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Journal : 3BIO: Journal of Biological Science, Technology and Management

The Primer Design and Optimization of Annealing Temperature for Analysis of Glutathione Reductase Gene Expression in Rice (Oryza sativa L.) Annisa Khaira; Afifatul Achyar; Zulyusri Zulyusri; Yusni Atifah; Dwi Hilda Putri; Violita Violita
3BIO: Journal of Biological Science, Technology and Management Vol. 5 No. 1 (2023)
Publisher : School of Life Sciences and Technology, Institut Teknologi Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.5614/3bio.2023.5.1.3

Abstract

Glutathione Reductase (GR) belongs to the NADPH-dependent flavoprotein oxidoreductase family and is found in both prokaryotes and eukaryotes. The GR gene is considered to play a key role in the elimination of oxidative reaction products by looking at the level of gene expression of GR rice in dealing with  drought stress using qPCR. One of the important steps to develop a specific, effective and efficient qPCR is the primer design. Several studies analyzing GR gene expression in rice have also designed primers. However, the primer still lacks an ideal characteristic of primer, as it still has a secondary structure. This studies aims to design rice GR specific primers and optimize the annealing temperature for GR gene expression analysis on rice. Primers were designed using the  Primer3 and Geneious Prime and checked for specificity using the Primer-BLAST tool. The selected primer pairs were then optimized for annealing  temperature using gradient PCR. The best primer design results were GR-Forward 5’-ACGATTGCAGCCAGTGAAGA-3’ and GR-Reverse 5’-TGCGGCAATACTATCAACATCC-3’, with an amplicon length of 204 bp, primer base lengths of 20 and 22 nucleotides, Tm values of 60°C and 58.9°C, %GC of 50% and 45.5%, respectively. This primer pair had no secondary structure, both hairpin and self dimer. Gradient PCR showed the optimum annealing temperature for this primer pair was 52.2oC so that the primer can be used as a specific primer to analyze  the GR gene expression in rice using qPCR.
Co-Authors Abdul Razak Abdul Razak Abubakar Abubakar Achyar, Afifatul Adinda, Diva Afrilliana, Friska Akbar, Imam Qodri Alsya Az Zahra Amalia, Windi Aprila Amsar Maulana Annisa Khaira Annisa Khaira Ardelia Febriana Ardi Ardi Arianti, Riri Putri Ayesa, Putri Az Zahra, Alsya Az zahra, Firda Azeli, Saskia Putri Azizah Mutmainah BR Tarigan, Siti Nadiah Zahra Dadang Mulyadi Saleh Des M Dezi Handayani Diana, Okta Dilla Wirmaningsih Dwi Hilda Putri Dwi Hilda Putri Dwi Junita Zega Elsa Badriyya Elsa Yuniarti Elwidani Siregar Fadhil Ramadhan, Bintang Fadika Hayyuni Fadillaturahmah, Fadillaturahmah Fathimah Azzahra Fatma Suryani Harahap Febi Permata Jingga Febiola, Cantika Riski Feby Djumaita Sari Ferix Riskierdi Fevria, Resti Fitra Arya Dwi Nugraha Fitra Nugraha, Fitra Fitri Agustina Lubis Fitri Arsih Fitria, Davina Foarota Harefa Fuadiyah, Sa’diyatul Fuji Zahara Zahara Gilang Amanda Gilang Amanda Hafizh Alza Afra Hafizh Alza Afra Hayu, Elvira Heffi Alberida Helendra Helendra . Helendra Helendra Helka Yuliati Helsa Rahmatika Hendro Pramono Iqra, Kuntum Nurul Irma Leilani Eka Putri Irma Leilani Eka Putri Iskandar Safri Hasibuan Iskandar Safri Hasibuan Jalilah Azizah Jalilah Azizah Lubis Jumatul Hafsah Keiko Kasy Billah Keiko Kasy Billah Khairunisa Khairunisa Kurnia, Aifa LAILA TUSSIFAH LUBIS Linda Advinda Lufri Lufri Marten, Threo Wanda Maulina, Adinda Rizky Mayang Anazalia Meilani Syaiful Meisya, Divia Yuda Melvariani Syari Batubara Miftahul Jannah Mita Ariani Monica, Della Trya Moralita Chatri Mutia, Ravena Mutiara Ghina Mutiara Lubis Nabila Latu Fany Najib Rahman. G Nella Fauziah Nurmaini Ginting Nurul Fathya NURUL HIDAYAH Nurul Hiza Putri Nurul Ilma Septiani Pasaribu, Surya Elita Putri Andriani Putri, Irma Leilani Eka Putri, Isna Aryunita Putri Putri, Nurul Hiza Rahma Amelia, Anisha Chahya Rahmadhani Fitri Rahmawati Darussyamsu Rahmi Holinesti Rahmi Suci Nadira Rani Mauliza Relsas Yogica, Relsas Reza Sapitri Rezi Nabilah Richi, Qori Dwi Rijal Satria Riri Putri Arianti Ristiono Ristiono Ristiono Ristiono S. Syamsurizal Sa'diatul Fuadiyah Sa'diah, Jihan Natul Sa'diah Sa’diyatul Fuadiyah safitri, fira Sahlan Tuah Saldi, Andini Putri Salsabila Juita Samsiah Samsiah Sandi Fransisco Satria, Rijal Sa’diatul Fuadiyah Silvira Ilhami Suci Fajrina Surya Elita Pasaribu Syamsurizal, S. Titisna Gumarni Vauzia Vauzia Vauzia, Vauzia Vauzia, Vauzia Verina, Farhanah Shofwah Violita Violita Violita Violita Violita Violita Widya Gusti Rahmawati D. Wulandari Wulandari Yogi Saputra, Yogi Yulia Sistina Yuliati, Netri Yuni Ahda Yuni Ahda Zahra, Fauziah Az Zega, Dwi Junita Zulfahmi Zulfahmi Zulhandri Zulhandri Zulyusri Zulyusri Zulyusri Zulyusri Zulyusri, Zulyusri Zulzusri, Zulzusri