Transcriptome and Metabolome Analyses Reveals the Pathway and Metabolites of Grain Quality Under Phytochrome B in Rice (Oryza sativa L.)
Abstract Background Grain size and chalkiness is a critical agronomic trait affecting rice yield and quality. The application of transcriptomics to rice has widened the understanding of complex molecular responsive mechanisms, differential gene expression, and regulatory pathways under varying condi...
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| Format: | Article |
| Language: | English |
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SpringerOpen
2022-10-01
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| Series: | Rice |
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| Online Access: | https://doi.org/10.1186/s12284-022-00600-5 |
| _version_ | 1797991754414161920 |
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| author | Fei Li Ye Liu Xiaohua Zhang Lingzhi Liu Yun Yan Xin Ji Fanshu Kong Yafan Zhao Junzhou Li Ting Peng Hongzheng Sun Yanxiu Du Quanzhi Zhao |
| author_facet | Fei Li Ye Liu Xiaohua Zhang Lingzhi Liu Yun Yan Xin Ji Fanshu Kong Yafan Zhao Junzhou Li Ting Peng Hongzheng Sun Yanxiu Du Quanzhi Zhao |
| author_sort | Fei Li |
| collection | DOAJ |
| description | Abstract Background Grain size and chalkiness is a critical agronomic trait affecting rice yield and quality. The application of transcriptomics to rice has widened the understanding of complex molecular responsive mechanisms, differential gene expression, and regulatory pathways under varying conditions. Similarly, metabolomics has also contributed drastically for rice trait improvements. As master regulators of plant growth and development, phys influence seed germination, vegetative growth, photoperiodic flowering, shade avoidance responses. OsPHYB can regulate a variety of plant growth and development processes, but little is known about the roles of rice gene OsPHYB in modulating grain development. Results In this study, rice phytochrome B (OsPHYB) was edited using CRISPR/Cas9 technology. We found that OsPHYB knockout increased rice grain size and chalkiness, and increased the contents of amylose, free fatty acids and soluble sugar, while the gel consistency and contents of proteins were reduced in mutant grains. Furthermore, OsPHYB is involved in the regulation of grain size and chalk formation by controlling cell division and complex starch grain morphology. Transcriptomic analysis revealed that loss of OsPHYB function affects multiple metabolic pathways, especially enhancement of glycolysis, fatty acid, oxidative phosphorylation, and antioxidant pathways, as well as differential expression of starch and phytohormone pathways. An analysis of grain metabolites showed an increase in the free fatty acids and lysophosphatidylcholine, whereas the amounts of sugars, alcohols, amino acids and derivatives, organic acids, phenolic acids, alkaloids, nucleotides and derivatives, and flavonoids decreased, which were significantly associated with grain size and chalk formation. Conclusions Our study reveals that, OsPHYB plays an important regulatory role in the growth and development of rice grains, especially grain size and chalkiness. Furthermore, OsPHYB regulates grain size and chalkiness formation by affecting gene metabolism interaction network. Thus, this study not only revealed that OsPHYB plays a vital role in regulating grain size and chalkiness of rice but reveal new functions and highlighted the importance and value of OsPHYB in rice grain development and provide a new strategy for yield and quality improvement in rice breeding. |
| first_indexed | 2024-04-11T08:57:19Z |
| format | Article |
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| institution | Directory Open Access Journal |
| issn | 1939-8425 1939-8433 |
| language | English |
| last_indexed | 2024-04-11T08:57:19Z |
| publishDate | 2022-10-01 |
| publisher | SpringerOpen |
| record_format | Article |
| series | Rice |
| spelling | doaj.art-72f6b8c5ada2473f88d092492d7356242022-12-22T04:33:09ZengSpringerOpenRice1939-84251939-84332022-10-0115111910.1186/s12284-022-00600-5Transcriptome and Metabolome Analyses Reveals the Pathway and Metabolites of Grain Quality Under Phytochrome B in Rice (Oryza sativa L.)Fei Li0Ye Liu1Xiaohua Zhang2Lingzhi Liu3Yun Yan4Xin Ji5Fanshu Kong6Yafan Zhao7Junzhou Li8Ting Peng9Hongzheng Sun10Yanxiu Du11Quanzhi Zhao12Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural UniversityHenan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural UniversityHenan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural UniversityHenan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural UniversityHenan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural UniversityHenan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural UniversityHenan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural UniversityHenan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural UniversityHenan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural UniversityHenan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural UniversityHenan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural UniversityHenan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural UniversityHenan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural UniversityAbstract Background Grain size and chalkiness is a critical agronomic trait affecting rice yield and quality. The application of transcriptomics to rice has widened the understanding of complex molecular responsive mechanisms, differential gene expression, and regulatory pathways under varying conditions. Similarly, metabolomics has also contributed drastically for rice trait improvements. As master regulators of plant growth and development, phys influence seed germination, vegetative growth, photoperiodic flowering, shade avoidance responses. OsPHYB can regulate a variety of plant growth and development processes, but little is known about the roles of rice gene OsPHYB in modulating grain development. Results In this study, rice phytochrome B (OsPHYB) was edited using CRISPR/Cas9 technology. We found that OsPHYB knockout increased rice grain size and chalkiness, and increased the contents of amylose, free fatty acids and soluble sugar, while the gel consistency and contents of proteins were reduced in mutant grains. Furthermore, OsPHYB is involved in the regulation of grain size and chalk formation by controlling cell division and complex starch grain morphology. Transcriptomic analysis revealed that loss of OsPHYB function affects multiple metabolic pathways, especially enhancement of glycolysis, fatty acid, oxidative phosphorylation, and antioxidant pathways, as well as differential expression of starch and phytohormone pathways. An analysis of grain metabolites showed an increase in the free fatty acids and lysophosphatidylcholine, whereas the amounts of sugars, alcohols, amino acids and derivatives, organic acids, phenolic acids, alkaloids, nucleotides and derivatives, and flavonoids decreased, which were significantly associated with grain size and chalk formation. Conclusions Our study reveals that, OsPHYB plays an important regulatory role in the growth and development of rice grains, especially grain size and chalkiness. Furthermore, OsPHYB regulates grain size and chalkiness formation by affecting gene metabolism interaction network. Thus, this study not only revealed that OsPHYB plays a vital role in regulating grain size and chalkiness of rice but reveal new functions and highlighted the importance and value of OsPHYB in rice grain development and provide a new strategy for yield and quality improvement in rice breeding.https://doi.org/10.1186/s12284-022-00600-5OsPHYBChalkinessGrain sizeTranscriptomeMetabolomeCorrelation analysis |
| spellingShingle | Fei Li Ye Liu Xiaohua Zhang Lingzhi Liu Yun Yan Xin Ji Fanshu Kong Yafan Zhao Junzhou Li Ting Peng Hongzheng Sun Yanxiu Du Quanzhi Zhao Transcriptome and Metabolome Analyses Reveals the Pathway and Metabolites of Grain Quality Under Phytochrome B in Rice (Oryza sativa L.) Rice OsPHYB Chalkiness Grain size Transcriptome Metabolome Correlation analysis |
| title | Transcriptome and Metabolome Analyses Reveals the Pathway and Metabolites of Grain Quality Under Phytochrome B in Rice (Oryza sativa L.) |
| title_full | Transcriptome and Metabolome Analyses Reveals the Pathway and Metabolites of Grain Quality Under Phytochrome B in Rice (Oryza sativa L.) |
| title_fullStr | Transcriptome and Metabolome Analyses Reveals the Pathway and Metabolites of Grain Quality Under Phytochrome B in Rice (Oryza sativa L.) |
| title_full_unstemmed | Transcriptome and Metabolome Analyses Reveals the Pathway and Metabolites of Grain Quality Under Phytochrome B in Rice (Oryza sativa L.) |
| title_short | Transcriptome and Metabolome Analyses Reveals the Pathway and Metabolites of Grain Quality Under Phytochrome B in Rice (Oryza sativa L.) |
| title_sort | transcriptome and metabolome analyses reveals the pathway and metabolites of grain quality under phytochrome b in rice oryza sativa l |
| topic | OsPHYB Chalkiness Grain size Transcriptome Metabolome Correlation analysis |
| url | https://doi.org/10.1186/s12284-022-00600-5 |
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