Identification of candidate genes and clarification of the maintenance of the green pericarp of weedy rice grains
The weedy rice (Oryza sativa f. spontanea) pericarp has diverse colors (e.g., purple, red, light-red, and white). However, research on pericarp colors has focused on red and purple, but not green. Unlike many other common weedy rice resources, LM8 has a green pericarp at maturity. In this study, the...
| Autores principales: | , , , , , , , , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Frontiers Media
2022
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/164045 |
| _version_ | 1855542481996742656 |
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| author | Han, Zhenyun Li, Fei Qiao, Weihua Nong, Baoxuan Cheng, Yunlian Zhang, Lifang Huang, Jingfen Wang, Yanyan Lou, Danjing Ge, Jinyue Xing, Meng Fan, Weiya Nie, Yamin Guo, Wenlong Wang, Shizhuang Liu, Ziran Li, Danting Zheng, Xiaoming Yang, Qingwen |
| author_browse | Cheng, Yunlian Fan, Weiya Ge, Jinyue Guo, Wenlong Han, Zhenyun Huang, Jingfen Li, Danting Li, Fei Liu, Ziran Lou, Danjing Nie, Yamin Nong, Baoxuan Qiao, Weihua Wang, Shizhuang Wang, Yanyan Xing, Meng Yang, Qingwen Zhang, Lifang Zheng, Xiaoming |
| author_facet | Han, Zhenyun Li, Fei Qiao, Weihua Nong, Baoxuan Cheng, Yunlian Zhang, Lifang Huang, Jingfen Wang, Yanyan Lou, Danjing Ge, Jinyue Xing, Meng Fan, Weiya Nie, Yamin Guo, Wenlong Wang, Shizhuang Liu, Ziran Li, Danting Zheng, Xiaoming Yang, Qingwen |
| author_sort | Han, Zhenyun |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | The weedy rice (Oryza sativa f. spontanea) pericarp has diverse colors (e.g., purple, red, light-red, and white). However, research on pericarp colors has focused on red and purple, but not green. Unlike many other common weedy rice resources, LM8 has a green pericarp at maturity. In this study, the coloration of the LM8 pericarp was evaluated at the cellular and genetic levels. First, an examination of their ultrastructure indicated that LM8 chloroplasts were normal regarding plastid development and they contained many plastoglobules from the early immature stage to maturity. Analyses of transcriptome profiles and differentially expressed genes revealed that most chlorophyll (Chl) degradation-related genes in LM8 were expressed at lower levels than Chl a/b cycle-related genes in mature pericarps, suggesting that the green LM8 pericarp was associated with inhibited Chl degradation in intact chloroplasts. Second, the F2 generation derived from a cross between LM8 (green pericarp) and SLG (white pericarp) had a pericarp color segregation ratio of 9:3:4 (green:brown:white). The bulked segregant analysis of the F2 populations resulted in the identification of 12 known genes in the chromosome 3 and 4 hotspot regions as candidate genes related to Chl metabolism in the rice pericarp. The RNA-seq and sqRT-PCR assays indicated that the expression of the Chl a/b cycle-related structural gene DVR (encoding divinyl reductase) was sharply up-regulated. Moreover, genes encoding magnesium-chelatase subunit D and the light-harvesting Chl a/b-binding protein were transcriptionally active in the fully ripened dry pericarp. Regarding the ethylene signal transduction pathway, the CTR (encoding an ethylene-responsive protein kinase) and ERF (encoding an ethylene-responsive factor) genes expression profiles were determined. The findings of this study highlight the regulatory roles of Chl biosynthesis- and degradation-related genes influencing Chl accumulation during the maturation of the LM8 pericarp. |
| format | Journal Article |
| id | CGSpace164045 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | Frontiers Media |
| publisherStr | Frontiers Media |
| record_format | dspace |
| spelling | CGSpace1640452025-12-08T10:29:22Z Identification of candidate genes and clarification of the maintenance of the green pericarp of weedy rice grains Han, Zhenyun Li, Fei Qiao, Weihua Nong, Baoxuan Cheng, Yunlian Zhang, Lifang Huang, Jingfen Wang, Yanyan Lou, Danjing Ge, Jinyue Xing, Meng Fan, Weiya Nie, Yamin Guo, Wenlong Wang, Shizhuang Liu, Ziran Li, Danting Zheng, Xiaoming Yang, Qingwen plant science The weedy rice (Oryza sativa f. spontanea) pericarp has diverse colors (e.g., purple, red, light-red, and white). However, research on pericarp colors has focused on red and purple, but not green. Unlike many other common weedy rice resources, LM8 has a green pericarp at maturity. In this study, the coloration of the LM8 pericarp was evaluated at the cellular and genetic levels. First, an examination of their ultrastructure indicated that LM8 chloroplasts were normal regarding plastid development and they contained many plastoglobules from the early immature stage to maturity. Analyses of transcriptome profiles and differentially expressed genes revealed that most chlorophyll (Chl) degradation-related genes in LM8 were expressed at lower levels than Chl a/b cycle-related genes in mature pericarps, suggesting that the green LM8 pericarp was associated with inhibited Chl degradation in intact chloroplasts. Second, the F2 generation derived from a cross between LM8 (green pericarp) and SLG (white pericarp) had a pericarp color segregation ratio of 9:3:4 (green:brown:white). The bulked segregant analysis of the F2 populations resulted in the identification of 12 known genes in the chromosome 3 and 4 hotspot regions as candidate genes related to Chl metabolism in the rice pericarp. The RNA-seq and sqRT-PCR assays indicated that the expression of the Chl a/b cycle-related structural gene DVR (encoding divinyl reductase) was sharply up-regulated. Moreover, genes encoding magnesium-chelatase subunit D and the light-harvesting Chl a/b-binding protein were transcriptionally active in the fully ripened dry pericarp. Regarding the ethylene signal transduction pathway, the CTR (encoding an ethylene-responsive protein kinase) and ERF (encoding an ethylene-responsive factor) genes expression profiles were determined. The findings of this study highlight the regulatory roles of Chl biosynthesis- and degradation-related genes influencing Chl accumulation during the maturation of the LM8 pericarp. 2022-07-22 2024-12-19T12:53:22Z 2024-12-19T12:53:22Z Journal Article https://hdl.handle.net/10568/164045 en Open Access Frontiers Media Han, Zhenyun; Li, Fei; Qiao, Weihua; Nong, Baoxuan; Cheng, Yunlian; Zhang, Lifang; Huang, Jingfen; Wang, Yanyan; Lou, Danjing; Ge, Jinyue; Xing, Meng; Fan, Weiya; Nie, Yamin; Guo, Wenlong; Wang, Shizhuang; Liu, Ziran; Li, Danting; Zheng, Xiaoming and Yang, Qingwen. 2022. Identification of candidate genes and clarification of the maintenance of the green pericarp of weedy rice grains. Front. Plant Sci., Volume 13 |
| spellingShingle | plant science Han, Zhenyun Li, Fei Qiao, Weihua Nong, Baoxuan Cheng, Yunlian Zhang, Lifang Huang, Jingfen Wang, Yanyan Lou, Danjing Ge, Jinyue Xing, Meng Fan, Weiya Nie, Yamin Guo, Wenlong Wang, Shizhuang Liu, Ziran Li, Danting Zheng, Xiaoming Yang, Qingwen Identification of candidate genes and clarification of the maintenance of the green pericarp of weedy rice grains |
| title | Identification of candidate genes and clarification of the maintenance of the green pericarp of weedy rice grains |
| title_full | Identification of candidate genes and clarification of the maintenance of the green pericarp of weedy rice grains |
| title_fullStr | Identification of candidate genes and clarification of the maintenance of the green pericarp of weedy rice grains |
| title_full_unstemmed | Identification of candidate genes and clarification of the maintenance of the green pericarp of weedy rice grains |
| title_short | Identification of candidate genes and clarification of the maintenance of the green pericarp of weedy rice grains |
| title_sort | identification of candidate genes and clarification of the maintenance of the green pericarp of weedy rice grains |
| topic | plant science |
| url | https://hdl.handle.net/10568/164045 |
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