Marker-Based Prediction of the Parental Genome Contribution to Inbred Lines Derived From Biparental Crosses

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Abstract
Molecular markers can be employed to predict the parental genome contribution to inbred lines. The proportion α of alleles originating from parent P1 at markers polymorphic between the parental lines P1 and P2 is commonly used as a predictor for the genome contribution of parent P1 to an offspring line. Our objectives were to develop a new marker-based predictor ξ 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 ξ with that of alternative methods. We derived formulas for ξ for inbreds derived from biparental crosses (F1 and backcrosses) with the single-seed descent or double-haploid method and presented an extension ξ* possessing statistical optimum properties. In a simulation study, α showed a systematic overestimation of large parental genome contribution that was not observed for ξ. The mean squared prediction error of ξ was at least 50% smaller than that of α 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 ξ. We conclude that ξ provides substantially greater prediction precision than the commonly used predictor α in a broad range of applications in genetics and breeding.