A high-quality bread wheat genome unravels the adaptive evolution of wheat end-use quality

Understanding the genetics of superior dough performance is essential for improving wheat end-use quality. Here we present a de novo assembly of the genome of JM44, a Chinese wheat cultivar known for its exceptional end-use quality. The JM44 genome achieved reference-level quality (with a quality value of 66.74), depicting a complete picture of complex regions containing gluten genes. Our microsynteny analysis across the Triticum-Aegilops complex showed that high-molecular-weight glutenin subunit loci are highly conserved, while low-molecular-weight glutenin subunits and α-/β-gliadins exhibited greater structural variation. These variable loci appear to have been preferentially selected by humans and contributed substantially to the evolution of wheat quality traits. Moreover, we observed that epistatic interactions between gluten genes are strong in modern cultivars but markedly weaker in landraces, indicating the importance of epistatic selection during modern breeding. Our findings shed light on the genomics and evolution of wheat quality traits, providing valuable guidance for future breeding efforts.