Dissection of the Genetic Basis of Genotype by Environment Interactions for Morphological Traits and Protein Content in Winter Wheat Panel Grown in Morocco and Spain

To fulfill the growing demand for wheat consumption, it is important to focus on enhancement breeding strategies targeting key parameters such as yield, thousand kernel weight (TKW), quality characteristics including morphological traits, and protein content. These elements are key to the ongoing and future objectives of wheat breeding programs. Prioritizing these factors will effectively help meet the rising demand for wheat, especially given the challenges posed by unpredictable weather patterns. This study evaluated the morphological traits and protein content of 249 winter wheat varieties and advanced lines grown in eleven different environments in Morocco and Spain incorporating three varied sowing dates. The results showed considerable variability in morphological traits and protein content. Significant correlations were observed among various grain traits, with most grain morphological parameters exhibiting negative correlations with protein content. Differences across environments (<i>p</i> ≤ 0.01) in all traits, genotypes, and genotype by environment interaction were significant. A factorial regression analysis revealed significant impacts of environmental conditions on all grain morphological parameters, protein content, and TKW during the three growth stages. The study identified several high-performing and stable genotypes across diverse environments, providing valuable insights for wheat breeding programs such as genotypes 129, 234, 241, and 243. Genome-Wide Association Studies pinpointed 603 significant markers across 11 environments, spread across chromosomes. Among these, 400 markers were linked with at least two traits or observed in at least two different environments. Moreover, twelve marker-trait associations were detected that surpassed the Bonferroni correction threshold. These findings highlight the importance of targeted breeding efforts to enhance wheat quality and adaptability to different environmental conditions.