Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden.
Institute of Marine Ecosystem and Fishery Science, Universität Hamburg, Hamburg, Germany.
J Evol Biol. 2021 Jun;34(6):879-892. doi: 10.1111/jeb.13699. Epub 2020 Sep 22.
Phenotypic variation plays an important role in how species cope with environmental challenges. Pinpointing which genes and genomic regions are underlying phenotypic variability thus helps to understand the processes of acclimation and adaptation. We used Daphnia as a system to identify candidates playing a role in phenotypic variation related to a predation risk environment with a genome-wide association approach. Furthermore, a gene co-expression network analysis allowed identifying clusters of co-expressed genes which correlated to life history traits. To enhance the understanding of the functional roles of the transcripts, we identified orthologs and paralogs from related species and used ontologies to annotate the candidates of interest. Our study revealed that only one life history trait and two morphometric traits have a genetic association in the presence of predation risk (fish kairomones), whereas most genotype-phenotype associations were detected in a genotype-environment interaction analysis for reproduction-related phenotypic traits. The gene co-expression network analysis identified a total of 44 modules, of which one module correlated to another life history trait namely the 'total number of broods'. The combined use of gene co-expression network and transcriptome-wide association analysis allowed the identification of 131 candidate transcripts associated with life history traits in Daphnia galeata. These results lay the ground for targeted studies to further understand phenotypic variability in this species.
表型变异在物种如何应对环境挑战方面起着重要作用。确定哪些基因和基因组区域是表型变异的基础，有助于理解适应和进化的过程。我们使用水蚤作为一个系统，通过全基因组关联分析来识别与捕食风险环境相关的表型变异中起作用的候选基因。此外，基因共表达网络分析允许识别与生活史特征相关的共表达基因簇。为了增强对转录本功能作用的理解，我们从相关物种中鉴定了同源基因和旁系同源基因，并使用本体论来注释感兴趣的候选基因。我们的研究表明，只有一个生活史特征和两个形态特征与捕食风险（鱼类信息素）有关，而大多数与繁殖相关的表型特征的基因型-表型关联是在基因型-环境相互作用分析中检测到的。基因共表达网络分析总共鉴定了 44 个模块，其中一个模块与另一个生活史特征（即“总产卵数”）相关。基因共表达网络和转录组关联分析的联合使用，确定了与水蚤 galeata 生活史特征相关的 131 个候选转录本。这些结果为有针对性的研究奠定了基础，以进一步了解该物种的表型变异。
