Repeated origins, widespread gene flow, and allelic interactions of target-site herbicide resistance mutations

eLife

Patrick J Tranel¹  John R Stinchcombe²  Stephen I Wright²  Julia M Kreiner²  George Sandler²  Detlef Weigel³  Aaron J Stern⁴ 

[1] Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, United States;Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada;Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany;Graduate Group in Computational Biology, University of California, Berkeley, Berkeley, United States;

关键词: herbicide resistance;    rapid adaptation;    gene flow;    de novo origins;    haplotype competition;    Amaranthus tuberculatus;    Agricultural weed;   

DOI  :  10.7554/eLife.70242

来源: eLife Sciences Publications, Ltd

【 摘 要 】

Causal mutations and their frequency in agricultural fields are well-characterized for herbicide resistance. However, we still lack understanding of their evolutionary history: the extent of parallelism in the origins of target-site resistance (TSR), how long these mutations persist, how quickly they spread, and allelic interactions that mediate their selective advantage. We addressed these questions with genomic data from 19 agricultural populations of common waterhemp (Amaranthus tuberculatus), which we show to have undergone a massive expansion over the past century, with a contemporary effective population size estimate of 8 x 107. We found variation at seven characterized TSR loci, two of which had multiple amino acid substitutions, and three of which were common. These three common resistance variants show extreme parallelism in their mutational origins, with gene flow having shaped their distribution across the landscape. Allele age estimates supported a strong role of adaptation from de novo mutations, with a median age of 30 suggesting that most resistance alleles arose soon after the onset of herbicide use. However, resistant lineages varied in both their age and evidence for selection over two different timescales, implying considerable heterogeneity in the forces that govern their persistence. Two such forces are intra- and inter-locus allelic interactions; we report a signal of extended haplotype competition between two common TSR alleles, and extreme linkage with genome-wide alleles with known functions in resistance adaptation. Together, this work reveals a remarkable example of spatial parallel evolution in a metapopulation, with important implications for the management of herbicide resistance.

【 授权许可】

CC BY