"zebra" mutants have alternating green and chlorotic crossbands on leaf blades and are widely distributed in monocotyledonous crops. Most recently, we cloned the first responsible gene from rice, ZEBRA2, which also leads to the phenotype of rice preharvest sprouting. ZEBRA2, a single-copy gene in the rice genome, encodes a carotenoid isomerase (CRTISO), the key enzyme catalyzing the conversion of cis-lycopene to all-trans lycopene. ZEBRA2 shares high identity with known CRTISOs from other species. Expression analysis via both RT-PCR and ZEBRA2-promoter-β-glucuronidase (GUS) transgenic rice indicates that ZEBRA2 is predominantly expressed in mesophyll cells of mature leaves where active photosynthesis occurs. Consistent with the alteration in agronomic traits, the zebra2 mutant exhibits decreased photosynthetic rate and chlorophyll content. Mutation of the ZEBRA2 gene results in the accumulation of all-trans-lycopene precursor, prolycopene (7Z,9Z,7'Z,9'Z tetra cis-lycopene), in dark-grown zebra2 tissues. Light-grown zebra2 mutant exhibits the characteristic "zebra" phenotype and decreased level of lutein, the xanthophyll that is essential for efficient chl triplet quenching. More severe phenotype of the zebra2 mutant under high light intensity indicates that "zebra" phenotype might be caused by photooxidative damages. We conclude that ZEBRA2 is involved in photoprotection in rice.