Accelerated development of rice near-isogenic lines based on rapid generation advance (RGA) and target capture...

Developing new crop cultivars with enhanced disease resistance, stress tolerance, and superior quality is urgently needed to address climate change and evolving agricultural demands. However, conventional breeding methods, particularly the development of near-isogenic lines (NILs), are notoriously time-consuming and labor-intensive. This study presents an innovative, integrated strategy to accelerate rice NIL development by combining a Rapid Generation Advance (RGA) system, Target Capture Sequencing (TCS), and a bulk DNA-based background selection approach applied at an advanced generation (BC₂F₆). Our strategy successfully established a NIL population within four years, a process traditionally requiring nearly a decade. The developed NILs exhibited a high recurrent parent genome (RPG) recovery rate, averaging 90.8% and reaching up to 97.2%. We validated the successful introgression of target genes, including x a5 (bacterial blight resistance) and Pita-2 (blast resistance), through both phenotypic and genotypic analyses. Notably, our RGA system utilized natural short-day conditions, effectively overcoming photoperiod sensitivity constraints in late-maturing cultivars and enabling two generations per year. This integrated strategy provides a scalable and efficient framework that dramatically reduces the time, labor, and costs associated with conventional NIL development while ensuring high precision, offering significant potential to accelerate functional genomics and marker-assisted breeding programs in rice and other major crop species.

The online version contains supplementary material available at 10.1007/s11032-026-01647-8.