Genomic Prediction with Genotype by Environment Interaction Analysis for Kernel Zinc Concentration in Tropical Maize Germplasm

• Main Authors: Edna K. Mageto, Jose Crossa, Paulino Pérez-Rodríguez, Thanda Dhliwayo, Natalia Palacios-Rojas, Michael Lee, Rui Guo, Félix San Vicente, Xuecai Zhang, Vemuri Hindu
• Format: Article
• Language: English
• Published: Oxford University Press 2020-08-01
• Series: G3: Genes, Genomes, Genetics
• Subjects: zea mays l.; genetics; breeding; zinc; prediction; genpred; shared data resources; genomic prediction
• Online Access: http://g3journal.org/lookup/doi/10.1534/g3.120.401172

Zinc (Zn) deficiency is a major risk factor for human health, affecting about 30% of the world’s population. To study the potential of genomic selection (GS) for maize with increased Zn concentration, an association panel and two doubled haploid (DH) populations were evaluated in three environments. Three genomic prediction models, M (M1: Environment + Line, M2: Environment + Line + Genomic, and M3: Environment + Line + Genomic + Genomic x Environment) incorporating main effects (lines and genomic) and the interaction between genomic and environment (G x E) were assessed to estimate the prediction ability (rMP) for each model. Two distinct cross-validation (CV) schemes simulating two genomic prediction breeding scenarios were used. CV1 predicts the performance of newly developed lines, whereas CV2 predicts the performance of lines tested in sparse multi-location trials. Predictions for Zn in CV1 ranged from -0.01 to 0.56 for DH1, 0.04 to 0.50 for DH2 and -0.001 to 0.47 for the association panel. For CV2, rMP values ranged from 0.67 to 0.71 for DH1, 0.40 to 0.56 for DH2 and 0.64 to 0.72 for the association panel. The genomic prediction model which included G x E had the highest average rMP for both CV1 (0.39 and 0.44) and CV2 (0.71 and 0.51) for the association panel and DH2 population, respectively. These results suggest that GS has potential to accelerate breeding for enhanced kernel Zn concentration by facilitating selection of superior genotypes.