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

• Published in: Plants (Basel) 2023-07, Vol.12 (15), p.2831
• Main Authors: Shim, Kyu-Chan, Kang, Yuna, Song, Jun-Ho, Kim, Ye Jin, Kim, Jae Kwang, Kim, Changsoo, Tai, Thomas H, Park, Inkyu, Ahn, Sang-Nag
• Format: Article
• Language: English
• Subjects: Albinism; Barley; Biological activity; Biomarkers; Biosynthesis; Carbohydrate metabolism; Carbohydrates; carotenoid; Carotenoids; Chlorophyll; Chloroplasts; Chromosomes; Frameshift mutation; Gene deletion; Gene mapping; Genes; Genetic aspects; Genetic crosses; Genotype & phenotype; Genotyping; Identification and classification; Leaves; Light microscopy; Magnesium; magnesium chelatase; Mesophyll; Microscopy; Mutants; Mutation; Optical microscopy; Parenchyma; Phenotypes; Photosynthesis; Physiological aspects; Pigments; Plant breeding; Plant mutation; Proteins; Quantitative trait loci; Rice; Seedlings; Seeds; Single-nucleotide polymorphism; Transcriptomes; Transmission electron microscopy; yellow seedling
• ISSN: 2223-7747; 2223-7747
• DOI: 10.3390/plants12152831

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 F plant derived from a backcross between Korean variety 'Hwaseong' ( ) and CR5029, which is mostly Hwaseong with a small amount of 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 gene, a magnesium (Mg)-chelatase subunit. A dCAPs marker was designed and genotyping of a segregating population ( = 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 was not. Chlorophyll- and carotenoid-related genes were also differentially expressed in the YS mutant. Our findings demonstrated that plays an important role in leaf pigment biosynthesis and leaf structure development in rice.