The number of generations to complete fixation (A) and the number of resulting founder segments (B) in two-way and eight-way RILs. On average, two-way RILs take 35.92 generations to reach complete fixation and have 91.95 segments. Eight-way RILs take 38.21 generations and have 145.12 segments on average. These figures are based on 100,000 simulations and are consistent with previous simulations (Broman 2005).

This image shows all possible JH states between a potential mating-pair and illustrates our notion of a genomic segment. DD stands for different-different and occurs in three variations. DD₄ occurs when both breeders are heterozygous and do not share any founder alleles among them. DD₃ occurs when both breeders are heterozygous and share one founder allele, whereas DD₂ refers to both breeders being heterozygous for the same two founder alleles. DS stands for different-same and occurs in two variations. DS₃ occurs when the heterozygous gene shares no founder alleles with the homozygous allele of its mate. DS₂ refers to when the heterozygous gene shares one founder allele with its mate. Ss is opposite same, where the male is homozygous for one founder allele and the female is homozygous for another allele. The final state, SS (same-same), is achieved when both male and female are homozygous for the same founder allele. All JH segments are depicted with a chromosome fraction of 0.15, except for Ss, with 0.10.

A state diagram showing the transitions between all JH states in a single generation. The directed edges are labeled with the transition probability. The grayed-out nodes represent transient states; once a segment moves away from these three states, there are no returning edges. Transient states tend to go away after a few generations and are rarely seen past the point of peak diversity (as shown in Figure 5). CC lines begin inbreeding in one of the states, DD₄, DD_3,, and DD₂. The desired inbred state for all intervals is SS. DS₂ is the most likely to become SS. DD₂ is the next most likely state to become fixed. It takes at least two generations to transit from Ss to SS, as there is no direct path between these two states.

A histogram of segments colored according to their JH state as a function of generation. In early generations, most segments have contributions from three or more founders, but by generation 10 (after the point of peak diversity), segments have contributions from two or fewer founders. This plot was created by tracking the JH states between breeder pairs and finding the average contribution of each state over 100,000 simulations.

A comparison of five breeder selection alternatives for generating an eight-way RIL, showing the number of generations to reach complete fixation (A) and the total number of segments (B) found in the final inbred lines. Random sib-pair mating is used as our baseline. The alternating backcross swaps between father−daughter and mother−son matings in successive generations. The father−daughter scheme alternates between father−daughter and random sibling matings in successive generations. MAI uses our weighted state metric to choose between 16 breeding pairs after the point of peak diversity. The selected advanced intercross modifies early stages of the breeding scheme to choose sib-pairs that maximize diversity, and then at a pre-established generation (10), it reverted to choosing sib-pairs to accelerate the inbreeding process.