Marker-based prediction of the parental genome contribution to inbred lines derived from biparental crosses

Molecular markets can be employed to predict the parental genome contribution to inbred lines. The proportion alpha of alleles originating from parent P-1 at markers polymorphic between the parental lines P-1 and P-2 is commonly used as a predictor xi for the genome contribution of parent P, to an offspring line. Our objectives were to develop a new marker-based predictor for the parental genome contribution, which takes into account not only the alleles at marker loci but also their map distance, and to compare the prediction precision of xi with that of alternative methods. We derived formulas for xi for inbreds derived from biparental crosses (F-1 and backcrosses) with the single-seed descent or double-haploid method and presented an extension xi* possessing statistical optimum properties. In a simulation Study, a showed a systematic overestimation of large parental genome contribution that was not observed for xi. The mean squared prediction error of xi was at least 50% smaller than that of alpha for linkage maps with unequal distances between adjacent markers. A data set from a study on plant variety protection in maize was used to illustrate the application of xi. We conclude that xi provides substantially greater prediction precision than the commonly used predictor a in a broad range of applications in genetics and breeding.