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 F<sub>...
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2023-07-01
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| author | Kyu-Chan Shim Yuna Kang Jun-Ho Song Ye Jin Kim Jae Kwang Kim Changsoo Kim Thomas H. Tai Inkyu Park Sang-Nag Ahn |
| author_facet | Kyu-Chan Shim Yuna Kang Jun-Ho Song Ye Jin Kim Jae Kwang Kim Changsoo Kim Thomas H. Tai Inkyu Park Sang-Nag Ahn |
| author_sort | Kyu-Chan Shim |
| collection | DOAJ |
| description | 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<sub>2</sub> 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. |
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| spelling | doaj.art-1585e65b1ed247d7a3f67489060a13982023-11-18T23:26:27ZengMDPI AGPlants2223-77472023-07-011215283110.3390/plants12152831A Frameshift Mutation in the Mg-Chelatase I Subunit Gene <i>OsCHLI</i> Is Associated with a Lethal Chlorophyll-Deficient, Yellow Seedling Phenotype in RiceKyu-Chan Shim0Yuna Kang1Jun-Ho Song2Ye Jin Kim3Jae Kwang Kim4Changsoo Kim5Thomas H. Tai6Inkyu Park7Sang-Nag Ahn8Department of Agronomy, College of Agriculture and Life Science, Chungnam National University, Daejeon 34134, Republic of KoreaDepartment of Agronomy, College of Agriculture and Life Science, Chungnam National University, Daejeon 34134, Republic of KoreaDepartment of Biology, Chungbuk National University, Cheongju 28644, Republic of KoreaDivision of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Republic of KoreaDivision of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Republic of KoreaDepartment of Agronomy, College of Agriculture and Life Science, Chungnam National University, Daejeon 34134, Republic of KoreaUSDA-ARS Crops Pathology and Genetics Research Unit, Davis, CA 95616, USADepartment of Biology and Chemistry, Changwon National University, Changwon 51140, Republic of KoreaDepartment of Agronomy, College of Agriculture and Life Science, Chungnam National University, Daejeon 34134, Republic of KoreaChlorophyll 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<sub>2</sub> 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.https://www.mdpi.com/2223-7747/12/15/2831yellow seedlingmagnesium chelatasechlorophyllcarotenoidrice |
| spellingShingle | Kyu-Chan Shim Yuna Kang Jun-Ho Song Ye Jin Kim Jae Kwang Kim Changsoo Kim Thomas H. Tai Inkyu Park Sang-Nag Ahn 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 Plants yellow seedling magnesium chelatase chlorophyll carotenoid rice |
| title | 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 |
| title_full | 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 |
| title_fullStr | 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 |
| title_full_unstemmed | 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 |
| title_short | 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 |
| title_sort | frameshift mutation in the mg chelatase i subunit gene i oschli i is associated with a lethal chlorophyll deficient yellow seedling phenotype in rice |
| topic | yellow seedling magnesium chelatase chlorophyll carotenoid rice |
| url | https://www.mdpi.com/2223-7747/12/15/2831 |
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