Wardhani, Fila Oxi (2021) Identifikasi In Silico Dan Profil Ekspresi Gen Famili NB-ARC Yang Berpotensi Sebagai Penanda Ketahanan Padi Dalam Cekaman Salinitas. Masters thesis, Institut Teknologi Sepuluh Nopember.
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Abstract
Padi merupakan tanaman pangan yang penting di dunia, terutama bagi penduduk negara Asia, khususnya penduduk Indonesia. Berkurangnya produksi padi akibat cekaman salinitas dapat diatasi dengan pengembangan bibit padi unggul, dan strategi ini dapat diawali dengan pengembangan gen penanda/marka padi tahan salinitas. Berdasarkan penelitian sebelumnya, kelompok gen NB-ARC merupakan kelompok gen yang sering digunakan untuk marka pada cekaman biotik. Namun sejauh ini belum banyak terdapat informasi mengenai potensi kelompok gen NB-ARC sebagai marka pada cekaman abiotik. Tujuan penelitian ini yaitu untuk mengetahui kandidat gen dari kelompok gen NB-ARC yang berpotensi sebagai marka molekuler pada cekaman salinitas. Metode yang digunakan pada penelitian ini yaitu: (1) melakukan pengolahan data secara in silico untuk mengidentifikasi kandidat gen dari kelompok NB-ARC sebagai marka molekuler; dan (2) melakukan validasi melalui studi ekspresi dengan metode real-time PCR untuk mengetahui tingkat ekspresi kandidat gen penanda dari kelompok NB-ARC pada padi tercekam salinitas. Berdasarkan hasil analisis heatmap pada parameter panjang akar dan tinggi tanaman, Inpari 35 merupakan varietas yang paling tahan terhadap cekaman salinitas. Sedangkan berdasarkan hasil analisis in silico didapatkan 3 kandidat gen penanda yaitu gen 24 (LOC_Os01g52304), 15 (LOC_Os11g38000), dan 7 (LOC_Os01g52270). Hasil validasi menggunakan metode real-time PCR menunjukkan bahwa ketiga gen mengalami kenaikan tingkat ekspresi relatif pada hari ke-3 dan penurunan tingkat ekspresi relatif pada hari ke-6.
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Rice is an important food crop in the world, especially in Asian countries. Unfortunately, there are many cases which current average crop yield is lower than its potential. Reduced rice production due to salinity stress can be handled by developing rice seedlings that are resistant to salinity stress, and this strategy can be initiated by developing a marker gene for salinity resistance. Based on previous study, NB-ARC gene family are often used for markers in biotic stress. However, so far there is not much information regarding the potential of the NB-ARC gene family as a marker for abiotic stress. The aim of this study was to determine candidate genes from the NB-ARC gene family that have potential as molecular markers on salinity stress. The methods used in this study were: (1) expression pattern identification of the NB-ARC gene family using in silico approach to determine its potential as molecular markers; (2) validation through gene expression studies using real-time PCR method to determine the expression level of candidate marker genes from NB-ARC family group in salinity stressed rice. The results of morphological observations showed that Inpari 35 was the most resistant variant to salinity stress, based on the heatmap analysis of the root length and plant height parameters. Moreover, three candidate marker genes were found based on silico study, which are gene 24 (LOC_Os01g52304), 15 (LOC_Os11g38000), and 7 (LOC_Os01g52270). The validation results using real-time PCR method showed that relative expression level from all three genes increase on day 3 then decrease on day 6.
| Item Type: | Thesis (Masters) |
|---|---|
| Uncontrolled Keywords: | Cekaman salinitas, gen famili NB-ARC, gen marka, padi, real-time PCR. marker gene, NB-ARC gene family, rice, real-time PCR, salinity stress. |
| Subjects: | Q Science > Q Science (General) Q Science > QH Biology > QH301 Biology Q Science > QK Botany > QK710 Plant physiology Q Science > QP Physiology > QP624 Molecular biology. |
| Divisions: | Faculty of Science and Data Analytics (SCIENTICS) > Biology > 46101-(S2) Master Thesis |
| Depositing User: | Fila Oxi Wardhani |
| Date Deposited: | 24 Aug 2021 10:32 |
| Last Modified: | 24 Aug 2021 10:32 |
| URI: | http://repository.its.ac.id/id/eprint/87066 |
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