A Frameshift Mutation in the Mg-Chelatase I Subunit Gene <i>OsCHLI</i> Is Associated with a Lethal Chlorophyll-Deficient, Yellow Seedling Phenotype in Rice

Chlorophyll biosynthesis is a crucial biological process in plants, and chlorophyll content is one of the most important traits in rice breeding programs. In this study, we identified a lethal, chlorophyll-deficient, yellow seedling (YS) phenotype segregating in progeny of CR5055-21, an F₂ plant derived from a backcross between Korean <i>japonica</i> variety ‘Hwaseong’ (<i>Oryza sativa</i>) and CR5029, which is mostly Hwaseong with a small amount of <i>Oryza grandiglumis</i> chromosome segments. The segregation of the mutant phenotype was consistent with a single gene recessive mutation. Light microscopy of YS leaf cross-sections revealed loosely arranged mesophyll cells and sparse parenchyma in contrast to wildtype. In addition, transmission electron microscopy showed that chloroplasts did not develop in the mesophyll cells of the YS mutant. Quantitative trait loci (QTL)-seq analysis did not detect any significant QTL, however, examination of the individual delta-SNP index identified a 2-bp deletion (AG) in the <i>OsCHLI</i> gene, a magnesium (Mg)-chelatase subunit. A dCAPs marker was designed and genotyping of a segregating population (<i>n</i> = 275) showed that the mutant phenotype co-segregated with the marker. The 2-bp deletion was predicted to result in a frameshift mutation generating a premature termination. The truncated protein likely affects formation and function of Mg-chelatase, which consists of three different subunits that together catalyze the first committed step of chlorophyll biosynthesis. Transcriptome analysis showed that photosynthesis and carbohydrate metabolism pathways were significantly altered although expression of <i>OsCHLI</i> was not. Chlorophyll- and carotenoid-related genes were also differentially expressed in the YS mutant. Our findings demonstrated that <i>OsCHLI</i> plays an important role in leaf pigment biosynthesis and leaf structure development in rice.