Choose a method for RIL simulation

Choose Fast Simulation Method to simulate RIL progenies that uses genetic properties from RIL population to bypass the need for many cycles of selfing to reach homozygosity. This method can be used whether a linkage map is available.

When.a linkage map is available, the recombination fractions are based on populations that have gone through just one cycle of meiosis. These fractions are then converted into recombination fractions that would be expected in a RIL population after many cycles of meiosis. Next, a RIL population, assuming two fictitious complete homozygous parental lines, are simulated using the converted recombination fractions. Then, for each simulated RIL progeny, all loci genotypes resulting from one of the two fictitious homozygous parental lines are replaced with the loci genotypes from one of the two real parental lines in the input data set. Likewise, all loci genotypes from the other fictitious homozygous parental line are replaced by the other real parental line. It should be noted that when either or both parental lines are not completely homozygous, there is possibility of RIL progeny are heterozygous when using this method. To circumvent this issue, for each locus for which the RIL progeny is heterozygous, either one or the other of the two alleles is randomly sampled with probability half each, then doubled to become diploid, and finally, the heterozygous genotype is replaced in the RIL progeny. Note: This method does not consist of selfing progenies for many generations until homozygosity is reached. Instead, the events of recombination, which can be expected after many generations of selfing needed to produce RIL progenies, are accounted for when converting the recombination fractions into the expected recombination fractions after many cycles of meiosis.

When linkage map is not available, each locus is assumed to segregate independently of each other, and RIL progeny are simulated by first crossing the real parental lines from the input data set and then, if the resulting genotype is homozygous, assigning it to the RIL progeny. When the resulting genotype is heterozygous, either one or the other of the two alleles is randomly sampled with probability half each, then doubled to become diploid, and finally, the heterozygous genotype is replaced in the RIL progeny.

Choose Single Seed Descent Method to simulate RIL progenies for each cross via the single seed descent (SSD) method, which consists of selfing one offspring per cross per generation through many selfing generations.