Predicting Hybrid Performances for Quality Traits through Genomic-Assisted Approaches in Central European Wheat

• Published in: PloS one 2016-07, Vol.11 (7), p.e0158635-e0158635
• Main Authors: Liu, Guozheng, Zhao, Yusheng, Gowda, Manje, Longin, C Friedrich H, Reif, Jochen C, Mette, Michael F
• Format: Article
• Language: English
• Subjects: Accuracy; Agricultural production; Biology and Life Sciences; Bread; Bread - standards; Breeding; Chromosome Mapping; Chromosomes, Plant - genetics; Corn; Europe; Gene mapping; Genes, Plant - genetics; Genetic aspects; Genome, Plant - genetics; Genomes; Genomics - methods; Genotype; Genotype & phenotype; Gluten; Hybrid Vigor - genetics; Hybridization, Genetic; Hybrids; Inbreeding; Marker-assisted selection; Performance prediction; Personality traits; Phenotype; Physical Sciences; Physiological aspects; Plant breeding; Plant Breeding - methods; Polymorphism; Polymorphism, Single Nucleotide; Population number; Quality; Quantitative genetics; Quantitative trait loci; Quantitative Trait Loci - genetics; Resampling; Research and Analysis Methods; Sedimentation & deposition; Single-nucleotide polymorphism; Species Specificity; Triticum - classification; Triticum - genetics; Triticum aestivum; Wheat
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0158635

Bread-making quality traits are central targets for wheat breeding. The objectives of our study were to (1) examine the presence of major effect QTLs for quality traits in a Central European elite wheat population, (2) explore the optimal strategy for predicting the hybrid performance for wheat quality traits, and (3) investigate the effects of marker density and the composition and size of the training population on the accuracy of prediction of hybrid performance. In total 135 inbred lines of Central European bread wheat (Triticum aestivum L.) and 1,604 hybrids derived from them were evaluated for seven quality traits in up to six environments. The 135 parental lines were genotyped using a 90k single-nucleotide polymorphism array. Genome-wide association mapping initially suggested presence of several quantitative trait loci (QTLs), but cross-validation rather indicated the absence of major effect QTLs for all quality traits except of 1000-kernel weight. Genomic selection substantially outperformed marker-assisted selection in predicting hybrid performance. A resampling study revealed that increasing the effective population size in the estimation set of hybrids is relevant to boost the accuracy of prediction for an unrelated test population.