Maternal deposition

Maternal deposition models the transfer of Cas9 protein (not DNA) from mother to offspring. In real gene drive systems, a mother carrying a Cas9 allele deposits Cas9 protein into her eggs. After fertilization but before the embryo's own transcription activates, this maternally deposited Cas9 can cut target alleles on the paternal chromosome via non-homologous end joining (NHEJ). Because this occurs before homology-directed repair (HDR) is active, the cut site is repaired imperfectly, producing resistance alleles rather than drive copies. This mechanism can generate resistance alleles even in offspring that did not inherit the drive allele.

Maternal deposition requires gene drives to be configured — it extends the behavior of an existing drive by adding a pre-embryonic cutting step. It is configured in the Maternal_Deposition array within Vector_Species_Params, on the same level and separately from the Drivers array. See vector-model-gene-drives for information on configuring gene drives and vector-model-genetics for the broader vector genetics system.

How maternal deposition works

During the fertilization pipeline in EMOD, maternal deposition is applied after gamete creation and germline mutations, but before gametes are combined into offspring genomes. For more details on the EMOD fertilization pipeline, see Mendelian inheritance. The sequence is:

Gene drive — applied during gamete merging (standard drive mechanics).
Gamete creation — eggs and sperm are generated from parent genomes.
Germline mutations — alleles may mutate in the gametes.
Maternal deposition — if the mother carries a Cas9-producing allele, the cutting likelihoods are applied to both the maternal and paternal gametes.
Genome combination — gametes are paired to form offspring genomes.

For each Maternal_Deposition entry, the system checks how many copies of the Cas9_gRNA_From allele the mother carries at the specified locus:

0 copies — no effect; maternal deposition is skipped for this entry.
1 copy (heterozygous) — the cutting likelihoods are applied once to all gametes carrying the target allele (Allele_To_Cut).
2 copies (homozygous) — the cutting likelihoods are applied twice in sequence. This produces a compound probability: if the per-allele cutting rate is p, the effective cutting rate for a homozygous mother is \(1 - (1 - p)^2\). For example, a 20% per-allele cutting rate becomes a 36% effective rate with two copies.

The cutting converts the wild-type allele into an allele that is resistant to the gene drive — Cut_To_Allele entry that matches Allele_To_Cut in Likelihood_Per_Cas9_gRNA_From represents the probability of no effect (the allele survives uncut).

Configuration example

{
    "Maternal_Deposition": [
        {
            "Cas9_gRNA_From": "Cd",
            "Allele_To_Cut": "Aw",
            "Likelihood_Per_Cas9_gRNA_From": [
                {"Cut_To_Allele": "Aw", "Likelihood": 0.8},
                {"Cut_To_Allele": "Am", "Likelihood": 0.15},
                {"Cut_To_Allele": "Ax", "Likelihood": 0.05}
            ]
        }
    ]
}

In this example, we have a maternal deposition derived from an INTEGRAL_AUTONOMOUS drive. When a mother carries the drive allele Cd, the wild-type allele Aw in the gametes has a 15% chance per maternal Cas9 copy of being cut into the drive resistance allele Am, a 5% chance of being cut into the drive resistance allele Ax, and an 80% chance of remaining Aw (no effect).

If the mother is homozygous for the Cd allele (Cd/Cd), the maternal deposition probabilities are applied twice to each Aw allele. After the first application, Aw splits into Aw at 0.8, Am at 0.15, and Ax at 0.05. The second application acts only on the remaining Aw fraction, so:

Aw = 0.8 × 0.8 = 0.64
Am = 0.8 × 0.15 = 0.12
Ax = 0.8 × 0.05 = 0.04

The final proportions for the A-locus alleles after maternal deposition are:

Aw = 0.64
Am = 0.15 + 0.12 = 0.27
Ax = 0.05 + 0.04 = 0.09

Multiple Maternal_Deposition entries can target different alleles from the same or different Cas9 sources. Each entry is evaluated independently.

Maternal deposition parameters

Note

Parameters are case-sensitive. For Boolean parameters, set to 1 for true or 0 for false. Minimum, maximum, or default values of "NA" indicate that those values are not applicable for that parameter.

EMOD does not use true defaults; that is, if the dependency relationships indicate that a parameter is required, you must supply a value for it. However, many of the tools used to work with EMOD will use the default values provided below.

JSON format does not permit comments, but you can add "dummy" parameters to add contextual information to your files. Any keys that are not EMOD parameter names will be ignored by the model.

Parameter	Type	Min	Max	Default	Description
Cas9_gRNA_From	string	NA	NA	UNINITIALIZED STRING	The allele in the mother that produces Cas9 protein. The mother's genome is checked for the presence of this allele to determine if additional gene drive resistance alleles will be formed via maternal deposition. This allele must be one of the Driving_Allele alleles defined in the Drivers array.
Allele_To_Cut	string	NA	NA	UNINITIALIZED STRING	The target allele from which gene drive resistance alleles might be formed due to maternal deposition. This must be one of the Allele_To_Replace alleles defined in the Drivers array for each of the Driving_Allele alleles defined in Cas9_gRNA_From.
Likelihood_Per_Cas9_gRNA_From	array of json objects	NA	NA	[]	An array of allele-to-likelihood objects applied for each copy of Cas9_gRNA_From present in the mother. Each object specifies a Cut_To_Allele and its Likelihood. If the mother is homozygous for the Cas9_gRNA_From allele, the likelihoods are applied twice in sequence. The sum of all Likelihood values in the array must equal 1.0. See example.
Cut_To_Allele	string	NA	NA	UNINITIALIZED STRING	The allele that will be formed at the cut site due to maternal deposition. This cannot be a driving allele and must be an allele of the same gene as Allele_To_Cut. If Cut_To_Allele equals Allele_To_Cut, this defines the likelihood that maternal deposition has no effect (the allele survives uncut).
Likelihood	float	0	1	0	The probability (0.0--1.0) that maternal deposition will produce the allele defined in Cut_To_Allele from the Allele_To_Cut allele. When Cut_To_Allele equals Allele_To_Cut, this represents the probability of no effect.

The following example shows a complete configuration including the gene, driver, and maternal deposition for an An. gambiae population with a classic gene drive and maternal Cas9 deposition.

{
    "Vector_Species_Params": [
        {
            "Name": "gambiae",
            "Genes": [
                {
                    "Is_Gender_Gene": 1,
                    "Alleles": [
                        {"Name": "X", "Initial_Allele_Frequency": 0.5, "Is_Y_Chromosome": 0},
                        {"Name": "Y", "Initial_Allele_Frequency": 0.5, "Is_Y_Chromosome": 1}
                    ]
                },
                {
                    "Is_Gender_Gene": 0,
                    "Alleles": [
                        {"Name": "Aw", "Initial_Allele_Frequency": 0.95, "Is_Y_Chromosome": 0},
                        {"Name": "Ad", "Initial_Allele_Frequency": 0.05, "Is_Y_Chromosome": 0},
                        {"Name": "Am", "Initial_Allele_Frequency": 0.0,  "Is_Y_Chromosome": 0}
                    ]
                }
            ],
            "Drivers": [
                {
                    "Driving_Allele": "Ad",
                    "Driver_Type": "CLASSIC",
                    "Alleles_Driven": [
                        {
                            "Allele_To_Copy": "Ad",
                            "Allele_To_Replace": "Aw",
                            "Copy_To_Likelihood": [
                                {"Copy_To_Allele": "Ad", "Likelihood": 0.95},
                                {"Copy_To_Allele": "Aw", "Likelihood": 0.03},
                                {"Copy_To_Allele": "Am", "Likelihood": 0.02}
                            ]
                        }
                    ]
                }
            ],
            "Maternal_Deposition": [
                {
                    "Cas9_gRNA_From": "Ad",
                    "Allele_To_Cut": "Aw",
                    "Likelihood_Per_Cas9_gRNA_From": [
                        {"Cut_To_Allele": "Aw", "Likelihood": 0.8},
                        {"Cut_To_Allele": "Am", "Likelihood": 0.2}
                    ]
                }
            ]
        }
    ]
}

Validation rules

Gene drives (Drivers) must be defined — maternal deposition cannot exist without a drive.
Cas9_gRNA_From must match a Driving_Allele in the Drivers array.
Allele_To_Cut must be an Allele_To_Replace for the corresponding driver.
All Cut_To_Allele entries must be alleles at the same locus as Allele_To_Cut.
Cut_To_Allele cannot be an Allele_To_Copy for the driver (cannot produce drive copies via maternal deposition).
The Allele_To_Cut allele must appear as one of the Cut_To_Allele entries (representing the probability of no cutting).
The sum of all Likelihood values must equal 1.0.
No two entries may have the same Cas9_gRNA_From and Allele_To_Cut combination.
For DAISY_CHAIN drives, Allele_To_Cut cannot be at the same locus as the driving allele (the driver cannot cut its own locus in daisy chain mode).