Wheat (Triticum aestivum L.) is an ancient and widely cultivated food source integral to global diets. As whole-grain wheat increasingly features in diets, grain quality, influenced by breeding programs and production practices, becomes critical. Excessive intake of refined wheat products is associated with health risks, including obesity, type 2 diabetes, and coronary diseases. Refined flour's functional properties stem from its protein and starch content, which averages between 7–15% and 54–72%, respectively. In contrast, whole wheat flour retains beneficial minerals, dietary fibers, B vitamins, and phytochemicals, which promote health. The aleurone layer is rich in antioxidants, thereby preserving bioactive compounds as dietary fiber aids in their digestion and colon health. Test weight, protein content, and gluten characteristics are significant indicators of wheat quality, affecting cereal baking performance by influencing dough properties. Proteins like gliadin and glutenin determine gluten’s impact on texture and quality. The relative contributions of environmental and genetic factors (GxE) in wheat quality are essential for effective breeding strategies, as they help delineate conditions impacting yield and stress tolerance.