Marka Molekuler Keragaman Genetik Plasma Nutfah Kelapa Indonesia Dan Penentuan Identitas Kelapa Hibrida Berdasarkan Marka Molekuler
Daftar Pustaka
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3 PENGEMBANGAN MARKA SNAP BERBASIS GEN WRKY DAN VALIDASI MENGGUNAKAN MULTIPLEX PCR
1
Abstrak
Pengembangan marka molekuler memberikan manfaat bagi program pemuliaan kelapa. Ketersediaan sekuens DNA memberikan peluang baru untuk
mengembangkan marka
molekuler yaitu:
single nucleotide
amplified polymorphism SNAP. Tujuan penelitian ini adalah mengevaluasi keragaman
sekuens nukleotida gen WRKY di database GenBank, desain primer spesifik gen untuk membuat marka SNAP berdasarkan gen WRKY, optimasi teknik multiplex
PCR, dan validasi efektivitas marka SNAP untuk evaluasi plasma nutfah kelapa Kopyor. Berdasarkan data 35 sekuens gen WRKY tanaman kelapa yang tersedia
di database GenBank, delapan titik SNP diidentifikasi dan digunakan untuk menghasilkan primer spesifik SNP. Delapan pasang primer didisain dan divalidasi
menggunakan singleplex PCR. Optimasi suhu Ta, konsentrasi primer, duplex dan triplex PCR dilakukan untuk multiplex PCR. Duplex PCR menggunakan dua
pasang primer lebih sesuai untuk genotyping plasma nuftah kelapa kopyor dibandingkan triplex PCR. Duplex PCR telah berhasil diaplikasikan untuk kelapa
Dalam Kopyor di Jember dan Kalianda, dan Genjah Kopyor di Pati. Pengembangan marka SNAP dapat digunakan sebagai alternatif sederhana marka
ko-dominan untuk analisis genetik kelapa. Ketersediaan marka SNAP dapat digunakan untuk investigasi kemungkinan asosiasi antara marka dan endosperma
Kopyor serta karakter fenotip penting lainnya pada tanaman kelapa.
Kata kunci: Kelapa Kopyor, Multiplex PCR, SNP
1
Bab ini telah disubmit pada Emirates Journal Food and Agriculture 2016, dengan judul: “Development of SNAP Markers Based on Nucleotide Variability of WRKY Genes in Coconut and
Their Validation Using Multiplex PCR ”.
Abstract
Development of molecular markers benefits coconut breeding program. Availability of DNA sequences for coconuts opens new possibility of developing
molecular markers such as: single nucleotide amplified polymorphism SNAP. The study objectives are to evaluate nucleotide sequence diversities of WRKY
gene in the GenBank database, design gene specific primers for generating WRKY specific SNAP markers, optimize multiplex PCR technique and validate
SNAP marker effectiveness for evaluating Kopyor coconut germplasm. Based on 35 sequence data of coconut WRKY genes available in the GenBank database,
eight informative SNPs were identified and used to generate SNP specific primers. Eight primer pairs were designed and validated using singleplex PCR.
Subsequently, optimization of the Ta, primer concentrations, and either duplex or triplex PCR were evaluated. Duplex PCR using two sets of primer pairs was more
reliable for genotyping Kopyor coconut germplasm than triplex PCR. Duplex PCR has successfully been demonstrated for genotyping Jember Tall, Kalianda
Tall, and Pati Dwarf Kopyor coconuts. Therefore, the developed SNAP markers can be used as simple alternative of co-dominant markers for genetic analysis of
coconuts. Availability of SNAP markers can be used to investigate possible association between markers and Kopyor endosperm and other important
phenotypes in coconuts.
Keywords: Kopyor coconut, Multiplex PCR, SNP