An introgression from <i>Triticum timopheevii</i> reduces grain protein content in winter wheat populations

Improving grain protein content (GPC) in wheat (Triticum aestivum L.) is crucial for enhancing end-use quality and ensuring efficient nitrogen (N) utilization, thereby reducing environmental damage caused by excess N. However, progress in increasing GPC has been limited because of the strong negative correlation between GPC and grain yield (GY), as well as the scarcity of multi-location, multi-year phenotypic data. In this study, we analyzed the variation in GPC, GY, and grain protein deviation (GPD) using multi-location, multi-year phenotypic data from winter wheat varieties in Scandinavian regions. As reported previously, we observed a negative correlation between GY and GPC, with recent cultivars showing higher GY but lower GPC. Additionally, a genome-wide association study (GWAS) in two independent populations identified significant marker-trait associations (MTAs) for GPC and GPD, with key MTAs located on chromosome 2B (chr2B), highlighting its central role in the regulation of these traits. Interestingly, the MTA for GPD on chr2B coincided with an introgression from Triticum timopheevii, which was associated with reduced GPC and GPD in elite lines carrying this region. This introgression, which contains a powdery mildew resistance gene (Pm6), appears to negatively affect GPC, likely due to linkage drag. These findings emphasize the importance of chr2B in wheat breeding and suggest that advanced genomic techniques, such as mutagenesis and CRISPR-Cas, could be employed to mitigate negative pleiotropic effects and improve GPC and GPD. Overall, this study provides valuable insights into the genetic architecture underlying GPC in wheat and offers directions for future breeding strategies aimed at enhancing protein content.