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All Journal HAYATI Journal of Biosciences MANAJEMEN HUTAN TROPIKA Journal of Tropical Forest Management Jurnal Ilmu Pertanian Indonesia Jurnal Silvikultur Tropika (JST) MEDIA KONSERVASI FORESTA BIOTROPIA - The Southeast Asian Journal of Tropical Biology Jurnal Penelitian Hutan dan Konservasi Alam Jurnal Penelitian Hutan Tanaman JURNAL PEMULIAAN TANAMAN HUTAN AGRIVITA, Journal of Agricultural Science Journal of Tropical Biodiversity and Biotechnology Abdimas Talenta : Jurnal Pengabdian Kepada Masyarakat ANNALES BOGORIENSES Jurnal Ilmu dan Teknologi Kayu Tropis Jurnal Teknik Mesin Indonesia JESBIO : Jurnal Edukasi dan Sains Biologi ALMUJTAMAE: Jurnal Pengabdian Masyarakat Jurnal Sylva Lestari Repong Damar: Jurnal Pengabdian Kehutanan dan Lingkungan Jurnal Pengabdian Pada Masyarakat Policy Brief Pertanian, Kelautan, dan Biosains Tropika Journal of Fisheries & Marine Annales Bogorienses
Ulfah Juniarti Siregar
Departement Of Silviculture, Faculty Of Forestry And Environment, IPB University, Bogor 16680, Indonesia
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Journal : HAYATI Journal of Biosciences

 1 
Development of Few Significant SNP Markers from Transcriptomic Data for Selection of Sengon (Falcataria falcata (L.) Greuter and R. Rankin) Resistant to Boktor Stem Borer and Gall Rust Disease Nugroho, Aditya; Anita, Vilda Puji Dini; Matra, Deden Derajat; Siregar, Iskandar Zulkarnaen; Siregar, Ulfah Juniarti
HAYATI Journal of Biosciences Vol. 31 No. 1 (2024): January 2024
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.31.1.110-125

Abstract

Sengon (Falcataria falcata (L.) Greuter and R. Rankin) plantations in Indonesia are threatened by attacks from Boktor stem borers and gall rust disease. Controlling pests and diseases is difficult therefore, planting resistant trees obtained from tree selection programs is necessary. Currently, genomic breeding often incorporates GWAS, which uses thousands of SNP markers to identify markers with significant associations with the traits studied. This study aimed to bypass such expensive studies by identifying and developing SNP markers from sequences of putative resistance genes to Boktor stem borer and gall rust disease, identified from sengon transcriptomic data analysis. A total of 496,194 putative SNP sites were identified from transcriptomic sequences using the SAMtools and BFCtools programs, of which 119 SNP sites were associated with resistance genes. Of the 101 non-synonymous SNPs selected, only 12 were located in the conserved domain of each gene and were used for primer design. Of the 13 primers designed, only 10 were successfully amplified. Validation of 10 developed SNP markers on 100 sengon accessions using the HRM method confirmed a significant association between SNP markers and resistance traits, with a -log 10 (P-value) between 10.49 and 16.63. A few SNPs markers developed from putative resistance gene sequences are associated with resistance traits in sengon. Therefore, the SNP markers could be applied in selection programs for sengon trees resistant to Boktor stem borers and gall rust disease.
Co-Authors Adam, Satria Adi Jaya, Adi Adisti Permatasari Putri Hartoyo Aditya Nugroho Aditya Nugroho Agus Kholik Agus Setiyono Ahmad Faqih Andi Sukendro Anita, Vilda Puji Dini Arief Budiman Arief Budiman Arif Kurnia Wijayanto Ario Damar Aris Tjahjoleksono Bayu Winata Bayu Winata, Bayu Cartealy, Imam Civi Chairil Anwar Siregar Chairil Anwar Siregar Chairil Anwar Siregar Dede J Sudrajat Dede J. Sudrajat Dede J. Sudrajat Dede Jajat Sudrajat Dede Jajat Sudrajat, Dede Jajat DEDE SUDRAJAT Deden D. Matra Deden Derajat Matra DIMAS ANDRIANTO Djiono Djiono Djufri Djufri Dodi Nandika Dodik Ridho Nurrochmat Eko Agus Suyono Eko Agus Suyono Erdy Santoso Esti Nurianti Evy Damayanthi Farosandi, Naufal Hilmi Fifi Gus Dwiyanti Fitta Setiajiati Hamzah, Hamzah Hartati Hartati Hartati, N Sri Hasim Hasyyati Shabrina Henti Rosdayanti Herman Daryono Herman Daryono I Made Mayun Maha Diputra I Wayan Windra Nugraha Idha Susanti Idha Susanti Idqan Fahmi Imam Wahyudi Indrawan, Imam Wahyudi IPB, DGB Irdika Mansur Iskandar Z Siregar Iskandar Z. Siregar Iskandar Z. Siregar ISKANDAR ZULKARNAEN SIREGAR Istikorini, Yunik Iswanto Jumadin Sidabutar Lala M Kolopaking Laura Flowrensia Lilik Maslachah Lina Karlinasari Lucia Tri Suwanti, Lucia Tri M Agus Setiadi M Iqbal Maulana Ginting M.Pd S.T. S.Pd. I Gde Wawan Sudatha . Ma'mun Sarma Madani, Hilmi Naufal Mahendra Pujiyanto Matra, Deden Derajat Mochamad Donny Koerniawan Mochammad Donny Koerniawan Mohammad Basyuni N. Sri Hartati Nahrowi Noor Farikhah Haneda Noor Farikhah Haneda Nurianti, Esti Nurul Khumaida Oemijati Rachmatsyah Oktariza, Wawan Pramisari, Yunita Pramisasi, Yunita Prijanto Pamoengkas PURNAMA HIDAYAT Purwiyatno Hariyadi Puti Awali Saimima Ramadhan, Rafli Ranny Dwita Olivia Rifana, Haikal Zaky rima siburian Rita Rahmawati Roisatuz Zakiyah Satriawan, Handi Sona Suhartana Sona Suhartana Sri Purwaningsih, Sri Sri Wilarso Budi Suci Rahayu Sudradjat Sugianto Sugianto Suharsono Suharsono Suharsono Suharsono Sumiati Supatmi Supatmi Suria Darma Tarigan Syamsidah Rahmawati, Syamsidah Tedi Yunanto Tedi Yunanto UTUT WIDYASTUTI Utut Widyastuti Vilda Puji Dini Anita Widiyatno, Thomas Valentinus Wirrahma . Zhaza Afililla Zidan, Mochammad