cubeClvR2 function

Inheritance Cube: 2-Locus ClvR (Cleave and Rescue)

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
)

Arguments

• cF: Female cutting rate, one ClvR allele
• crF: Female functional resistance rate, one ClvR allele
• ccF: Female cutting rate, two ClvR alleles
• ccrF: Female functional resistance rate, two ClvR alleles
• cM: Male cutting rate, one ClvR allele
• crM: Male functional resistance rate, one ClvR allele
• ccM: Male cutting rate, two ClvR alleles
• ccrM: Male functional resistance rate, two ClvR alleles
• dW: Female deposition cutting rate
• drW: Female deposition functional resistance rate
• ddW: Female deposition (HH) cutting rate
• ddrW: Female deposition (HH) functional resistance rate
• hSuf: Haplosufficiency level, default is completely sufficient
• crossF: Crossover rate in females, 0 is completely linked, 0.5 is unlinked, 1.0 is complete divergence
• crossM: Crossover rate in males, 0 is completely linked, 0.5 is unlinked, 1.0 is complete divergence
• eta: Genotype-specific mating fitness
• phi: Genotype-specific sex ratio at emergence
• omega: Genotype-specific multiplicative modifier of adult mortality
• xiF: Genotype-specific female pupatory success
• xiM: Genotype-specific male pupatory success
• s: Genotype-specific fractional reduction(increase) in fertility

Returns

Named list containing the inheritance cube, transition matrix, genotypes, wild-type allele, and all genotype-specific parameters.

Details

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.