Research ArticlePOPULATION GENETICS

CRISPR/Cas9 gene drives in genetically variable and nonrandomly mating wild populations

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Science Advances  19 May 2017:
Vol. 3, no. 5, e1601910
DOI: 10.1126/sciadv.1601910

Figures

  • Fig. 1 Schematic of the propagation of a CRISPR/Cas9-based gene drive.

    (i) A plasmid expressing Cas9 and gRNA flanked by DNA homologous to the sequences flanking the gRNA target site is expressed in the organism. Cas9 cleaves DNA at the gRNA-specified target site. (ii) The drive cassette, containing Cas9 and gRNA, is integrated into the target locus via HDR, resulting in (iii) heterozygosity for the drive allele. (iv) The remaining wild-type allele is targeted by Cas9 and gRNA expressed from the drive allele, leading to (v) HDR-mediated copying of the drive allele into the wild-type locus and (vi) homozygosity for the drive allele.

  • Fig. 2 Genetic variation in Cas9 target sequences.

    Each component of the Cas9 target sequence is highlighted according to its potential to affect Cas9 cleavage [red, PAM (complete abrogation of cleavage); yellow, seed (reduced cleavage efficiency); green, outer protospacer (little to no effect on cleavage efficiency)]. The frequency of each SNP in the analyzed population is given below each gRNA sequence. Note that all regions harbor SNP variants in some population and an obstructing variant in the critical PAM region of Ace2 occurs at a frequency of 0.375 in the Peru population.

  • Fig. 3 ITDs limit drive propagation.

    (A) In the absence of an ITD and inbreeding, a strongly deleterious drive rapidly spreads to fixation. (B) Addition of an ITD at a frequency of 0.01 severely impairs propagation of a strongly deleterious drive and leads to its removal from the population, as well as a substantial increase in ITD frequency. (C) In the presence of an ITD at a frequency of 0.01, a moderately deleterious drive remains at high frequency for several tens of generations but is eventually eliminated from the population. The populations considered in this figure are considered to be randomly mating (F = 0).

  • Fig. 4 Inbreeding impairs drive spread.

    (A) Inbreeding at a rate of 0.15 in the absence of an ITD leads to rapid cessation of the spread of a strongly deleterious drive and its removal from the population. (B) Addition of an ITD at a frequency of 0.01 to the population inbreeding at a rate of 0.15 again leads to rapid loss of the strongly deleterious drive from the population, as well as a moderate increase in ITD frequency. (C) In the presence of an ITD at a frequency of 0.01, a moderately deleterious drive remains high for several generations but is effectively eliminated (frequency, <0.01) after 39 generations.

  • Fig. 5 Analysis of systematic variation of model parameters.

    (A) Plot showing the effect of varying the drive fitness penalty s from 0.1 to 0.9 on the generation at which the drive is eliminated (considered to be the generation at which drive frequency is first <0.01) and ITD frequency. (B) Plot showing the effect of varying the inbreeding coefficient F from 0 to 1 on the generation at which the drive is eliminated and ITD frequency. (C) Plot showing the effect of varying the drive efficiency c from 0.9 to 1 on the generation at which the drive is eliminated and ITD frequency. For the plots shown in (B) and (C), we assumed s = 0.8.