Hybrid Wheat Prediction Using Genomic, Pedigree, and Environmental Covariables Interaction Models

• Main Authors: Bhoja Raj Basnet, Jose Crossa, Susanne Dreisigacker, Paulino Pérez-Rodríguez, Yann Manes, Ravi P. Singh, Umesh R. Rosyara, Fatima Camarillo-Castillo, Mercedes Murua
• Format: Article
• Language: English
• Published: Wiley 2019-03-01
• Series: The Plant Genome
• Online Access: https://dl.sciencesocieties.org/publications/tpg/articles/12/1/180051

In this study, we used genotype × environment interactions (G×E) models for hybrid prediction, where similarity between lines was assessed by pedigree and molecular markers, and similarity between environments was accounted for by environmental covariables. We use five genomic and pedigree models (M1–M5) under four cross-validation (CV) schemes: prediction of hybrids when the training set (i) includes hybrids of all males and females evaluated only in some environments (T2FM), (ii) excludes all progenies from a randomly selected male (T1M), (iii) includes all progenies from 20% randomly selected females in combination with all males (T1F), and (iv) includes one randomly selected male plus 40% randomly selected females that were crossed with it (T0FM). Models were tested on a total of 1888 wheat ( L.) hybrids including 18 males and 667 females in three consecutive years. For grain yield, the most complex model (M5) under T2FM had slightly higher prediction accuracy than the less complex model. For T1F, the prediction accuracy of hybrids for grain yield and other traits of the most complete model was 0.50 to 0.55. For T1M, Model M3 exhibited high prediction accuracies for flowering traits (0.71), whereas the more complex model (M5) demonstrated high accuracy for grain yield (0.5). For T0FM, the prediction accuracy for grain yield of Model M5 was 0.61. Including genomic and pedigree gave relatively high prediction accuracy even when both parents were untested. Results show that it is possible to predict unobserved hybrids when modeling genomic general combining ability (GCA) and specific combining ability (SCA) and their interactions with environments.