Figure 3. Performance of contemporary gene drive systems for population modification with a single release.

(A) Simulations of carrier frequency trajectories (i.e. heterozygotes and homozygotes) for one-locus versions of ClvR, TARE, HomeR, and HGD for ideal parameters (see 'Materials and methods'), and HomeR for experimental parameters (HomeR-Exp, see 'Materials and methods'). Twenty-five repetitions (lighter lines) were used to calculate the average behavior of each drive (thicker, dashed lines). Populations were initialized with 50% wildtype (+/+) adult females, 25% wildtype (+/+) adult males, and 25% drive homozygous (drive/drive) males. (B) Heatmaps depicting drive efficacy for one-locus versions of ClvR, TARE, HomeR, and HGD for a range of fitness and transmission rate parameter values. Fitness costs were incorporated as a dominant, female-specific fecundity reduction. Transmission rate was varied based on cleavage rate, using HDR rates consistent with ideal parameters, when applicable (see 'Materials and methods'). Drive efficacy is defined as the average carrier frequency at generation 20 (approximately 1 year, given a generation period of 2-3 weeks) based on 100 stochastic simulations with the same initial conditions as (A). (C) Simulations of carrier frequency trajectories for two-locus (split-drive) versions of ClvR, TARE, HomeR, and HGD for ideal parameters (see 'Materials and methods'), and HomeR for experimental parameters (HomeR-Exp, see 'Materials and methods'). Twenty-five repetitions (lighter lines) were used to calculate the average behavior of each drive (thicker, dashed lines). Populations were initialized with 50% wildtype (+/+; +/+) adult females, 25% wildtype (+/+; +/+) males, and 25% drive homozygous (Cas9/Cas9; gRNA/gRNA) males. (D) Heatmaps depicting drive efficacy for two-locus versions of ClvR, TARE, HomeR, and HGD for a range of fitness and transmission rate parameter values, implemented as in panel (B), with initial conditions given in (C).

Figure 3—figure supplement 1. Mechanistic comparison of contemporary split-drives for population modification.

Each diagram depicts the cross between females trans-heterozygous for a split gene drive (GD) and wildtype (wt) males. A two-locus toxin-antidote recessive embryo (TARE) (A) and two-locus cleave and rescue (ClvR) (B) are non-homing toxin-antidote (TA)-based drives. TARE and ClvR force their inheritance by disrupting an essential gene (EsGene^WT) in oocytes as well as in embryos using maternal carryover of Cas9/guideRNA (Cas9/gRNA), and rescuing only those embryos that inherit the drive element harboring the re-coded essential target gene, which is resistant to Cas9/gRNA-mediated cleavage. As a result, mating between trans-heterozygous females and wt males generates 50% non-viable embryos. The TARE is integrated at the target gene locus (referred to as same-site teal diamond) and uses its native promoter to drive expression of the re-coded rescue, hence it is referred to as EsGene^TARE. Panel (B) depicts the two-locus version of ClvR, in which a ClvR harbors a re-coded rescue using a non-native promoter and 3’ UTR, and both ClvR and Cas9 are inserted into two distant loci separate from the target gene (referred to as distant-site red ellipse). Since both TARE and ClvR use multiple gRNAs to target an essential gene, only very rare functional resistant alleles (R1) can survive. (C) A homing-based gene drive (HGD) with no rescue targeting a non-essential gene (gene) can bias transmission in germ cells by cleaving a non-essential gene (gene) and homing, or copying itself, at the cut site (gene^GD). However, since the disruption of a non-essential gene does not cause lethality and sterility, maternal carryover of Cas9/gRNA disrupts paternal alleles in embryos, and end joining (EJ) induces both R2 and R1 (gene^R2 and gene^R1) resistant alleles that survive and eventually hinder the spread of HGD in a population. (D) The HGD with a rescue (HGD+R) targeting a non-essential gene can preserve the function of the target gene and possibly reduce fitness effects. However, given that the gene is non-essential, resistant alleles can accumulate and impede the spread of HGD+R. (E) A homing gene drive with HGD+R targeting a haploinsufficient gene (HiGene) requires two functional alleles for viability and fertility of its carriers. Therefore, any somatic cleavage that does not result in precise homing during development of the trans-heterozygous individuals can induce high fitness costs via lethal biallelic mosaicism (LBM). Maternal carryover and somatic expression of Cas9/gRNA are known to promote generation of resistant alleles and will increase fitness costs of HiGene^HGD+R. Ideally this type of drive system needs to function exclusively in the male germline and avoid problematic maternal deposition issues. (F) Home-and-rescue (HomeR) drives as a toxin-antidote homing drive designed to target a haplosufficient essential gene. HomeR harbors a re-coded essential gene, and its precise homing at the cut site rescues the wt function of the essential gene (EsGene^HomeR). Maternal carryover of HomeR’s Cas9/gRNA induces cleavage of paternal EsGene^WT alleles in embryos, which are rescued by only EsGene^HomeR but not EsGene^R2 maternal alleles resulting in the removal of non-rescued LOF resistant alleles (EsGene^R2) via LBM (see Figure 1—figure supplement 4). HomeR targets an essential gene to increase transmission and impair the survival of resistant alleles that disrupt the function of the target gene (R2). Red strikethrough defines an LOF (R2) allele.