DataSheet1_Genomic characterisation and dissection of the onset of resistance to acetyl CoA carboxylase-inhibiting herbicides in a large collection of Digitaria insularis from Brazil.PDF

An in-depth genotypic characterisation of a diverse collection of Digitaria insularis was undertaken to explore the neutral genetic variation across the natural expansion range of this weed species in Brazil. With the exception of Minas Gerais, populations from all other states showed high estimates of expected heterozygosity (HE > 0.60) and genetic diversity. There was a lack of population structure based on geographic origin and a low population differentiation between populations across the landscape as evidenced by average Fst value of 0.02. On combining haloxyfop [acetyl CoA carboxylase (ACCase)-inhibiting herbicide] efficacy data with neutral genetic variation, we found evidence of presence of two scenarios of resistance evolution in this weed species. Whilst populations originating from north-eastern region demonstrated an active role of gene flow, populations from the mid-western region displayed multiple, independent resistance evolution as the major evolutionary mechanism. A target-site mutation (Trp2027Cys) in the ACCase gene, observed in less than 1% of resistant populations, could not explain the reduced sensitivity of 15% of the populations to haloxyfop. The genetic architecture of resistance to ACCase-inhibiting herbicides was dissected using a genome wide association study (GWAS) approach. GWAS revealed association of three SNPs with reduced sensitivity to haloxyfop and clethodim. In silico analysis of these SNPs revealed important non-target site genes belonging to families involved in herbicide detoxification, including UDPGT91C1 and GT2, and genes involved in vacuolar sequestration-based degradation pathway. Exploration of five genomic prediction models revealed that the highest prediction power (≥0.80) was achieved with the models Bayes A and RKHS, incorporating SNPs with additive effects and epistatic interactions, respectively.

本研究对采集自巴西的一套多样化海岛马唐（Digitaria insularis）种群集合开展了深入的基因型鉴定，以探究该杂草物种自然扩散范围内的中性遗传变异。除米纳斯吉拉斯州（Minas Gerais）的种群外，其余各州的种群均表现出较高的期望杂合度（expected heterozygosity, HE > 0.60）与遗传多样性水平。基于地理起源的种群结构并不显著，且种群间的遗传分化程度极低，全区域观测的平均Fst值仅为0.02。将高效氟吡甲禾灵（haloxyfop，乙酰辅酶A羧化酶（ACCase）抑制型除草剂）的药效数据与中性遗传变异相结合后，本研究发现该杂草存在两种抗性演化模式的相关证据：其中东北部种群的抗性演化主要依赖基因流的活跃介导，而中西部种群则以多起独立的抗性演化事件作为主要的演化机制。ACCase基因中发现的靶标位点突变Trp2027Cys仅在不足1%的抗性种群中被检测到，无法解释15%的种群对高效氟吡甲禾灵敏感性下降的现象。本研究通过全基因组关联分析（Genome Wide Association Study, GWAS）解析了ACCase抑制型除草剂的抗性遗传结构，结果显示共有3个单核苷酸多态性位点（Single Nucleotide Polymorphism, SNPs）与高效氟吡甲禾灵和烯草酮（clethodim）的敏感性下降存在显著关联。对上述SNP位点的计算机模拟分析（in silico analysis）显示，其中存在多个重要的非靶标抗性基因，分别隶属于除草剂解毒相关基因家族（如UDPGT91C1与GT2）以及参与液泡隔离降解通路的基因家族。对5种基因组预测模型的测试结果表明，贝叶斯A（Bayes A）与RKHS模型的预测能力最强（预测精度≥0.80），二者分别纳入了具有加性效应和上位性互作效应的SNP位点。