Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA.
Rothamsted Research, Protecting Crops and the Environment, Harpenden, Hertfordshire AL5 2JQ, UK.
Genes (Basel). 2023 Oct 4;14(10):1905. doi: 10.3390/genes14101905.
(blackgrass) is a problematic weed of Western European winter wheat, and its success is largely due to widespread multiple-herbicide resistance. Previous analysis of F2 seed families derived from two distinct blackgrass populations exhibiting equivalent non-target site resistance (NTSR) phenotypes shows resistance is polygenic and evolves from standing genetic variation. Using a CIDER-seq pipeline, we show that herbicide-resistant (HR) and herbicide-sensitive (HS) F3 plants from these F2 seed families as well as the parent populations they were derived from carry extra-chromosomal circular DNA (eccDNA). We identify the similarities and differences in the coding structures within and between resistant and sensitive populations. Although the numbers and size of detected eccDNAs varied between the populations, comparisons between the HR and HS blackgrass populations identified shared and unique coding content, predicted genes, and functional protein domains. These include genes related to herbicide detoxification such as Cytochrome P450s, ATP-binding cassette transporters, and glutathione transferases including . eccDNA content was mapped to the reference genome, revealing genomic regions at the distal end of chromosome 5 and the near center of chromosomes 1 and 7 as regions with a high number of mapped eccDNA gene density. Mapping to 15 known herbicide-resistant QTL regions showed that the eccDNA coding sequences matched twelve, with four QTL matching HS coding sequences; only one region contained HR coding sequences. These findings establish that, like other pernicious weeds, blackgrass has eccDNAs that contain homologs of chromosomal genes, and these may contribute genetic heterogeneity and evolutionary innovation to rapidly adapt to abiotic stresses, including herbicide treatment.
（黑麦草）是西欧冬小麦的一种有害杂草，其成功在很大程度上归因于广泛的多种除草剂抗性。先前对来自两个具有等效非靶标位点抗性（NTSR）表型的不同黑麦草种群的 F2 种子家族进行的分析表明，抗性是多基因的，并且源自现有遗传变异。使用 CIDER-seq 管道，我们表明，来自这些 F2 种子家族的除草剂抗性（HR）和除草剂敏感（HS）F3 植物以及它们源自的亲本种群携带额外染色体环状 DNA（eccDNA）。我们在抗性和敏感种群内和之间鉴定了编码结构的相似性和差异。尽管检测到的 eccDNA 的数量和大小在种群之间有所不同，但 HR 和 HS 黑麦草种群之间的比较确定了共享和独特的编码内容、预测基因和功能蛋白结构域。这些包括与除草剂解毒相关的基因，如细胞色素 P450s、ATP 结合盒转运蛋白和谷胱甘肽转移酶，包括.eccDNA 内容被映射到参考基因组上，揭示了染色体 5 的远端和染色体 1 和 7 的近中心作为具有高 mapped eccDNA 基因密度的基因组区域。映射到 15 个已知的除草剂抗性 QTL 区域表明，eccDNA 编码序列与 12 个匹配，其中 4 个 QTL 与 HS 编码序列匹配；只有一个区域包含 HR 编码序列。这些发现表明，像其他有害杂草一样，黑麦草具有包含染色体基因同源物的 eccDNA，这些可能有助于遗传异质性和进化创新，以快速适应非生物胁迫，包括除草剂处理。
