Linear, funnel, and multiple funnel schemes for stacking chromosomes that carry targeted recombinations in plants

Up to five chromosomes that carry targeted recombinations can be stacked via a multiple funnel scheme, provided that the probabilities of inheriting intact chromosomes from donor parents are high. Targeted recombination involves inducing or selecting for recombination events at specific points in the genome to maximize genetic gain. Practical application of targeted recombination requires efficient breeding strategies to stack multiple chromosomes that carry such recombinations. Our objectives were to determine how many chromosomes with targeted recombinations can be feasibly stacked in a breeding program, and how the feasibility of stacking is affected by the crossing design, homozygosity versus heterozygosity of the donor lines, size of the chromosomal segment showing recombination, and probability of an intact chromosome being inherited. Based on a genetic model for maize (Zea mays L.) with 10 pairs of chromosomes, we examined different crossing schemes by simulation experiments and analytical studies with the goal of minimizing the number of generations and population sizes required for stacking. We found that targeted recombinations on up to five chromosomes can be stacked within practical constraints on time and resources. Linear and funnel schemes were less efficient than a multiple funnel scheme, which involved making all possible crosses in the first generation and stacking two additional chromosomes across multiple lines in subsequent generations. Homozygosity versus heterozygosity of the donor lines did not affect stacking efficiency. Population sizes and stacking efficiency were largely determined by the probability of intact chromosomal transfer from a donor parent to offspring. Such probability increased as the size of the chromosome segment from the donor decreased. When the probability of inheriting an intact chromosome was less than 0.15, population sizes needed for stacking became infeasibly large.