Analisis In Silico Data Transkriptomik Famili Gen NAC pada Padi (Oryza sativa L.) Terinduksi Kekeringan dan Salinitas

Ahmadi, Bihar Hikam (2025) Analisis In Silico Data Transkriptomik Famili Gen NAC pada Padi (Oryza sativa L.) Terinduksi Kekeringan dan Salinitas. Other thesis, Institut Teknologi Sepuluh Nopember.

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Abstract

Padi (Oryza sativa L.) merupakan tanaman pangan utama yang menjadi sumber makanan pokok bagi sebagian besar populasi dunia. Namun, produktivitas padi menghadapi tantangan besar akibat cekaman abiotik seperti kekeringan dan salinitas yang dapat menurunkan hasil panen dan berdampak pada ketahanan pangan global. Salah satu mekanisme pertahanan tanaman terhadap cekaman tersebut melibatkan faktor transkripsi yang berfungsi mentransduksi sinyal stres menjadi aktivasi gen-gen responsif. Keluarga gen NAC (NAM, ATAF1/2, CUC) diketahui berperan penting dalam merespons berbagai jenis cekaman abiotik. Analisis transkriptomik secara in silico memungkinkan eksplorasi ekspresi gen secara menyeluruh untuk mengidentifikasi mekanisme molekuler yang mendasari respons tanaman terhadap cekaman. Penelitian ini bertujuan untuk menganalisis data transkriptomik secara in silico untuk mengeksplorasi respons gen NAC pada padi varietas Pokkali dan N22 yang terpapar kekeringan dan salinitas. Analisis dilakukan melalui identifikasi differentially expressed genes (DEG), analisis SNP pada gen, protein, dan promotor, prediksi elemen cis pada daerah promotor, serta analisis filogenetik. Hasil analisis DEG menunjukkan bahwa varietas N22 memiliki 8.891 gen yang terekspresi signifikan (4.526 upregulated dan 4.365 downregulated), sedangkan Pokkali memiliki 2.081 gen (1.201 upregulated dan 880 downregulated). Ditemukan empat gen NAC yang terekspresi pada kedua varietas, yaitu LOC_Os01g60020, LOC_Os03g60080, LOC_Os07g12340, dan LOC_Os11g05614. Di antara keempatnya, LOC_Os03g60080 dipilih untuk dianalisis lebih lanjut karena menunjukkan pola ekspresi yang konsisten meningkat dikeduanya serta berlokasi di nukleus. Analisis SNP gen menunjukkan satu mutasi sinonim di daerah CDS. Sedangkan analisis SNP pada promotor (0–2000 bp upstream) diperoleh 12 SNP yang berpotensi memengaruhi ekspresi gen. Analisis elemen cis-regulatori menemukan lima cis elemen (DPBFCOREDCDC3, GT1GMSCAM4, MYCCONSENSUSAT, RAV1AAT, MYCATERD1) lebih banyak pada varietas Pokkali dan N22 dibandingkan Nipponbare, yang kemungkinan berkontribusi terhadap peningkatan ekspresi gen dalam kondisi cekaman. Analisis filogenetik juga menunjukkan bahwa LOC_Os03g60080 berkerabat dekat dengan LOC_Os01g60020, LOC_Os07g12340 AT5G08790, dan AT5G63790 yang diduga berfungsi dalam regulasi cekaman kekeringan dan salinitas.
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Rice (Oryza sativa L.) is a major food crop and serves as the staple food for a large portion of the global population. However, rice productivity faces significant challenges due to abiotic stresses such as drought and salinity, which can reduce crop yields and threaten global food security. One of the plant’s defense mechanisms against such stresses involves transcription factors, which function to transduce stress signals into the activation of responsive genes. The NAC (NAM, ATAF1/2, CUC) gene family is known to play a crucial role in responding to various abiotic stresses. In silico transcriptomic analysis enables comprehensive exploration of gene expression to identify the molecular mechanisms underlying plant stress responses. This study aims to analyze transcriptomic data in silico to explore the response of NAC genes in rice varieties Pokkali and N22 under drought and salinity stress. The analysis includes identification of differentially expressed genes (DEGs), SNP analysis of genes, proteins, and promoters, prediction of cis-regulatory elements in promoter regions, and phylogenetic analysis. The DEG analysis revealed that the N22 variety had 8,891 significantly expressed genes (4,526 upregulated and 4,365 downregulated), while Pokkali had 2,081 genes (1,201 upregulated and 880 downregulated). Four NAC genes were found to be expressed in both varieties, namely LOC_Os01g60020, LOC_Os03g60080, LOC_Os07g12340, and LOC_Os11g05614. Among them, LOC_Os03g60080 was selected for further analysis due to its consistently increased expression in both varieties and its predicted nuclear localization. SNP analysis of the gene revealed one synonymous mutation in the CDS region. Meanwhile, SNP analysis of the promoter region (0–2000 bp upstream) identified 12 SNPs that may affect gene expression. The cis-regulatory element analysis found five elements (DPBFCOREDCDC3, GT1GMSCAM4, MYCCONSENSUSAT, RAV1AAT, MYCATERD1) that were more abundant in Pokkali and N22 compared to the reference variety Nipponbare, potentially contributing to increased gene expression under stress conditions. Phylogenetic analysis also showed that LOC_Os03g60080 is closely related to LOC_Os01g60020, AT5G08790, and AT5G63790, which are suspected to function in regulating drought and salinity stress responses.

Item Type:	Thesis (Other)
Uncontrolled Keywords:	Cekaman Kekeringan, Cekaman Salinitas, In Silico, Padi, Transkriptomik Drought Stress, In Silico, Rice Plant, Salinity Stress, Transcriptomic
Subjects:	Q Science > QK Botany > QK754.7.D75 Droughts. Drought tolerance Q Science > QP Physiology > QP624 Molecular biology.
Divisions:	Faculty of Science and Data Analytics (SCIENTICS) > Biology > 46201-(S1) Undergraduate Thesis
Depositing User:	Bihar Hikam Ahmadi
Date Deposited:	01 Aug 2025 01:25
Last Modified:	01 Aug 2025 01:25
URI:	http://repository.its.ac.id/id/eprint/124608

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