Genetic structure, KASP markers, and core germplasm resources of rice landraces from the Taihu Lake Basin

Rice (Oryza sativa L.), a global staple crop, is crucial to food security, particularly in Asia. The Taihu Lake Basin, located in the middle and lower reaches of the Yangtze River, is a secondary origin center for rice, with a cultivation history dating back over 8000 years. However, the genetic diversity of traditional rice landraces in this region faces significant threats due to the widespread adoption of high-yielding cultivars. This study aimed to characterize the genetic structure of rice landraces from the Taihu Lake Basin, develop KASP markers for precise identification, and establish a core germplasm collection, using high-throughput resequencing technologies. A total of 114 rice landrace accessions from the Taihu Lake Basin were sampled and analyzed. Population genetic structure analysis revealed seven distinct genetic groups. Utilizing this dataset, a set of 27 kompetitive allele specific PCR (KASP) markers were developed, enabling accurate genotyping and efficient landrace identification. Furthermore, a core germplasm collection was established, representing 99 % of the genetic diversity of the original collection. Overall, this study provides a valuable resource for the conservation and sustainable utilization of rice landraces in the Taihu Lake Basin, supporting future rice breeding programs and ensuring the preservation of genetic resources crucial for crop improvement.