Spatiotemporal expression profile of novel and known small RNAs throughout rice plant development focussing on seed tissues
Abstract Background Small RNAs (sRNAs) regulate numerous plant processes directly related to yield, such as disease resistance and plant growth. To exploit this yield-regulating potential of sRNAs, the sRNA profile of one of the world’s most important staple crops – rice – was investigated throughou...
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| Format: | Article |
| Language: | English |
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BMC
2022-01-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-021-08264-z |
| _version_ | 1828138459109261312 |
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| author | Anikó Meijer Tim De Meyer Klaas Vandepoele Tina Kyndt |
| author_facet | Anikó Meijer Tim De Meyer Klaas Vandepoele Tina Kyndt |
| author_sort | Anikó Meijer |
| collection | DOAJ |
| description | Abstract Background Small RNAs (sRNAs) regulate numerous plant processes directly related to yield, such as disease resistance and plant growth. To exploit this yield-regulating potential of sRNAs, the sRNA profile of one of the world’s most important staple crops – rice – was investigated throughout plant development using next-generation sequencing. Results Root and leaves were investigated at both the vegetative and generative phase, and early-life sRNA expression was characterized in the embryo and endosperm. This led to the identification of 49,505 novel sRNAs and 5581 tRNA-derived sRNAs (tsRNAs). In all tissues, 24 nt small interfering RNAs (siRNAs) were highly expressed and associated with euchromatic, but not heterochromatic transposable elements. Twenty-one nt siRNAs deriving from genic regions in the endosperm were exceptionally highly expressed, mimicking previously reported expression levels of 24 nt siRNAs in younger endosperm samples. In rice embryos, sRNA content was highly diverse while tsRNAs were underrepresented, possibly due to snoRNA activity. Publicly available mRNA expression and DNA methylation profiles were used to identify putative siRNA targets in embryo and endosperm. These include multiple genes related to the plant hormones gibberellic acid and ethylene, and to seed phytoalexin and iron content. Conclusions This work introduces multiple sRNAs as potential regulators of rice yield and quality, identifying them as possible targets for the continuous search to optimize rice production. |
| first_indexed | 2024-04-11T18:37:12Z |
| format | Article |
| id | doaj.art-18e6de63380e47119c51b2d071a5b038 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-11T18:37:12Z |
| publishDate | 2022-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-18e6de63380e47119c51b2d071a5b0382022-12-22T04:09:13ZengBMCBMC Genomics1471-21642022-01-0123111710.1186/s12864-021-08264-zSpatiotemporal expression profile of novel and known small RNAs throughout rice plant development focussing on seed tissuesAnikó Meijer0Tim De Meyer1Klaas Vandepoele2Tina Kyndt3Department of Biotechnology, Ghent UniversityDepartment of Data Analysis and Mathematical Modelling, Ghent UniversityDepartment of Plant Biotechnology and Bioinformatics, Ghent UniversityDepartment of Biotechnology, Ghent UniversityAbstract Background Small RNAs (sRNAs) regulate numerous plant processes directly related to yield, such as disease resistance and plant growth. To exploit this yield-regulating potential of sRNAs, the sRNA profile of one of the world’s most important staple crops – rice – was investigated throughout plant development using next-generation sequencing. Results Root and leaves were investigated at both the vegetative and generative phase, and early-life sRNA expression was characterized in the embryo and endosperm. This led to the identification of 49,505 novel sRNAs and 5581 tRNA-derived sRNAs (tsRNAs). In all tissues, 24 nt small interfering RNAs (siRNAs) were highly expressed and associated with euchromatic, but not heterochromatic transposable elements. Twenty-one nt siRNAs deriving from genic regions in the endosperm were exceptionally highly expressed, mimicking previously reported expression levels of 24 nt siRNAs in younger endosperm samples. In rice embryos, sRNA content was highly diverse while tsRNAs were underrepresented, possibly due to snoRNA activity. Publicly available mRNA expression and DNA methylation profiles were used to identify putative siRNA targets in embryo and endosperm. These include multiple genes related to the plant hormones gibberellic acid and ethylene, and to seed phytoalexin and iron content. Conclusions This work introduces multiple sRNAs as potential regulators of rice yield and quality, identifying them as possible targets for the continuous search to optimize rice production.https://doi.org/10.1186/s12864-021-08264-zOryza sativaEmbryoEndospermSeedSmall RNAsiRNA |
| spellingShingle | Anikó Meijer Tim De Meyer Klaas Vandepoele Tina Kyndt Spatiotemporal expression profile of novel and known small RNAs throughout rice plant development focussing on seed tissues BMC Genomics Oryza sativa Embryo Endosperm Seed Small RNA siRNA |
| title | Spatiotemporal expression profile of novel and known small RNAs throughout rice plant development focussing on seed tissues |
| title_full | Spatiotemporal expression profile of novel and known small RNAs throughout rice plant development focussing on seed tissues |
| title_fullStr | Spatiotemporal expression profile of novel and known small RNAs throughout rice plant development focussing on seed tissues |
| title_full_unstemmed | Spatiotemporal expression profile of novel and known small RNAs throughout rice plant development focussing on seed tissues |
| title_short | Spatiotemporal expression profile of novel and known small RNAs throughout rice plant development focussing on seed tissues |
| title_sort | spatiotemporal expression profile of novel and known small rnas throughout rice plant development focussing on seed tissues |
| topic | Oryza sativa Embryo Endosperm Seed Small RNA siRNA |
| url | https://doi.org/10.1186/s12864-021-08264-z |
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