Based on the Cleave-and-Rescue system of Oberhofer,
this is a 3-locus Cas9-based toxin-antidote system. The first locus carries the
Cas9, the second locus carries the gRNAs, and a recoded copy of an essential gene.
The third locus is the targeted essential gene. This gene can be completely
haplosufficient (hSuf = 1) or completely haploinsufficient (hSuf = 0).
It is assumed that having 2 copies of the gene (be it wild-type at the second
locus or recoded at the first) confers complete viability. Additionally, loci
1 and 2 can be linked, given crM and crF, imitating the original
2-locus ClvR system.
For this construct, the first locus will have 2 alleles, the second will have 2
alleles, and the third will have 3 alleles:
Locus 1
W: Wild-type
C: Cas9
Locus 2
W: Wild-type
G: gRNAs and recoded essential gene
Locus 3
W: Wild-type
R: Functional resistant
B: Non-functional resistant
cubeClvR2(
cF = 1,
crF = 0,
ccF = cF,
ccrF = crF,
cM = 1,
crM = 0,
ccM = cM,
ccrM = crM,
dW = 0,
drW = 0,
ddW = dW,
ddrW = drW,
hSuf = 1,
crossF = 0.5,
crossM = 0.5,
eta = NULL,
phi = NULL,
omega = NULL,
xiF = NULL,
xiM = NULL,
s = NULL
)Female cutting rate, one ClvR allele
Female functional resistance rate, one ClvR allele
Female cutting rate, two ClvR alleles
Female functional resistance rate, two ClvR alleles
Male cutting rate, one ClvR allele
Male functional resistance rate, one ClvR allele
Male cutting rate, two ClvR alleles
Male functional resistance rate, two ClvR alleles
Female deposition cutting rate
Female deposition functional resistance rate
Female deposition (HH) cutting rate
Female deposition (HH) functional resistance rate
Haplosufficiency level, default is completely sufficient
Crossover rate in females, 0 is completely linked, 0.5 is unlinked, 1.0 is complete divergence
Crossover rate in males, 0 is completely linked, 0.5 is unlinked, 1.0 is complete divergence
Genotype-specific mating fitness
Genotype-specific sex ratio at emergence
Genotype-specific multiplicative modifier of adult mortality
Genotype-specific female pupatory success
Genotype-specific male pupatory success
Genotype-specific fractional reduction(increase) in fertility
Named list containing the inheritance cube, transition matrix, genotypes, wild-type allele, and all genotype-specific parameters.
Female deposition is implemented incorrectly. Right now, it is performed on male alleles prior to zygote formation - it should happen post-zygote formation. Since this construct doesn't have HDR, this should be fine. Additionally, it is assumed that deposition requries loaded Cas9-RNP complexes from the mother, having Cas9 and no maternal gRNA, even in the presence of paternal gRNA, will not result in maternal deposition mediated cleavage.
Copy-number dependent rates are based on Cas9, not gRNA. The assumption is that RNA is easier to produce, and therefore won't limit cleavage by Cas9.