- Description: Parameters that decide how animals are mated and the algorithm utilized to optimize matings.
- Options:
- Mating Option:
- random: Males and female parents are randomly mated.
- random5: Relationships ≥ 0.5 are not allowed to mate otherwise same as random mating option.
- random25: Relationships ≥ 0.25 are not allowed to mate otherwise same as random5 mating option.
- random125: Relationships ≥ 0.125 are not allowed to mate otherwise same as random25 mating option.
- minPedigree: Minimize parental co-ancestries based on a pedigree relationship matrix.
- minGenomic: Minimize parental co-ancestries based on a genomic relationship matrix (Van Raden 2008).
- minROH: Minimize parental co-ancestries based on a ROH relationship matrix (Howard et al. 2016).
- pos_assort: Positive assortative mating based on the value animals are being selected on.
- neg_assort: Negative assortative mating based on the value animals are being selected on.
- index: Mating is done based on an index of multiple values and is parameterized by 'MATING_INDEX' option.
- Optimization Method:
- simu_anneal: Adaptive simulated annealing algorithm to assign mates (Ingber 1993).
- linear_prog: Uses the Hungarian algorithm to find an exact solution to the best possible mating design.
- sslr: Sequential selection of least related mates algorithm to assign mates (Pryce et al. 2011).
- gp: Genetic programming to find assign mating pairs (Chu & Beasley, 1997).
- Usage: '
MATING: minPedigree sslr'.
- Type: Mandatory. Only the first option is required for random, pos_assort, and neg_assort.
- Note:
For avoidance mating's (i.e. random5, random25, random 125) any coancestry below the threshold is zeroed out and mating are optimized. If utilizing the index mating parameter, the only options are can be utilized are 'gp' or 'sslr'. The 'gp' option can only be used for index mating.