The current state of the use of DNA markers for improving the efficiency of rice breeding in Japan.

In response to recent environmental and geopolitical changes, Japan requires rice cultivars with high adaptability and production efficiency. Advances in rice genomics have enabled precise genetic mapping and the use of DNA markers for efficient selection. Marker-assisted selection (MAS) reduces labor and environmental influences, and co-dominant markers allow accurate genotyping. When combined with backcrossing, MAS enables rapid pyramiding of multiple traits. Marker-assisted breeding has been widely applied to improving elite cultivars across Japan. This review highlights the practical applications of DNA markers in rice breeding programs in Japan. Specifically, we examine how molecular markers have been used to improve resistance to diseases and pests, improve grain quality, strengthen tolerance to abiotic stresses, and support the selection of agronomically important quantitative traits such as heading date and yield. We also provide an overview of a practical approach to accelerating breeding through MAS and generation advancement for efficient trait stacking. Finally, we present future perspectives on expanding the use of molecular markers to further improve the efficiency and precision of rice breeding.