Perancangan Primer Gen Toleransi Salinitas pada Tanaman Padi (Oryza sativa L.) Sebagai Dasar Validasi Ekspresi Gen Berbasis qPCR

Ramadhan, Muhammad Gilang (2026) Perancangan Primer Gen Toleransi Salinitas pada Tanaman Padi (Oryza sativa L.) Sebagai Dasar Validasi Ekspresi Gen Berbasis qPCR. Other thesis, Institut Teknologi Sepuluh Nopember.

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Abstract

Faktor transkripsi NAC merupakan salah satu famili gen penting yang berperan dalam regulasi respons cekaman abiotik pada tanaman padi (Oryza sativa L.). Analisis ekspresi gen NAC memerlukan primer PCR yang spesifik dan efisien untuk menghasilkan data molekuler yang akurat. Penelitian ini bertujuan untuk merancang dan mengevaluasi primer gen OsNAC4 dan OsNAC19 secara in silico sebagai dasar analisis ekspresi gen terkait toleransi cekaman pada padi. Desain primer dilakukan menggunakan pendekatan bioinformatika dengan mempertimbangkan parameter utama primer PCR, meliputi panjang sekuens, suhu leleh (Tm), kandungan GC, nilai self-complementarity, serta ukuran produk amplifikasi. Hasil menunjukkan bahwa primer OsNAC4 memiliki panjang 20–21 nukleotida dengan Tm sekitar 60 °C, kandungan GC 52,38–55,00%, dan menghasilkan produk amplifikasi sepanjang 121 bp. Sementara itu, primer OsNAC19 memiliki panjang 20 nukleotida, Tm ±60 °C, kandungan GC 55,00–60,00%, serta menghasilkan produk amplifikasi sepanjang 107 bp. Analisis in silico PCR menunjukkan bahwa kedua pasangan primer hanya menghasilkan satu pita amplifikasi pada target transkrip masing-masing, menegaskan tingkat spesifisitas yang tinggi tanpa indikasi amplifikasi nonspesifik. Nilai self-complementarity dan self 3′-complementarity yang rendah pada seluruh primer mengindikasikan risiko minimal terbentuknya primer dimer dan struktur sekunder. Dengan demikian, primer OsNAC4 dan OsNAC19 yang dirancang dalam penelitian ini dinilai layak dan andal untuk digunakan pada analisis ekspresi gen menggunakan PCR konvensional maupun RT-qPCR, serta mendukung penelitian lanjutan mengenai peran gen NAC dalam respons cekaman abiotik pada tanaman padi.
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Transcription factor NAC is one of the important gene families involved in the regulation of abiotic stress responses in rice plants (Oryza sativa L.). Analysis of NAC gene expression requires specific and efficient PCR primers to generate accurate molecular data. This study aimed to design and evaluate primers for the OsNAC4 and OsNAC19 genes in silico as a basis for gene expression analysis related to stress tolerance in rice. Primer design was performed using a bioinformatics approach by considering the main PCR primer parameters, including sequence length, melting temperature (Tm), GC content, self-complementarity values, and amplification product size. The results showed that the OsNAC4 primers had a length of 20–21 nucleotides with a Tm of approximately 60 °C, GC content of 52.38–55.00%, and produced an amplification product of 121 bp. Meanwhile, the OsNAC19 primers had a length of 20 nucleotides, a Tm of approximately 60 °C, GC content of 55.00–60.00%, and produced an amplification product of 107 bp. In silico PCR analysis demonstrated that both primer pairs generated only a single amplification band for their respective target transcripts, confirming high specificity without indications of nonspecific amplification. Low self-complementarity and self 3′-complementarity values for all primers indicate a minimal risk of primer dimer formation and secondary structures. Therefore, the OsNAC4 and OsNAC19 primers designed in this study are considered suitable and reliable for use in gene expression analysis using conventional PCR and RT-qPCR, and they support further research on the role of NAC genes in abiotic stress responses in rice plants.

Item Type:	Thesis (Other)
Uncontrolled Keywords:	Cekaman Salinitas, OsNAC4, OsNAC19, Oryza sativa, qPCR, Salinity Stress, OsNAC4, OsNAC19, Oryza sativa, qPCR
Subjects:	Q Science Q Science > QH Biology Q Science > QK Botany Q Science > QK Botany > QK754.7.D75 Droughts. Drought tolerance Q Science > QK Botany > QK870 Plant-water relationships Q Science > QR Microbiology
Divisions:	Faculty of Mathematics and Science > Biology > 46201-(S1) Undergraduate Thesis Faculty of Science and Data Analytics (SCIENTICS) > Biology > 46201-(S1) Undergraduate Thesis
Depositing User:	Muhammad Gilang Ramadhan
Date Deposited:	03 Feb 2026 04:06
Last Modified:	03 Feb 2026 04:06
URI:	http://repository.its.ac.id/id/eprint/131916

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