Transcriptome profiling of high and low somatic embryogenesis rate of oil palm (Elaeis guineensis Jacq. var. Tenera)
Oil palm micropropagation through tissue culture is a technique to provide elite oil palms to meet the desired traits. This technique is commonly carried out through somatic embryogenesis. However, the oil palm’s somatic embryogenesis rate is quite low. Several approaches have been made to overcome...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-05-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2023.1142868/full |
| _version_ | 1797828942796685312 |
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| author | Asri Sahara Roberdi Roberdi Ni Made Armini Wiendi Tony Liwang |
| author_facet | Asri Sahara Roberdi Roberdi Ni Made Armini Wiendi Tony Liwang |
| author_sort | Asri Sahara |
| collection | DOAJ |
| description | Oil palm micropropagation through tissue culture is a technique to provide elite oil palms to meet the desired traits. This technique is commonly carried out through somatic embryogenesis. However, the oil palm’s somatic embryogenesis rate is quite low. Several approaches have been made to overcome this problem, including transcriptome profiling through RNA-seq to identify key genes involved in oil palm somatic embryogenesis. RNA sequencing was applied in high- and low-embryogenic ortets of Tenera varieties based on the somatic embryoid rate at the callus, globular, scutellar, and coleoptilar embryoid stages. Cellular analysis of embryoid inductions and proliferations showed that high-embryogenic ortets resulted in higher embryoid proliferation and germinations than low-embryogenic ortets. Transcriptome profiling showed that there are a total of 1,911 differentially expressed genes (DEGs) between high- and low-embryogenic ortets. ABA signaling-related genes such as LEA, DDX28, and vicilin-like protein are upregulated in high-embryogenic ortets. Furthermore, DEGs associated with other hormone signaling, such as HD-ZIP associated with brassinosteroids and NPF associated with auxin, are upregulated in high-embryogenic ortets. This result suggests a physiological difference between high- and low-embryogenic ortets that is connected to their capacity for somatic embryogenesis. These DEGs will be used as potential biomarkers for high-embryogenic ortets and will be validated in further studies. |
| first_indexed | 2024-04-09T13:12:30Z |
| format | Article |
| id | doaj.art-83a2f0317545465b9af4245a381e42ed |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-09T13:12:30Z |
| publishDate | 2023-05-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-83a2f0317545465b9af4245a381e42ed2023-05-12T06:15:46ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2023-05-011410.3389/fpls.2023.11428681142868Transcriptome profiling of high and low somatic embryogenesis rate of oil palm (Elaeis guineensis Jacq. var. Tenera)Asri Sahara0Roberdi Roberdi1Ni Made Armini Wiendi2Tony Liwang3Biotechnology Department, Plant Production and Biotechnology Division, PT SMART Tbk, Bogor, IndonesiaBiotechnology Department, Plant Production and Biotechnology Division, PT SMART Tbk, Bogor, IndonesiaAgronomy and Horticulture Department, Agriculture Faculty, Bogor Agricultural University, Bogor, IndonesiaBiotechnology Department, Plant Production and Biotechnology Division, PT SMART Tbk, Bogor, IndonesiaOil palm micropropagation through tissue culture is a technique to provide elite oil palms to meet the desired traits. This technique is commonly carried out through somatic embryogenesis. However, the oil palm’s somatic embryogenesis rate is quite low. Several approaches have been made to overcome this problem, including transcriptome profiling through RNA-seq to identify key genes involved in oil palm somatic embryogenesis. RNA sequencing was applied in high- and low-embryogenic ortets of Tenera varieties based on the somatic embryoid rate at the callus, globular, scutellar, and coleoptilar embryoid stages. Cellular analysis of embryoid inductions and proliferations showed that high-embryogenic ortets resulted in higher embryoid proliferation and germinations than low-embryogenic ortets. Transcriptome profiling showed that there are a total of 1,911 differentially expressed genes (DEGs) between high- and low-embryogenic ortets. ABA signaling-related genes such as LEA, DDX28, and vicilin-like protein are upregulated in high-embryogenic ortets. Furthermore, DEGs associated with other hormone signaling, such as HD-ZIP associated with brassinosteroids and NPF associated with auxin, are upregulated in high-embryogenic ortets. This result suggests a physiological difference between high- and low-embryogenic ortets that is connected to their capacity for somatic embryogenesis. These DEGs will be used as potential biomarkers for high-embryogenic ortets and will be validated in further studies.https://www.frontiersin.org/articles/10.3389/fpls.2023.1142868/fulldifferentially expressed genesglobular embryoidhigh embryogenicoil palmsomatic embryogenesisRNA-seq |
| spellingShingle | Asri Sahara Roberdi Roberdi Ni Made Armini Wiendi Tony Liwang Transcriptome profiling of high and low somatic embryogenesis rate of oil palm (Elaeis guineensis Jacq. var. Tenera) Frontiers in Plant Science differentially expressed genes globular embryoid high embryogenic oil palm somatic embryogenesis RNA-seq |
| title | Transcriptome profiling of high and low somatic embryogenesis rate of oil palm (Elaeis guineensis Jacq. var. Tenera) |
| title_full | Transcriptome profiling of high and low somatic embryogenesis rate of oil palm (Elaeis guineensis Jacq. var. Tenera) |
| title_fullStr | Transcriptome profiling of high and low somatic embryogenesis rate of oil palm (Elaeis guineensis Jacq. var. Tenera) |
| title_full_unstemmed | Transcriptome profiling of high and low somatic embryogenesis rate of oil palm (Elaeis guineensis Jacq. var. Tenera) |
| title_short | Transcriptome profiling of high and low somatic embryogenesis rate of oil palm (Elaeis guineensis Jacq. var. Tenera) |
| title_sort | transcriptome profiling of high and low somatic embryogenesis rate of oil palm elaeis guineensis jacq var tenera |
| topic | differentially expressed genes globular embryoid high embryogenic oil palm somatic embryogenesis RNA-seq |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2023.1142868/full |
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