Integrative Transcriptomic and Proteomic Analyses of Quality Differences in Wheat Cultivars Grown in Two Ecological Regions

Advancements in the grain industry and evolving dietary patterns have made the processing quality of wheat a key determinant governing the diversification and industrial application of flour products. Characterizing genotype-dependent environmental responses is important for quality-oriented breeding of high-quality bread wheat. In this study, two winter wheat cultivars with distinct gluten properties—the strong-gluten Xindong 23 and the medium-gluten Xindong 53—were grown in two ecological regions of Xinjiang (Yili and Tacheng) during the 2024–2025 season. Integrative transcriptomic and proteomic analyses were performed on developing grains at three nominal grain-filling stages (10, 20, and 30 days after anthesis). Blocked factorial analysis detected genotypic differences, site effects and genotype-by-site interactions for six of eight processing quality traits. Specifically, Xindong 23 exhibited superior processing quality potential but displayed substantial ecological variation between the two experimental sites. In contrast, Xindong 53 showed smaller site-associated differences in several rheological traits within this trial. Multi-omics analysis further showed extensive site-associated transcriptomic and proteomic responses in Xindong 23. In Xindong 23, endoplasmic reticulum protein processing and ribosome-related pathways were enriched at early and middle grain filling, respectively. Direct transcript–protein matching showed positive, stage-dependent agreement, including a concordant omega-gliadin candidate at middle filling. Collectively, this study identifies candidate molecular associations with cultivar-specific quality responses, providing preliminary evidence for further environmental trials and functional investigation of specialized wheat varieties.