Prediction of single-cross hybrid performance in maize using haplotype blocks associated with QTL for grain yield |
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Authors: | Tobias A Schrag Hans Peter Maurer Albrecht E Melchinger Hans-Peter Piepho Johan Peleman Matthias Frisch |
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Institution: | (1) Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70593 Stuttgart, Germany;(2) Bioinformatics Unit of the Institute for Crop Production and Grassland Research, University of Hohenheim, 70599 Stuttgart, Germany;(3) Keygene, P.O. Box 216, 6700 AE Wageningen, The Netherlands |
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Abstract: | Marker-based prediction of hybrid performance facilitates the identification of untested single-cross hybrids with superior
yield performance. Our objectives were to (1) determine the haplotype block structure of experimental germplasm from a hybrid
maize breeding program, (2) develop models for hybrid performance prediction based on haplotype blocks, and (3) compare hybrid
performance prediction based on haplotype blocks with other approaches, based on single AFLP markers or general combining
ability (GCA), under a validation scenario relevant for practical breeding. In total, 270 hybrids were evaluated for grain
yield in four Dent × Flint factorial mating experiments. Their parental inbred lines were genotyped with 20 AFLP primer–enzyme
combinations. Adjacent marker loci were combined into haplotype blocks. Hybrid performance was predicted on basis of single
marker loci and haplotype blocks. Prediction based on variable haplotype block length resulted in an improved prediction of
hybrid performance compared with the use of single AFLP markers. Estimates of prediction efficiency (R
2
) ranged from 0.305 to 0.889 for marker-based prediction and from 0.465 to 0.898 for GCA-based prediction. For inter-group
hybrids with predominance of general over specific combining ability, the hybrid prediction from GCA effects was efficient
in identifying promising hybrids. Considering the advantage of haplotype block approaches over single marker approaches for
the prediction of inter-group hybrids, we see a high potential to substantially improve the efficiency of hybrid breeding
programs.
Tobias A. Schrag and Hans Peter Maurer contributed equally to this work. |
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