Gene Expression in the Developing Seed of Wild and Domesticated Rice
The composition and nutritional properties of rice are the product of the expression of genes in the developing seed. RNA-Seq was used to investigate the level of gene expression at different stages of seed development in domesticated rice (<i>Oryza sativa</i> ssp. <i>japonica</...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-11-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/23/21/13351 |
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| author | Sharmin Hasan Agnelo Furtado Robert Henry |
| author_facet | Sharmin Hasan Agnelo Furtado Robert Henry |
| author_sort | Sharmin Hasan |
| collection | DOAJ |
| description | The composition and nutritional properties of rice are the product of the expression of genes in the developing seed. RNA-Seq was used to investigate the level of gene expression at different stages of seed development in domesticated rice (<i>Oryza sativa</i> ssp. <i>japonica</i> var. Nipponbare) and two Australian wild taxa from the primary gene pool of rice (<i>Oryza meridionalis</i> and <i>Oryza rufipogon</i> type taxa). Transcriptome profiling of all coding sequences in the genome revealed that genes were significantly differentially expressed at different stages of seed development in both wild and domesticated rice. Differentially expressed genes were associated with metabolism, transcriptional regulation, nucleic acid processing, and signal transduction with the highest number of being linked to protein synthesis and starch/sucrose metabolism. The level of gene expression associated with domestication traits, starch and sucrose metabolism, and seed storage proteins were highest at the early stage (5 days post anthesis (DPA)) to the middle stage (15 DPA) and declined late in seed development in both wild and domesticated rice. However, in contrast, black hull colour (<i>Bh4</i>) gene was significantly expressed throughout seed development. A substantial number of novel transcripts (38) corresponding to domestication genes, starch and sucrose metabolism, and seed storage proteins were identified. The patterns of gene expression revealed in this study define the timing of metabolic processes associated with seed development and may be used to explain differences in rice grain quality and nutritional value. |
| first_indexed | 2024-03-09T18:59:16Z |
| format | Article |
| id | doaj.art-1388fa30871d49e584e5f19b104bca9f |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T18:59:16Z |
| publishDate | 2022-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-1388fa30871d49e584e5f19b104bca9f2023-11-24T05:06:30ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-11-0123211335110.3390/ijms232113351Gene Expression in the Developing Seed of Wild and Domesticated RiceSharmin Hasan0Agnelo Furtado1Robert Henry2Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, AustraliaQueensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, AustraliaQueensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, AustraliaThe composition and nutritional properties of rice are the product of the expression of genes in the developing seed. RNA-Seq was used to investigate the level of gene expression at different stages of seed development in domesticated rice (<i>Oryza sativa</i> ssp. <i>japonica</i> var. Nipponbare) and two Australian wild taxa from the primary gene pool of rice (<i>Oryza meridionalis</i> and <i>Oryza rufipogon</i> type taxa). Transcriptome profiling of all coding sequences in the genome revealed that genes were significantly differentially expressed at different stages of seed development in both wild and domesticated rice. Differentially expressed genes were associated with metabolism, transcriptional regulation, nucleic acid processing, and signal transduction with the highest number of being linked to protein synthesis and starch/sucrose metabolism. The level of gene expression associated with domestication traits, starch and sucrose metabolism, and seed storage proteins were highest at the early stage (5 days post anthesis (DPA)) to the middle stage (15 DPA) and declined late in seed development in both wild and domesticated rice. However, in contrast, black hull colour (<i>Bh4</i>) gene was significantly expressed throughout seed development. A substantial number of novel transcripts (38) corresponding to domestication genes, starch and sucrose metabolism, and seed storage proteins were identified. The patterns of gene expression revealed in this study define the timing of metabolic processes associated with seed development and may be used to explain differences in rice grain quality and nutritional value.https://www.mdpi.com/1422-0067/23/21/13351gene expressionRNA-Seqseed developmentdifferentially expressed genesdomestication locistarch and sucrose metabolism |
| spellingShingle | Sharmin Hasan Agnelo Furtado Robert Henry Gene Expression in the Developing Seed of Wild and Domesticated Rice International Journal of Molecular Sciences gene expression RNA-Seq seed development differentially expressed genes domestication loci starch and sucrose metabolism |
| title | Gene Expression in the Developing Seed of Wild and Domesticated Rice |
| title_full | Gene Expression in the Developing Seed of Wild and Domesticated Rice |
| title_fullStr | Gene Expression in the Developing Seed of Wild and Domesticated Rice |
| title_full_unstemmed | Gene Expression in the Developing Seed of Wild and Domesticated Rice |
| title_short | Gene Expression in the Developing Seed of Wild and Domesticated Rice |
| title_sort | gene expression in the developing seed of wild and domesticated rice |
| topic | gene expression RNA-Seq seed development differentially expressed genes domestication loci starch and sucrose metabolism |
| url | https://www.mdpi.com/1422-0067/23/21/13351 |
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