INRAE, Agroécologie, Dijon, France.
Université de Lyon, Anses, INRAE, USC CASPER, Lyon, France.
BMC Plant Biol. 2023 Oct 24;23(1):510. doi: 10.1186/s12870-023-04524-0.
Non-target site resistance (NTSR) to herbicides is a polygenic trait that threatens the chemical control of agricultural weeds. NTSR involves differential regulation of plant secondary metabolism pathways, but its precise genetic determinisms remain fairly unclear. Full-transcriptome sequencing had previously been implemented to identify NTSR genes. However, this approach had generally been applied to a single weed population, limiting our insight into the diversity of NTSR mechanisms. Here, we sought to explore the diversity of NTSR mechanisms in common ragweed (Ambrosia artemisiifolia L.) by investigating six field populations from different French regions where NTSR to acetolactate-synthase-inhibiting herbicides had evolved.
A de novo transcriptome assembly (51,242 contigs, 80.2% completeness) was generated as a reference to seek genes differentially expressed between sensitive and resistant plants from the six populations. Overall, 4,609 constitutively differentially expressed genes were identified, of which none were common to all populations, and only 197 were shared by several populations. Similarly, population-specific transcriptomic response was observed when investigating early herbicide response. Gene ontology enrichment analysis highlighted the involvement of stress response and regulatory pathways, before and after treatment. The expression of 121 candidate constitutive NTSR genes including CYP71, CYP72, CYP94, oxidoreductase, ABC transporters, gluco and glycosyltransferases was measured in 220 phenotyped plants. Differential expression was validated in at least one ragweed population for 28 candidate genes. We investigated whether expression patterns at some combinations of candidate genes could predict phenotype. Within populations, prediction accuracy decreased when applied to an additional, independent plant sampling. Overall, a wide variety of genes linked to NTSR was identified within and among ragweed populations, of which only a subset was captured in our experiments.
Our results highlight the complexity and the diversity of NTSR mechanisms that can evolve in a weed species in response to herbicide selective pressure. They strongly point to a non-redundant, population-specific evolution of NTSR to ALS inhibitors in ragweed. It also alerts on the potential of common ragweed for rapid adaptation to drastic environmental or human-driven selective pressures.
非靶标位点抗性（NTSR）是一种威胁农业杂草化学防治的多基因性状。NTSR 涉及植物次生代谢途径的差异调节，但其确切的遗传决定因素仍相当不清楚。全转录组测序此前已被用于鉴定 NTSR 基因。然而，这种方法通常仅应用于单个杂草种群，限制了我们对 NTSR 机制多样性的了解。在这里，我们通过研究来自法国不同地区的六个田间种群，探索普通豚草（Ambrosia artemisiifolia L.）中 NTSR 机制的多样性，这些种群中已进化出对乙酰乳酸合酶抑制剂类除草剂的 NTSR。
生成了从头组装的转录组（51242 个串联，80.2%的完整性），作为参考，用于从六个种群中寻找敏感和抗性植物之间差异表达的基因。总体而言，鉴定出 4609 个组成型差异表达基因，其中没有一个在所有种群中共同存在，只有 197 个在多个种群中共享。同样，在研究早期除草剂反应时，也观察到种群特异性的转录组反应。基因本体富集分析强调了应激反应和调节途径的参与，在处理前后。在 220 个表型植物中测量了 121 个候选组成型 NTSR 基因（包括 CYP71、CYP72、CYP94、氧化还原酶、ABC 转运蛋白、葡萄糖和糖基转移酶）的表达。在至少一个豚草种群中验证了 28 个候选基因的差异表达。我们研究了某些候选基因组合的表达模式是否可以预测表型。在种群内，当应用于额外的独立植物样本时，预测准确性降低。总体而言，在豚草种群内和种群间鉴定出了与 NTSR 相关的大量基因，其中只有一部分在我们的实验中被捕获。
我们的结果强调了在杂草物种中，NTSR 机制可以在应对除草剂选择压力下进化的复杂性和多样性。它们强烈表明，在豚草中，NTSR 对 ALS 抑制剂的非冗余、种群特异性进化。这也提醒人们，普通豚草有快速适应剧烈环境或人为驱动的选择压力的潜力。
