Seeing Red, Selecting True: RUBY-Reported Seed Marker Streamlines CRISPR-Clean Rice Breeding

The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated protein (Cas)9 genome-editing technology has become a cornerstone for generating knockout mutations in plant functional genomics. To obtain genetically stable CRISPR-edited plants, the removal of exogenous CRISPR constructs through genetic segregation is imperative. However, current transgene-free strategies lack universality and operational simplicity. Here, we developed a modular CRISPR toolkit integrated with the widely applicable visual RUBY marker. This system achieved 100% editing efficiency in three independent CRISPR-Cas9 editing events in rice (cv. Zhonghua 11), enabled rapid visual identification of transgene-free progeny, and may provide a framework for future adaptation of CRISPR vectors to other plant species. Our design significantly accelerates the identification of edited lines while bypassing laborious molecular validation steps.