Main Data File Setup

Your data file contains the candidates for selection and as much of their pedigree as you choose to handle. You need to include individuals that are not candidates but that are ancestors of candidates if you want to fully account for coancestry when managing genetic diversity. However, even with no pedigree, coancestry is accommodated as much as is possible - equivalent to using classical concepts of effective population size. If you intend to use a Genomic Relationship Matrix (GRM) instead of (or in addition to) pedigree information, please see the section on GRM.

Note

Are you launching MateSel via a Breed Society portal? If so, you can skip this page since all the required data are generated for you.

File Formats Accepted

MateSel only supports the CSV (Comma-Separated Values) format for the fields mentioned below. If you are looking to integrate MateSel with your organisations database, we also support the JSON format, please contact us for more information.

Data File Templates

Below we have 2 Data File Templates for you to review. All fields are further explained below.

Template	Description
MateSelClassicDemo.csv	Our classic MateSel dataset with 40 male candidates, 108 female candidates, 615 pedigree individuals, 6 traits, and 4 genetic markers.
MateSelBisexDemo.csv	Our bisexual plants MateSel dataset allows candidate max/min/must usage constraints to be specified per sex e.g. Max use of 50 as a male and 25 as a female.

Standard Fields

Field	Required	DataType	Description
Id	True	Text (20)	Unique identifier for the individual. Text fields are case sensitive, such that “bert” and “Bert” are recognised as different individuals. Must not contain spaces.
Sire	True	Text (20)	Father’s Id. Must not contain spaces.
Dam	True	Text (20)	Mother’s Id. Must not contain spaces.
Sex	True	Text (1)	Either “M” or male or “F” for female. This field is not required for non-candidates i.e. individual included for pedigree purposes only. This field should not be included for BiSexual datasets.
MaxUse	True	Integer	The maximum value for number of matings permitted for each candidate. What is a mating? It is a planned pregnancy. See here for more information. For example, MaxUse = 1 mating for natural mating females, MaxUse =30 matings for natural mating bulls, and possibly MaxUse =1,000 matings for AI bulls, or the number of semen doses left for a deceased bull. Enter 0 for non-candidates i.e. individuals included for pedigree purposes only. It is not recommended that you set MaxUse values low with the intention of conserving genetic diversity. Let Optimal Contributions Selection (OCS) manage that through your chosen Balance Strategy. Better to set MaxUse according to reasonable biological and/or logistical limits.
MinUse	False	Integer	Minimum number of matings if selected. E.g. If this Individual is selected, MateSel will use the Individual at least this many times in the mating list. Zero means ‘No Minimum’.
MustUse	False	Integer	The absolute minimum number of matings. This is generally zero, but may be set higher, for example where a breeder has a given number of doses of semen available for a favoured bull, and insists that these should all be used.
MatingGroup	False	Text (20)	Needed if dividing individuals into mating groups. This field must contain the Id of the group that represents group membership. Entries for non-candidates can be set to blank/empty – they are not used. Groups are different for each sex, even if they have the same label (e.g. “Group6” for males is treated differently from “Group6” for females), so you can use the same labels across sexes. Must not contain spaces.
Index	True	Numeric	This should contain the selection index value for each individual, which will typically be a multi-trait BLUP index value or other similar selection index value that is a measure of genetic merit across traits. It can be simply the EBV for the single trait of interest. Do not use scientific notation for numerical values.

Tip

The Id, Sire, and Dam fields must be the first three fields, in the order shown above. However, you can name them as you like e.g. TagId, Ram, Ewe to better match your industry terminology. All other fields can be in any order but must be named as presented above.

Warning

It does not make sense to specify non-zero values for both MinUse and MustUse for any one individual. E.g. If MustUse is 1 and MinUse is 10, then this effectively makes MustUse=10, as 1 mating is illegal under Minuse=10.

Warning

Take care if setting MinUse equal to MaxUse. For example, if for males you set MinUse=MaxUse=10 and you ask for 55 matings, there is no valid solution and an error will be reported. Moreover, by setting equal contributions, you will be losing much of the potential benefit of Optimal Contributions Selection (OCS).

Genetic Marker Fields

Genetic Marker Fields will begin with a “g_” in their name. Genetic Marker Probability Fields will begin with a “gp_” in their name. Please see the Genetic Markers Overview to learn more.

Trait Fields

Any unrecognised field in the CSV file is treated as a trait (e.g. EBV). This means that fields such as Age, DateOfBirth, SemenDoseCost, and YearOfBirth are treated as traits which is useful as information and for setting targets. For example, you can make constraints on YearOfBirth and DateOfBirth of selected individuals by using the Trait Management tool to manage trait distributions.

Validation of Trait Fields:

• The values for trait information must be numeric only. Alpha-numeric values cannot be plotted on trait histograms so are not supported.
• Do not use scientific notation for numerical values

Missing information

• Unknown parents should be denoted as a blank value in the CSV e.g ”,,,”
• Missing numerical trait and index information should be given as a decimal point (.), as the value 0 will be taken as an observed value.

Supported Fields for BiSexual datasets

We support slightly different fields when using BiSexual datasets. Please visit the Accommodating Bisexuality in Plants page for more information.

Supported Fields for handling multiple lethal recessives

MateSel supports two additional fields “LethalA” and “LethalG” for handling multiple lethal recessives. For more information, please see Handling Multiple Lethal Recessives

Video Guide

If you need additional information around preparing your main data file for MateSel, please see the video guide below. Please note this video showcases the MateSel Legacy version, however, the fundamentals are the same in the newer version of MateSel.