IFM Biology, University of Linköping, Linköping 581 83, Sweden.
Science for Life Laboratory, Department of Environmental Science, Stockholm University, Stockholm 106 91, Sweden.
G3 (Bethesda). 2022 Aug 25;12(9). doi: 10.1093/g3journal/jkac174.
How sexual selection affects the genome ultimately relies on the strength and type of selection, and the genetic architecture of the involved traits. While associating genotype with phenotype often utilizes standard trait morphology, trait representations in morphospace using geometric morphometric approaches receive less focus in this regard. Here, we identify genetic associations to a sexual ornament, the comb, in the chicken system (Gallus gallus). Our approach combined genome-wide genotype and gene expression data (>30k genes) with different aspects of comb morphology in an advanced intercross line (F8) generated by crossing a wild-type Red Junglefowl with a domestic breed of chicken (White Leghorn). In total, 10 quantitative trait loci were found associated to various aspects of comb shape and size, while 1,184 expression QTL were found associated to gene expression patterns, among which 98 had overlapping confidence intervals with those of quantitative trait loci. Our results highlight both known genomic regions confirming previous records of a large effect quantitative trait loci associated to comb size, and novel quantitative trait loci associated to comb shape. Genes were considered candidates affecting comb morphology if they were found within both confidence intervals of the underlying quantitative trait loci and eQTL. Overlaps between quantitative trait loci and genome-wide selective sweeps identified in a previous study revealed that only loci associated to comb size may be experiencing on-going selection under domestication.
性选择如何影响基因组最终取决于选择的强度和类型，以及涉及性状的遗传结构。虽然将基因型与表型相关联通常利用标准的性状形态，但在这方面，使用几何形态测量方法在形态空间中表现性状的表示形式受到的关注较少。在这里，我们确定了与鸡系统（Gallus gallus）中的性装饰物 - 鸡冠 - 相关的遗传关联。我们的方法将全基因组基因型和基因表达数据（>30k 个基因）与通过杂交野生型红原鸡和家鸡品种（白来亨鸡）产生的高级杂交系（F8）中的鸡冠形态的不同方面结合在一起。总共发现了 10 个与鸡冠形状和大小的各个方面相关的数量性状位点，而发现了 1184 个与基因表达模式相关的表达数量性状位点，其中 98 个与数量性状位点的置信区间重叠。我们的结果突出了已知的基因组区域，这些区域证实了先前记录的与鸡冠大小相关的大型数量性状位点的记录，以及与鸡冠形状相关的新的数量性状位点。如果基因在潜在数量性状位点和 eQTL 的置信区间内都被发现，则被认为是影响鸡冠形态的候选基因。先前研究中发现的数量性状位点和全基因组选择清除之间的重叠表明，只有与鸡冠大小相关的位点可能在驯化过程中经历持续选择。
