Population genomics of selectively neutral genetic structure and herbicide resistance in UK populations of Alopecurus myosuroides
Population genomics of selectively neutral genetic structure and herbicide resistance in UK populations of Alopecurus myosuroides
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DOI：
10.1002/ps.6174
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发表时间：
2020-12-11
影响因子：
4.1
通讯作者：
Neve, Paul
中科院分区：
文献类型：
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作者：
Dixon, Andrea;Comont, David;Neve, Paul
背景：麦草(Alopecurus Myosuroides)是欧洲的一种主要杂草，已知对多种除草剂的作用方式具有抗性。在英国，有证据表明黑草已经经历了范围的扩大。本文利用测序基因分型和种群水平的除草剂抗性表型来探索选择性中性遗传变异和抗性的空间格局。我们还进行了初步的全基因组关联研究和基因组预测分析，以评估这些方法在研究非靶点除草剂抗性方面的潜力。结果：从不列颠群岛的47个田间采集了黑草，每个田间群体(n=369)多达8株通过限制性内切酶相关DNA(RAD)测序进行了基因分型。共检测到20426个多态基因座，用于群体遗传分析。表型分析表明，种群间对除草剂的抗性存在显著差异。种群结构较弱(F-ST=0.024-0.048)，但空间格局与正在向西和向北的范围扩展相一致。我们检测到了强烈且一致的瓦伦德效应(F-IS=0.30)。没有除草剂抗性的空间格局或与种群结构相混淆的证据。结合群体水平和基因组预测，发现前20个、200个和2000个基因座对除草剂的抗性具有较高的预测能力。结论：在全国范围内，杂草黑草田间种群间可能存在广泛的人为介导的基因流动。缺乏适应性和中性遗传变异的混淆，可以使未来更广泛的GWAS分析能够识别进化的除草剂抗性的遗传结构。(C)2020年化学工业学会
BACKGROUND: Alopecurus myosuroides (blackgrass) is a major weed in Europe with known resistance to multiple herbicide modes of action. In the UK, there is evidence that blackgrass has undergone a range expansion. In this paper, genotyping-by-sequencing and population-level herbicide resistance phenotypes are used to explore spatial patterns of selectively neutral genetic variation and resistance. We also perform a preliminary genome-wide association study (GWAS) and genomic prediction analysis to evaluate the potential of these approaches for investigating nontarget site herbicide resistance.RESULTS: Blackgrass was collected from 47 fields across the British Isles and up to eight plants per field population (n = 369) were genotyped by Restriction site-associated DNA (RAD)-sequencing. A total of 20 426 polymorphic loci were identified and used for population genetic analyses. Phenotypic assays revealed significant variation in herbicide resistance between populations. Population structure was weak (F-ST = 0.024-0.048), but spatial patterns were consistent with an ongoing westward and northward range expansion. We detected strong and consistent Wahlund effects (F-IS = 0.30). There were no spatial patterns of herbicide resistance or evidence for confounding with population structure. Using a combination of population-level GWAS and genomic prediction we found that the top 20, 200, and 2000 GWAS loci had higher predictive abilities for fenoxaprop resistance compared to all markers.CONCLUSION: There is likely extensive human-mediated gene flow between field populations of the weed blackgrass at a national scale. The lack of confounding of adaptive and neutral genetic variation can enable future, more extensive GWAS analyses to identify the genetic architecture of evolved herbicide resistance. (c) 2020 Society of Chemical Industry