Selection strategies for the development of rye introgression libraries

Computer simulations can be employed to find optimal procedures for developing introgression libraries in rye with marker-assisted backcrossing. Our objectives were to investigate the effects of the employed (1) breeding scheme, (2) selection strategy, and (3) population sizes on the donor genome coverage of the library, the number of introgression lines carrying additional donor chromosome segments outside the target regions, and the number of required marker data points. With respect to these target criteria, a BC3S2 breeding scheme and increasing population sizes from early to advanced generations were superior to a BC2S3 breeding scheme and constant population sizes. The smallest number of donor segments outside the target regions was reached with a three-stage selection strategy, which consists on selection for the target segment, selection for recombination at flanking markers and selection for recurrent parent alleles across the entire genome. Omitting the selection for flanking markers in generation BC1 reduced considerably the number of required marker data points. A pre-selection of chromosomes consisting completely of donor genome in BC1 was advantageous, if the effort in the breeding nursery should kept minimum. Adopting the described designs can help rye breeders to successfully develop introgression libraries.