Carlier Jean, Bonnot François, Roussel Véronique, Ravel Sébastien, Martinez Reina Teresa, Perez-Vicente Luis, Abadie Catherine, Wright Stephen
CIRAD, UMR PHIM, Montpellier, France
PHIM, Plant Health Institute, Univ Montpellier, INRAe, CIRAD, Institut Agro, Montpellier, France.
mBio. 2021 Feb 23;12(1):e03129-20. doi: 10.1128/mBio.03129-20.
Plant pathogens can adapt to quantitative resistance, eroding its effectiveness. The aim of this work was to reveal the genomic basis of adaptation to such a resistance in populations of the fungus , a major devastating pathogen of banana, by studying convergent adaptation on different cultivars. Samples from populations showing a local adaptation pattern on new banana hybrids with quantitative resistance were compared, based on a genome scan approach, with samples from traditional and more susceptible cultivars in Cuba and the Dominican Republic. Whole-genome sequencing of pools of isolates (pool-seq) sampled from three locations per country was conducted according to a paired population design. The findings of different combined analyses highly supported the existence of convergent adaptation on the study cultivars between locations within but not between countries. Five to six genomic regions involved in this adaptation were detected in each country. An annotation analysis and available biological data supported the hypothesis that some genes within the detected genomic regions may play a role in quantitative pathogenicity, including gene regulation. The results suggested that the genetic basis of fungal adaptation to quantitative plant resistance is at least oligogenic, while highlighting the existence of specific host-pathogen interactions for this kind of resistance. Understanding the genetic basis of pathogen adaptation to quantitative resistance in plants has a key role to play in establishing durable strategies for resistance deployment. In this context, a population genomic approach was developed for a major plant pathogen (the fungus causing black leaf streak disease of banana) whereby samples from new resistant banana hybrids were compared with samples from more susceptible conventional cultivars in two countries. A total of 11 genomic regions for which there was strong evidence of selection by quantitative resistance were detected. An annotation analysis and available biological data supported the hypothesis that some of the genes within these regions may play a role in quantitative pathogenicity. These results suggested a polygenic basis of quantitative pathogenicity in this fungal pathogen and complex molecular plant-pathogen interactions in quantitative disease development involving several genes on both sides.
植物病原体能够适应数量抗性，从而削弱其有效性。本研究的目的是通过研究在不同品种上的趋同适应，揭示香蕉主要毁灭性病原菌——该真菌种群中适应这种抗性的基因组基础。基于基因组扫描方法，将在具有数量抗性的新型香蕉杂交品种上呈现局部适应模式的种群样本，与古巴和多米尼加共和国传统的、更易感品种的样本进行比较。根据配对种群设计，对每个国家三个地点采集的分离株池（池测序）进行全基因组测序。不同组合分析的结果有力地支持了在各国国内不同地点的研究品种之间存在趋同适应，但各国之间不存在趋同适应。每个国家检测到五到六个参与这种适应的基因组区域。注释分析和现有生物学数据支持这样的假设，即检测到的基因组区域内的一些基因可能在数量致病性中发挥作用，包括基因调控。结果表明，真菌适应植物数量抗性的遗传基础至少是寡基因的，同时突出了这种抗性存在特定的宿主 - 病原体相互作用。了解病原体适应植物数量抗性的遗传基础对于制定持久的抗性部署策略具有关键作用。在此背景下，针对一种主要的植物病原体（导致香蕉黑叶条斑病的真菌）开发了一种种群基因组方法，将来自新型抗性香蕉杂交品种的样本与两个国家更易感的传统品种的样本进行比较。总共检测到11个有充分证据表明受到数量抗性选择的基因组区域。注释分析和现有生物学数据支持这样的假设，即这些区域内的一些基因可能在数量致病性中发挥作用。这些结果表明这种真菌病原体的数量致病性具有多基因基础，并且在数量病害发展过程中涉及双方多个基因的复杂分子植物 - 病原体相互作用。
