Marker-based selection as a tool for enhancing the efficiency of two conventional breeding methods of self-fertilizing crop plants, the generation-accelerated bulk breeding and doubled haploid breeding

The effectiveness of marker-based selection (MBS) for enhancing the efficiency of two conventional breeding methods of self-fertilizing crop plants, i.e., generation-accelerated bulk breeding (GAB) and doubled haploid breeding (DHB), is evaluated. When incorporated into GAB, MBS is assumed to be applied in Fsub(2) and Fsub(3) generations based on DNA markers that are linked with desirable trait genes. The effectiveness of MBS is evaluated based on its contribution to increasing the probability of obtaining the desired genotype. Our calculations of the probability show that the effectiveness of MBS depends on the number of trait genes involved in the breeding objective as well as the number of available markers; MBS will produce a great increase in the probability when more than about 12 genes are involved in the breeding objective and markers are available for several or more of these trait genes. In such a case, MBS is useful even when as few as 100 plants are tested in Fsub(2) and Fsub(3) generations, compared to conventional GAB in which 2000 plants are grown for generation acceleration. The effectiveness of MBS increases in the presence of repulsion linkage between desirable trait genes, whereas it decreases in the presence of coupling linkage. Although codominant markers are superior under most practically possible conditions, dominant markers (linked with desirable trait genes) could be superior when relatively few, roughly fewer than 12, genes are involved in the breeding objective and desirable trait genes are linked prevalently in the coupling phase. When MBS is based on more than several codominant markers, it is important to widen the range of the marker genotypes to be selected; not only the best but also the second and third best, partially heterozygous genotypes should be selected. Linkage between trait genes and markers needs not to be perfect; when many markers are available, the advantage of MBS is not lost even with a map distance as long as 10 cM. When desirable trait genes are linked prevalently in the repulsion phase, MBS could effectively be combined with DHB for eliminating unpromising doubled haploid genotypes prior to field test, or for selecting from an Fsub(2) population, plants that should be treated for doubled haploidization.