Identification and Characterization of a Novel Yellow Leaf Mutant yl1 in Rice

Leaf-color mutants play an important role in the study of chlorophyll metabolism, chloroplast development, andphotosynthesis system. In this study, the yellow leaf 1 (yl1) rice mutant was identified from the ethyl methanesulfonate-treated mutant progeny of Lailong, a glutinous japonica rice landrace cultivated in Guizhou Province,China. Results showed that yl1 exhibited yellow leaves with decreased chlorophyll content throughout the growthperiod. Chloroplast development in the yl1 mutant was disrupted, and the grana lamellae was loosely packed anddisordered. RNA sequencing and real-time quantitative polymerase chain reaction (qRT-PCR) analysis revealedthat the chlorophyll synthesis-related genes OsCHLH, OsCHLM, OsCHLG, PORB, and YGL8, as well as the chloroplast development-related genes FtsZ, OsRpoTp, and RbcL, were down-regulated in the yl1 mutant. Genetic analysis revealed that the yellow leaf phenotype of yl1 was controlled by recessive nuclear gene. By employing theMutMap method, the mutation responsible for the phenotype was mapped to a 6.17 Mb region between17.34 and 23.51 Mb on chromosome 3. Two non-synonymous single-nucleotide polymorphisms (SNPs) locatedin the gene locus LOC_Os03g31210 and LOC_Os03g36760 were detected in this region. The two SNPs werefurther confirmed by PCR and Sanger sequencing. The expression patterns of the two candidate genes indicatedthat LOC_Os03g36760 showed greater potential for functional verification. Subcellular protein localizationrevealed that the encoded product of LOC_Os03g36760 was localized in the nucleus, cytoplasm, and plasma membrane. These results will be useful for further characterization and cloning of the yl1 gene, and for research on themolecular mechanisms controlling biogenesis and chloroplast biochemical processes.