Claim Missing Document
Check
Articles

Improved Performance of SiDREB2-SNAP Marker in Foxtail Millet by Optimum Primer Concentration, PCR Cycle, and DNA Polymerase Specificity Wospakrik, Andrean Heskiel; Rizqullah, Ramadaniarto; Pahlevi, M Reza; Yudiansyah, Yudiansyah; Purwoko, Bambang Sapta; Suwarno, Willy Bayuardi; ARDIE, Sintho Wahyuning
Journal of Tropical Crop Science Vol. 13 No. 01 (2026): Journal of Tropical Crop Science
Publisher : Department of Agronomy and Horticulture, IPB University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29244/jtcs.13.01.103-113

Abstract

Foxtail millet (Setaria italica L. Beauv.) is an emerging carbohydrate-producing crop. It is considered a climate-resilient crop due to its tolerance to abiotic stresses. Breeding for abiotic-tolerant crops requires powerful tools such as molecular markers. The single-nucleotide amplified polymorphism (SNAP) marker, developed from a single-nucleotide DNA variation at a specific location in the plant genome, is a simple yet powerful PCR-based marker widely used in phenotype-related selection. A SiDREB2-based SNAP marker was previously developed based on a base variation at the 558th base pair (an A/G transition) in the SiDREB2 gene and used to estimate the drought tolerance in foxtail millet. However, the specificity of the marker depends on technical aspects, including the type of DNA polymerase used, primer concentration, and the number of PCR cycles. Here, we reported that non-specific and false positive amplicons can be eliminated by utilizing DNA polymerase with no 3’ to 5’ proofreading activity and reducing the final primer concentration to 1.25 μM. PCR cycle number 25 yielded the optimum specificity, while increasing the cycle to 30 resulted in false positive results. Altogether, our results showed that technical optimization is necessary for improving the specificity of the SNAP marker.
Co-Authors , Krisantini , Supartopo , Suwarno Abdul Qadir Adlan Adriwan Siregar, Heri Agus Purwito Ajitama, Trio Fanny Akbar, Miftahur Rizqi Alfian Helmi Amalia Nurul Huda AMIN NUR Amin Nur Amy Estiati Anas Dinurrohman Susila Andayani, Nining Anggara, Heru Anggita Duhita Anindyajati Anggraeny, Bunga Anshori, Muhammad Fuad Aprilianti, Devi Kurnia Aris Hairmansis Awang Maharijaya Ayub Darmanto Azis Boing Sitanggang Azrai, dan Muhammad Badrieh, Haian Amin Baharuddin Baharuddin Bambang Sapta Purwoko Bambang Suprihatno Bayu Pramono Wibowo Budi Indra Setiawan Butarbutar, Lidya Kristina Sari Chusnah, Uswatun Chusnul Arif Constantin, Mondjeli Cucu Gunarsih da Cunha, Rojino Danu Kuncoro Deden Derajat Matra Desi Anugra Safitri Dewi Sukma Dewi, dan Iswari Saraswati Diah Setiowati, Retno Dian Rakhmad Diny Dinarti Efendi, Darda Efendy, Roy Ekasari Putri, Nurwanita Endang Gunawan Eny Widajati Fadhilah Sitepu, Annisa Fadhli, Nur Farid, Muh Fidya Novita Firmansyah, Muh HAJRIAL ASWIDINNOOR Hishar Mirsam I Made Legawa I Putu Adi Saputra, I Putu Indrastuti A. Rumanti Indrastuti Apri Rumanti Iskandar Lubis Iskandar Lubis Iswari Saraswati Dewi Iswari Saraswati Dewi Iswari Saraswati Dewi Jayaningsih, Elvita Dwi Juharni Jundi Aiman Abdullah Kusuma, I Gede Artha Surya Kuswandi Kuswandi Lianda Dewi Sartika Lopes Hornai, Ermelinda Maria Maharijaya, dan Awang Matsuda, Hiroshi Maya Melati Mohammad Syafii Muhamad Askari Muhamad Syukur Muhammad Azrai, Muhammad Muhammad Jauhar Firdaus Muhammad Roiyan Romadhon Munandar, Arief Munif Ghulamahdi Nafisah Nailatul Karomah Ni Made Armini Wiendi Nindita, Anggi Novianti, Fira Nugroho, Rizki Anjal Puji Nugroho, Rizki Bagus Nugroho, Syarul Nurul Khumaida Pahlevi, M Reza Priyanto, Slamet Bambang Purwoko, Bambang Sapta Purwoko Purwoko, Bambang Sapto Rahmah, Syifaur Ramadaniarto Rizqullah Ramadhan, Fitrah Ramadhani, Nabilah Zulfah Reswari, Helvi Ardana Ridwani, Sobir Rika Miftakhul Jannah Rina Hapsari Wening, Rina Hapsari Rizqullah, Ramadaniarto Rokhana Faizah rudiyanto Rusianto Saenal, Nirwanti Safitri, dan Heni Salengke, Salengke Sani, Mutiyara Sari, Dewi Citra Sari, Siti Hapita Satyanto Krido Saptomo Sherly Rahayu Sintho Wahyuning Ardie Siti Nurhidayah Siti Nurhidayah Siti Yuriyah Slamet Susanto Sobir Sobir Sobir Sri Ratnawati Sri Wahjuni Sri Wening Sri Wening, Sri Wening Sugiyanta, dan Suriani Suriani Surjono Hadi Sutjahjo Susila, Anas Dinnurohman Suwarno, Punjung Medaraji Syah, Uswah Trywulan Syaifullah Rahim Syawaluddin, Dwi Dana Syilvia Nosya Pratama Tamura, Koremasa THAMRIN, SULAEHA TRI HASTINI Trias Sitaresmi Trikoesoemaningtyas Tsugama, Daisuke Tutik Kuswinanti Umi Salamah Untung Susanto Wage Ratna Rohaeni Wida W. Khumaero Widodo Widodo Wijaya, Aldi Kamal Winarso D. Widodo Wira Hadianto, Wira Wospakrik, Andrean Heskiel Yudiansyah Yudiansyah Yudiwanti Wahyu E. Kusumo Yuli Irvana Dewi Yuli Rahmadi, Hernawan YUNUS MUSA Z, Bunyamin Zakiah, Rizqi Alifahasni