Advanced: Handling Multiple Lethal Recessives
Moves are underway to discover hopefully many low-frequency recessive lethals by looking for loci with ‘missing homozygotes’ in the population(s) of interest.
You can enter these loci as markers using the genotype or the genotype probability format. Of course the latter is useful where not all candidates are genotyped, and e.g. GeneProb is used to extend the information on hand.
However, with possibly hundreds of these markers in your main data file, we need a special way to manipulate them.
LethalA and LethalG Fields
Section titled “LethalA and LethalG Fields”In your main data file, create two extra Trait fields/columns. These are basically LethalA (for Lethal Alleles) and LethalG (for Lethal Genotypes). However we hitch-hike on these field names to also point to which markers are to be included in this way. For example:
- LethalA1 and LethalG100 means that marker numbers 1 to 100 are to be included.
- LethalA23 and LethalG49 means that marker numbers 23 to 49 are to be included.
Marker numbers are deduced from the alphabetical order of your Marker Names as supplied in the datafile.
The individual values in these columns is of no consequence. Please set them all to zero. MateSel will populate them on the fly according to the selections and mate allocations of the current solution, and you will see histograms for these “traits” that show:
| Field | Description |
|---|---|
| LethalA | Use this for longer-term objectives, by selecting against recessive lethal alleles in the population. LethalA for each progeny is the probability of mortality in their offspring (i.e. in grand-progeny of the current candidates), given that the progeny will be randomly mated to the population at large, with recessive allele frequencies equal to those observed (or implied from genotype probabilities) among the current candidates. |
| LethalG | Use this for short-term objectives by selecting against the incidence of lethally affected progeny from the current matings. LethalG for each progeny is the probability of mortality due to lethal homozygosity at one or more of the loci concerned. Given that the parents have zero probability of being homozygous lethal at any locus, the minimum predicted probability of survival is (1 - 0.5 * 0.5) = 0.75 for each locus, where both parents are heterozygotes. Across n loci, the minimum probability of survival is thus 0.75n, giving a maximum value for LethalG of 1-0.75n. So LethalG ranges 0 to 1-0.75n for n loci considered. |
You can manipulate LethalA and LethalG using their histograms under Trait Management. As frequencies are generally very low, the scales shown will be well below the maximum possible. Rescaling will occur as you find success in reducing allele and genotypes frequencies to very low levels. But look out for the impact on other issues!
You can view the response for these “traits” by navigating to Matings tab > Dashboards tab > Trait Responses Dashboard, as for all other traits.
Some rules
Section titled “Some rules”- You must include either both these fields, or neither of them.
- Column order is free except for the first 3 ID columns.
- Whatever your column order, these field names must be LethalA
and LethalG . These two column names are case sensitive.