Genetic diversity analysis of newly approved rice cultivars in southern China from 2014 to 2022

The advancement of rice breeding technology, coupled with the persistent endeavors of breeders, has led to a marked improvement in both yield and quality of new rice cultivars in China. The accelerated dissemination of exemplary new rice cultivars, such as Shan-you-63 and Tian-you-hua-zhan, has contributed to year-on-year increases in total rice production. This study evaluated 1,914 newly approved rice cultivars from 2014 to 2022, covering 11 major ecological types in southern China. Our analysis focused on genetic diversity, population structure, and developmental trends, utilizing simple sequence repeat (SSR) markers to categorize these cultivars based on approval year and suitable planting regions. Using 48 SSR markers, we identified 390 alleles and 986 genotypes. The polymorphic information content (PIC) indices varied from 0.09 to 0.773, while the gene diversity ranged from 0.09 to 0.800. Principal component analysis (PCA), neighbor-joining trees, and model-based structure analysis revealed that the 1,914 new rice cultivars form two distinct population structures. From a temporal perspective, the average PIC and gene diversity indices declined. In terms of suitable planting areas, the 1,914 new rice cultivars were aligned with 11 ecological types across the rice cultivation regions of southern China, which could be primarily categorized into four components. Notably, the PIC of japonica rice cultivars in the middle and lower reaches of the Yangtze River was the highest, and genetic distance analysis revealed that these cultivars had the greatest genetic divergence from indica rice cultivars. Over time, the PIC index for the 11 ecological groups demonstrated varied transformation trends, with 48 markers displaying differential polymorphisms across these groups. Certain loci exhibited a polymorphism of zero. Our findings provide an essential data foundation and critical perspectives to inform strategies for variety protection, cross-regional introduction, and the future design of breeding programs. The limitations identified also highlight the need for optimizing molecular marker systems for these applications.