A frameshift mutation in the Mg-Chelatase I subunit gene OsCHLI is associated with a lethal chlorophyll-deficient, yellow seedling phenotype in rice

Authors: SHIM, KYU-CHAN - Chungnam National University; KANG, YUNA - Chungnam National University; SONG, JUN-HO - Chungbuk National University; KIM, YE JIN - Incheon National University; KIM, JAE KWANG - Incheon National University; KIM, CHANGSOO - Chungnam National University; Tai, Thomas; PARK, INKYU - Changwon National University; AHN, SANG-NAG - Chungnam National University

Submitted to: Plants
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/28/2023
Publication Date: 7/31/2023
Citation: Shim, K., Kang, Y., Song, J., Kim, Y., Kim, J., Kim, C., Tai, T., Park, I., Ahn, S. 2023. A frameshift mutation in the Mg-Chelatase I subunit gene OsCHLI is associated with a lethal chlorophyll-deficient, yellow seedling phenotype in rice. Plants. 12/2831. https://doi.org/10.3390/plants12152831.
DOI: https://doi.org/10.3390/plants12152831

Interpretive Summary: Plants have an array of pigments that function in various physiological processes. The pigments that impart the characteristic green color of most plants are chlorophylls which play a key role in harvesting light energy using it to convert carbon dioxide and water into food in the form of carbohydrates in a process called photosynthesis. In this research, a chlorophyll-deficient, yellow colored rice seedling mutant was identified. The lack of chlorophyll in these mutant seedlings resulted in their death after a few weeks. Using genetic and genomic approaches, the nature of the mutation responsible for this lethal, yellow seedling mutant was identified as a 2-base pair deletion in a gene, OsCHLI, that encodes one of three protein subunits that make up the enzyme magnesium chelatase. This enzyme catalyzes the first critical step in the biosynthesis of chlorophyll pigments. In addition to identifying the mutation, characterization of the leaf pigment contents and global gene expression in the yellow and normal green seedlings was performed and the potential effect of the deletion mutation on the OsCHI protein was examined using a protein structure prediction program.

Technical Abstract: Chlorophyll biosynthesis is a crucial biological process in plants, and chlorophyll content is one of the most important traits in rice breeding programs. Magnesium (Mg) chelatase catalyzes the insertion of Mg2+ into protoporphyrin IX to produce Mg-protoporphyrin, which is essential for the chlorophyll biosynthesis pathway. In this study, we identified a lethal chlorophyll-deficient yellow seedling (YS) mutant from the F3 line, CR5055-21, derived from a cross between Hwaseong and CR5029, an introgression line that includes Oryza grandiglumis chromosome segments. YS and green seedlings (GS) were segregated in the CR5055-21 F3 line at a 1:3 ratio, indicating that one locus might be associated with the YS phenotype. Loosed mesophyll cells and sparse parenchyma were observed in the microscopic analysis of YS leaves. In addition, chloroplasts did not develop in the mesophyll cells of the YS. Quantitative trait loci (QTL)-seq analysis was performed to identify the locus responsible for the YS phenotype. However, no significant QTL were detected in the sliding window analysis. Examination of the individual delta-SNP index identified a 2-bp deletion (AG) in the OsCHLI gene, a magnesium-chelatase subunit. To validate the 2-bp InDel, the dCAPs marker was designed, and 275 YS and GS plants were co-segregated with dCAPs markers. The 2-bp deletion led to a frameshift mutation with a truncated protein, and the three-dimensional structure of the OsCHLI protein of YS and GS was compared by protein structure alignment. Furthermore, transcriptome analysis of YS and GS leaves was performed to understand the regulatory mechanism of OsCHLI better, and the photosynthesis and carbohydrate metabolism pathways were significantly altered. Chlorophyll- and carotenoid-related genes were also differentially expressed in the YS plants. Our findings demonstrated that OsCHLI plays an important role in leaf pigment biosynthesis and leaf structure development in rice.