Genetic Diversity, Population Structure and Temporal Dynamics of Wheat Cultivars in China

Abstract

Molecular characterization of wheat varieties is of high importance for wheat breeding. In the present study, 1883 Chinese wheat cultivars released between 1971 and 2025 were genotyped using a wheat 90K SNP array. Analysis of genetic diversity indicated a consistent A > B > D pattern, with the D subgenome showing the lowest genetic diversity and fastest LD decay (4.2 Mb), indicating diminished genetic diversity driven by breeding and selection. Population structure analysis revealed ten genetic clusters with clear ecological preferences, whereas genetic differentiation was weak (FST < 0.05) and gene flow extensive (Nem > 1), indicating the co-existence of strong ecological adaptation and frequent interregional germplasm exchange. Selective sweeps were identified on chromosome 5A (TaVRN1) and 2D (Rht8/RNHL-D1) regions controlling vernalization, plant height, and stress tolerance. Despite high gene flow, these loci for variety adaptiveness remained differentiated, highlighting the impact of artificial selection. Average pairwise genetic similarity was 0.56, but only a minority of cultivar pairs exceeded 0.98, especially in the Northeastern Spring Wheat and Middle-Lower Yangtze River Facultative Wheat regions, revealing severe genetic homogeneity from the excessive use of core parents. Nucleotide diversity increased to a peak in 2011–2015. These findings indicate that Chinese wheat cultivars still harbor significant potential for genetic improvement, highlighting the critical need to integrate exotic germplasm into core breeding parents to drive future advancements.