A yellow and green zebra leaf mutant zebraleaf 2 (zl2) displayed a distinctive zebra leaf at seedling stage, and the leaves of the mutant gradually turned yellow after heading. Compared with wild type, the chlorophyll and carotenoid contents of zl2 were significantly reduced at trileaf stage, tillering stage, heading stage and mature stage. The seed setting rate, grain weight and plant height of zl2 also decreased significantly. The ultrastructures of chloroplasts in the mesophyll cells of the yellow part of seedling of zl2 have obvious differences from that of wild type. Genetic analysis showed that the phenotype of zl2 was controlled by a single recessive nuclear gene. Total 1607 zebra leaf plants selected from the F2 population of zl2 / Nanjing 11 were used to finemap the mutant gene. Finally, ZL2 gene was narrowed to the 164.3 kb region on chromosome 11. There are 13 ORFs in this region, and a single base mutation was found in the ORF12 which encode a carotenoid isomerase. And as a result, four bases were missed in cDNA of ORF12 of zl2, leading to frameshift and the amino acid premature termination at the 395th. Compared with the wild type, the expression level of ZL2 and the genes involved in the control of leaf color and photosynthesis, such as PORA, RbcL, RbcS， Cab1， Cab2， psaA, psbA and OsDVR decreased significantly in the mutant, while those of HEMA1, YGL1, V1, V2, SPP and OsPPR increase significantly. The results suggested that ZL2 act a very important role in chlorophyll biosynthesis, chloroplast development and photosynthesis in rice.
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