A Frameshift Mutation in the Mg-Chelatase I Subunit Gene OsCHLI Is Associated with a Lethal Chlorophyll-Deficient, Yellow Seedling Phenotype in Rice
Abstract
:1. Introduction
2. Results
2.1. Identification of YS Mutant
2.2. Examination of Pigments in YS Mutant Leaves
2.3. Microscopy Revealed Differences in Leaf Anatomy and an Absence of Chloroplasts
2.4. QTL-Seq Analysis Identified a Candidate Gene for the YS Phenotype
2.5. The 2-bp Deletion in OsCHLI Co-Segregated with YS
2.6. Prediction and Alignment of the Protein Structure of OsCHLI
2.7. The Mutation in OsCHLI Altered the Expression of Photosynthesis and Carbohydrate Metabolism Pathway Genes
2.8. Leaf Pigment- and Photosynthesis-Related Gene Expression Was Changed in YS Mutant
3. Discussion
4. Materials and Methods
4.1. Plant Materials
4.2. Anatomical and Ultrastructural Observation
4.3. Measurement of Chlorophylls and Carotenoids
4.4. DNA Extraction and PCR
4.5. QTL-Seq Analysis
4.6. Protein Structure Prediction and Alignment
4.7. RNA-Seq Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Chr. | Position | Variant | p99 | SNP Index | Gene ID | Gene Name | Variant Location | Description | ||
---|---|---|---|---|---|---|---|---|---|---|
GS | YS | Delta | ||||||||
3 | 20,248,858 | indel | 0.41 | 0.22 | 1.00 | 0.78 | Os03g0563300 | ELL, OsCHLI | Exon (Frameshift) | Magnesium-chelatase subunit ChlI, Mg-chelatase I subunit |
3 | 20,693,214 | indel | 0.53 | 0.12 | 0.76 | 0.65 | Os03g0570300 | Promoter | Zinc finger, C2H2-like domain-containing protein. | |
5 | 3,101,365 | indel | 0.48 | 0.00 | 1.00 | 1.00 | Intergenic | |||
7 | 24,595,098 | indel | 0.48 | 1.00 | 0.00 | −1.00 | Os07g0602200 | Intron | Similar to HDA1. | |
7 | 24,595,109 | indel | 0.49 | 0.05 | 1.00 | 0.95 | Os07g0602200 Intergenic | Intron | Similar to HDA1. | |
7 | 24,599,596 | indel | 0.46 | 0.00 | 0.76 | 0.76 | ||||
7 | 26,805,909 | indel | 0.59 | 0.00 | 1.00 | 1.00 | Intergenic | |||
9 | 12,636,359 | indel | 0.49 | 0.00 | 0.91 | 0.91 | Intergenic | |||
9 | 12,721,564 | indel | 0.44 | 0.03 | 1.00 | 0.97 | Os09g0378100 | Exon (Frameshift) | ND * | |
9 | 12,832,179 | indel | 0.54 | 0.00 | 0.94 | 0.94 | Os09g0380300 | Exon | Hypothetical conserved gene | |
11 | 8,522,066 | indel | 0.52 | 0.05 | 1.00 | 0.95 | Intergenic | |||
11 | 9,368,578 | indel | 0.49 | 1.00 | 0.00 | −1.00 | Intergenic | |||
12 | 5,109,930 | indel | 0.47 | 0.05 | 0.94 | 0.89 | Intergenic | |||
12 | 5,702,114 | indel | 0.48 | 0.09 | 0.93 | 0.84 | Os12g0209200 | OsBBX30 | Exon | Similar to CONSTANS-LIKE a. |
12 | 6,749,621 | indel | 0.49 | 0.94 | 0.00 | −0.94 | Intergenic |
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Shim, K.-C.; Kang, Y.; Song, J.-H.; Kim, Y.J.; Kim, J.K.; Kim, C.; Tai, T.H.; Park, I.; Ahn, S.-N. A Frameshift Mutation in the Mg-Chelatase I Subunit Gene OsCHLI Is Associated with a Lethal Chlorophyll-Deficient, Yellow Seedling Phenotype in Rice. Plants 2023, 12, 2831. https://doi.org/10.3390/plants12152831
Shim K-C, Kang Y, Song J-H, Kim YJ, Kim JK, Kim C, Tai TH, Park I, Ahn S-N. A Frameshift Mutation in the Mg-Chelatase I Subunit Gene OsCHLI Is Associated with a Lethal Chlorophyll-Deficient, Yellow Seedling Phenotype in Rice. Plants. 2023; 12(15):2831. https://doi.org/10.3390/plants12152831
Chicago/Turabian StyleShim, Kyu-Chan, Yuna Kang, Jun-Ho Song, Ye Jin Kim, Jae Kwang Kim, Changsoo Kim, Thomas H. Tai, Inkyu Park, and Sang-Nag Ahn. 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, no. 15: 2831. https://doi.org/10.3390/plants12152831