Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, 29634, USA.
Protecting Crops and the Environment, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK.
New Phytol. 2023 Mar;237(5):1891-1907. doi: 10.1111/nph.18655. Epub 2023 Jan 12.
Globally, weedy plants are a major constraint to sustainable crop production. Much of the success of weeds rests with their ability to rapidly adapt in the face of human-mediated management of agroecosystems. Alopecurus myosuroides (blackgrass) is a widespread and impactful weed affecting agriculture in Europe. Here we report a chromosome-scale genome assembly of blackgrass and use this reference genome to explore the genomic/genetic basis of non-target site herbicide resistance (NTSR). Based on our analysis of F2 seed families derived from two distinct blackgrass populations with the same NTSR phenotype, we demonstrate that the trait is polygenic and evolves from standing genetic variation. We present evidence that selection for NTSR has signatures of both parallel and non-parallel evolution. There are parallel and non-parallel changes at the transcriptional level of several stress- and defence-responsive gene families. At the genomic level, however, the genetic loci underpinning NTSR are different (non-parallel) between seed families. We speculate that variation in the number, regulation and function of stress- and defence-related gene families enable weedy species to rapidly evolve NTSR via exaptation of genes within large multi-functional gene families. These results provide novel insights into the potential for, and nature of plant adaptation in rapidly changing environments.
在全球范围内，杂草是可持续作物生产的主要制约因素。杂草之所以能在面对人类对农业生态系统的管理时迅速适应，很大程度上是因为它们的这种能力。节节麦是一种广泛存在且具有重大影响的杂草，对欧洲的农业造成了影响。在这里，我们报告了节节麦的染色体规模基因组组装，并利用这个参考基因组来探索非靶标位点除草剂抗性（NTSR）的基因组/遗传基础。基于对来自两个具有相同 NTSR 表型的不同节节麦群体的 F2 种子家系的分析，我们证明了该性状是多基因的，并且是由现有遗传变异进化而来的。我们提出的证据表明，对 NTSR 的选择具有平行和非平行进化的特征。在几个应激和防御反应基因家族的转录水平上存在平行和非平行变化。然而，在基因组水平上，NTSR 所依赖的遗传基因座在种子家系之间是不同的（非平行）。我们推测，应激和防御相关基因家族数量、调控和功能的变化使杂草物种能够通过大型多功能基因家族中基因的适应来快速进化出 NTSR。这些结果为快速变化的环境中植物适应的潜力和本质提供了新的见解。
