Taylor Katherine L, Quackenbush Jane, Lamberty Cara, Hamby Kelly A, Fritz Megan L
Department of Entomology, University of Maryland, College Park, MD, 20742, USA.
Department of Biology, Hofstra University, Hempstead, NY, 11549, USA.
BMC Genomics. 2024 Dec 26;25(1):1247. doi: 10.1186/s12864-024-11160-x.
Strong and shifting selective pressures of the Anthropocene are rapidly shaping phenomes and genomes of organisms worldwide. Crops expressing pesticidal proteins from Bacillus thuringiensis (Bt) represent one major selective force on insect genomes. Here we characterize a rapid response to selection by Bt crops in a major crop pest, Helicoverpa zea. We reveal the polygenic architecture of Bt resistance evolution in H. zea and identify multiple genomic regions underlying this trait. In the genomic region of largest effect, we identified a gene amplification event, where resistant individuals showed variation in copy number for multiple genes. Signals of this amplification increased over time, consistent with the history of field-evolved Bt resistance evolution. Modern wild populations from disparate geographical regions are positive for this variant at high, but not fixed, allele frequencies. We also detected selection against single copy variants at this locus in wild H. zea collected from Bt expressing plants, further supporting its role in resistance. Multiple genes were annotated in this genomic region, and all appeared to be significantly upregulated in Bt resistant H. zea. We functionally characterized genes within the copy number variant (CNV), providing insight into their potential roles in resistance evolution. Our findings reveal the nature of rapid genome evolution in a major crop pest following anthropogenic selection and highlight the role that CNVs can have in rapid evolutionary responses.
人类世强大且不断变化的选择压力正在迅速塑造全球生物体的表型和基因组。表达来自苏云金芽孢杆菌（Bt）杀虫蛋白的作物是昆虫基因组的一种主要选择力量。在此，我们描述了主要作物害虫玉米棉铃虫对Bt作物选择的快速反应。我们揭示了玉米棉铃虫Bt抗性进化的多基因结构，并确定了该性状背后的多个基因组区域。在影响最大的基因组区域，我们发现了一个基因扩增事件，抗性个体在多个基因的拷贝数上存在变异。这种扩增的信号随时间增加，与田间进化的Bt抗性进化历史一致。来自不同地理区域的现代野生种群中，该变异的等位基因频率较高但未固定。我们还在从表达Bt的植物中采集的野生玉米棉铃虫中检测到针对该位点单拷贝变异的选择，进一步支持了其在抗性中的作用。该基因组区域注释了多个基因，且在Bt抗性玉米棉铃虫中所有这些基因似乎都显著上调。我们对拷贝数变异（CNV）内的基因进行了功能表征，深入了解了它们在抗性进化中的潜在作用。我们的研究结果揭示了人为选择后主要作物害虫快速基因组进化的本质，并突出了CNV在快速进化反应中可能发挥的作用。
