Mutations that cause lethality in the gametophyte phase pose a major challenge for studying postfertilization gene function. When both male and female haploid cells require a functional gene copy, null alleles cause developmental arrest before the formation of the zygote, precluding further investigation. The Arabidopsis thaliana Rb homolog RETINOBLASTOMA-RELATED (RBR) has an important function in the stem cell niche, but its requirement in both male and female gametophytes has prevented full loss-of-function studies. To circumvent this obstacle, we designed a clonal deletion system named BOB (Brother of Brainbow) in which nullmutant sectors marked by double fluorescence are generated in a fully complemented wildtype background. In this system, both copies of a complementing RBR transgene are eliminated by tissue-specific and inducible CRE expression, and homozygous mutant clones can be distinguished visually. Since mutant sectors can be produced in a homozygous, rather than a heterozygous, background, this system facilitates clonal deletion analysis not only for gametophytic lethal alleles but also for any type of mutation. Using the BOB system, we show that RBR has unique cellautonomous functions in different cell types within the root stem cell niche.