Department of Botany, Biodiversity Research Centre, University of British Columbia.
Department of Ecology & Evolutionary Biology, University of Toronto.
PLoS Genet. 2023 Dec 27;19(12):e1010865. doi: 10.1371/journal.pgen.1010865. eCollection 2023 Dec.
Genome size variation, largely driven by repeat content, is poorly understood within and among populations, limiting our understanding of its significance for adaptation. Here we characterize intraspecific variation in genome size and repeat content across 186 individuals of Amaranthus tuberculatus, a ubiquitous native weed that shows flowering time adaptation to climate across its range and in response to agriculture. Sequence-based genome size estimates vary by up to 20% across individuals, consistent with the considerable variability in the abundance of transposable elements, unknown repeats, and rDNAs across individuals. The additive effect of this variation has important phenotypic consequences-individuals with more repeats, and thus larger genomes, show slower flowering times and growth rates. However, compared to newly-characterized gene copy number and polygenic nucleotide changes underlying variation in flowering time, we show that genome size is a marginal contributor. Differences in flowering time are reflected by genome size variation across sexes and marginally, habitats, while polygenic variation and a gene copy number variant within the ATP synthesis pathway show consistently stronger environmental clines than genome size. Repeat content nonetheless shows non-neutral distributions across the genome, and across latitudinal and environmental gradients, demonstrating the numerous governing processes that in turn influence quantitative genetic variation for phenotypes key to plant adaptation.
基因组大小的变异主要由重复序列驱动，但在种群内和种群间的了解甚少，这限制了我们对其在适应中的重要性的理解。在这里，我们描述了 186 个 Amaranthus tuberculatus 个体的基因组大小和重复序列含量的种内变异，Amaranthus tuberculatus 是一种普遍存在的本地杂草，它在其分布范围内表现出对气候的开花时间适应，并对农业做出响应。基于序列的基因组大小估计在个体之间变化高达 20%，这与转座元件、未知重复序列和 rDNA 在个体之间的丰度的巨大变异性一致。这种变异的累加效应具有重要的表型后果——具有更多重复序列和更大基因组的个体表现出较慢的开花时间和生长速度。然而，与新描述的开花时间变异的基因拷贝数和多基因核苷酸变化相比，我们表明基因组大小是一个边缘贡献者。开花时间的差异反映在基因组大小的个体间变异上，跨性别和边缘生境，而多基因变异和 ATP 合成途径内的一个基因拷贝数变异比基因组大小表现出更一致的环境梯度。尽管如此，重复序列含量在整个基因组、纬度和环境梯度上表现出非中性分布，这表明了许多控制过程，这些过程反过来又影响着对植物适应至关重要的表型的数量遗传变异。
