Accommodating Bisexuality in Plants

If your main data file has individuals that are candidates to be used as both male and female parents (including candidates for selfing) then this page describes how MateSel supports this scenario.

Enable BiSexual Data Sets

To use BiSexual data sets:

1. Login to MateSel
2. Navigate to “Settings”
3. Scroll down to the “Plant Breeding” section
4. Check the Max/Min/Must Use parameters can be defined per gender option
5. Click the “Save” button at the bottom of the page

You can now load data sets that contain the supported bisexual fields mentioned below.

Supported Fields for BiSexual datasets

BiSexual datasets follow the same standard, marker, and trait fields, however, the MaxUse, MinUse, MustUse, and MatingGroup fields must be removed and replaced with the following per-gender equivalent:

Field	Required	DataType	Description
MaxUseMale	True	Integer	See MaxUse description in Standard Fields
MaxUseFemale	True	Integer	See MaxUse description in Standard Fields
MinUseMale	True	Integer	The minimum number of matings. Used in conjuntion with MustUseMale to determine if MateSel “Must Use” this individual in the mating list. Zero means ‘No Minimum’.
MinUseFemale	True	Integer	As above
MustUseMale	True	Boolean	If True, the MinUseMale integer value will be taken as “Must Use” (also know as AbsMinUse)
MustUseFemale	True	Boolean	As above
MatingGroupMale	False	Text (20)	See MatingGroup description in Standard Fields
MatingGroupFemale	False	Text (20)	See MatingGroup description in Standard Fields

Reading the usage parameters above for each gender (MaxUse, MinUse and MustUse) is essentially the same as for no bisexuality. If using grouping, usage parameters can be read from the Group definition except when the “Different Per Individual” option is used, in which case the values for individuals of that sex (or sex/Group) in the datafile will be used. In this way it is possible that, for example, male usage is taken from the Group definition, and female usage is taken from the values for individuals in the datafile.

Supported Crossing Policies

MateSel supports the following crossing policies that can be set on the “Mating Rules” tab of the pre-run inputs:

Policy	Description
For each crossing of a female plant, you can use pollen from a different male plant	This operates in the same documented manner as IVF in animal species
For all crossings of a female plant, you must use pollen from a single male plant	This operates in the same documented manner as MOET in animal species

Avoid matings that are duplicate, reciprocal, or selfings

Where at least some members of each sex have MaxUse > 1 there is the possibility of duplicate matings. Under bisexuality, there is also the possibility of reciprocal matings and/or self matings. To avoid these, please select the scenarios you want to avoid on the “Mating Rules” tab of the pre-run inputs:

Warning

When “Avoid Duplicate Crossings” is checked, you must use the For each crossing of a female plant, you can use pollen from a different male plant crossing policy.

Tip

MateSel supports an alternative (more direct) way to avoid self matings using the GMS facility.

When avoiding certain crossings, you need to specify an emphasis or weighting to tell MateSel how important this contraint is compared to other targets (e.g. marker/trait/inbreeding targets). If you still see duplicate, reciprocal or self matings in the converged result, increase this weighting until you get the outcome you desire. The downside of using a stronger weighting is possibly slower convergence, but this may be a minor issue for relatively large problems where such matings will probably occur at lower frequency. The compromises made in progeny index and parental coancestry can be large. You must ask yourself if these compromises are worth it.

Note that the feature to avoid duplicate matings also operates on non-bisexual (Sire-Dam) matings, typically in IVF programs where duplications are possible.