,就必须适应不断变化的世界。然而,我们往往无法对物种的适应潜力做出可靠的预测。基因组选择是研究物种适应潜力的有力工具,但对于相关表型的潜在基因组结构而言,它是一个 "盲目的过程"。在这里,我们利用大山雀(Parus major)雌鸟的产卵日期基因组选择实验来放大这一盲目过程。我们的目的是鉴定对基因组选择做出反应的遗传变异,以及伴随这种反应的表观遗传变异,从而在表观遗传水平上反映可遗传的遗传变异。我们对第三代早产和晚产双向基因组选择系的大山雀雌性个体的血液样本进行了全基因组亚硫酸氢盐测序。基因组选择导致了遗传和表观遗传水平的差异。显示出选择特征的基因变异位于主要与大脑发育和功能有关的基因中,包括LOC107203824(类SOX3)。SOX3 是下丘脑-垂体轴正常发育和功能所需的转录因子,是生殖轴的重要组成部分。在表观遗传分化方面,早期选择系相对于晚期选择系表现出低甲基化。存在DNA甲基化差异的位点位于对包括性腺功能在内的各种生物过程非常重要的基因上(如MSTN和PIK3CB)。总之,禽类产蛋期的基因组选择深入揭示了产蛋期遗传变异在基因组中的位置,选择可以作用于这些变异,并表明其中一些变异可能通过表观遗传变异反映出来。
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来源期刊
Evolutionary Applications
Evolutionary Applications 生物-进化生物学
CiteScore
8.50
自引率
7.30%
发文量
175
审稿时长
6 months
期刊介绍: Evolutionary Applications is a fully peer reviewed open access journal. It publishes papers that utilize concepts from evolutionary biology to address biological questions of health, social and economic relevance. Papers are expected to employ evolutionary concepts or methods to make contributions to areas such as (but not limited to): medicine, agriculture, forestry, exploitation and management (fisheries and wildlife), aquaculture, conservation biology, environmental sciences (including climate change and invasion biology), microbiology, and toxicology. All taxonomic groups are covered from microbes, fungi, plants and animals. In order to better serve the community, we also now strongly encourage submissions of papers making use of modern molecular and genetic methods (population and functional genomics, transcriptomics, proteomics, epigenetics, quantitative genetics, association and linkage mapping) to address important questions in any of these disciplines and in an applied evolutionary framework. Theoretical, empirical, synthesis or perspective papers are welcome.
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