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

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.