Browsing by Person "Mayer, Manfred"

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Calibration and validation of predicted genomic breeding values in an advanced cycle maize population
(2021) Auinger, Hans-Jürgen; Lehermeier, Christina; Gianola, Daniel; Mayer, Manfred; Melchinger, Albrecht E.; da Silva, Sofia; Knaak, Carsten; Ouzunova, Milena; Schön, Chris-Carolin
The transition from phenotypic to genome-based selection requires a profound understanding of factors that deter- mine genomic prediction accuracy. We analysed experimental data from a commercial maize breeding programme to inves- tigate if genomic measures can assist in identifying optimal calibration sets for model training. The data set consisted of six contiguous selection cycles comprising testcrosses of 5968 doubled haploid lines genotyped with a minimum of 12,000 SNP markers. We evaluated genomic prediction accuracies in two independent prediction sets in combination with calibration sets differing in sample size and genomic measures (effective sample size, average maximum kinship, expected reliability, number of common polymorphic SNPs and linkage phase similarity). Our results indicate that across selection cycles pre- diction accuracies were as high as 0.57 for grain dry matter yield and 0.76 for grain dry matter content. Including data from all selection cycles in model training yielded the best results because interactions between calibration and prediction sets as well as the effects of different testers and specific years were attenuated. Among genomic measures, the expected reliability of genomic breeding values was the best predictor of empirical accuracies obtained with different calibration sets. For grain yield, a large difference between expected and empirical reliability was observed in one prediction set. We propose to use this difference as guidance for determining the weight phenotypic data of a given selection cycle should receive in model retraining and for selection when both genomic breeding values and phenotypes are available.
Discovery of beneficial haplotypes for complex traits in maize landraces
(2020) Mayer, Manfred; Hölker, Armin C.; González-Segovia, Eric; Bauer, Eva; Presterl, Thomas; Ouzunova, Milena; Melchinger, Albrecht E.; Schön, Chris-Carolin
Genetic variation is of crucial importance for crop improvement. Landraces are valuable sources of diversity, but for quantitative traits efficient strategies for their targeted utilization are lacking. Here, we map haplotype-trait associations at high resolution in ~1000 doubled-haploid lines derived from three maize landraces to make their native diversity for early development traits accessible for elite germplasm improvement. A comparative genomic analysis of the discovered haplotypes in the landrace-derived lines and a panel of 65 breeding lines, both genotyped with 600k SNPs, points to untapped beneficial variation for target traits in the landraces. The superior phenotypic performance of lines carrying favorable landrace haplotypes as compared to breeding lines with alternative haplotypes confirms these findings. Stability of haplotype effects across populations and environments as well as their limited effects on undesired traits indicate that our strategy has high potential for harnessing beneficial haplotype variation for quantitative traits from genetic resources.