Pitfalls of genetic analysis using a doubled-haploid backcrossed to its parent.

A population derived from a doubled-haploid backcrossed to its parent has a unique genetic structure, which affects the mapping and genetic analysis of molecular-marker data. In such a cross: (1) repulsion linkages are reduced dramatically and can be detected only in restricted chromosome sections; each repulsion-linkage group represents a section of a chromosome carrying a crossover that occurred in the meiosis that produced the gamete from which the doubled-haploid was derived; (2) the number of coupling-linkage groups observed depends on how many crossovers occurred during the meiosis; the observed size of a linkage group will be only a fraction of a total chromosome if the chromosome carried in the doubled-haploid resulted from crossover exchanges; (3) the size covered by all the observed linkages is only equivalent to the haploid genome; and (4) the ratio of single-dose to multi-dose markers is inflated. These features have not been recognized in previous reports, resulting in misinterpretations in genetic mapping and analysis of the molecular-marker data. The ratio of single- to multi-dose markers has been used inappropriately to distinguish polyploid type.