Keragaman Runutan Nukleotida Gen matK Parsial Asal Empat Spesies Salacca

Abstract

ABSTRAK KAYLA MAR’ATI SHOLIHAH. Keragaman Runutan Nukleotida Gen matK Parsial Asal Empat Spesies Salacca. Dibimbing oleh SUDARSONO dan AWANG MAHARIJAYA. Salacca tergolong ke dalam famili Arecaceae yang berpotensi berkembang lebih signifikan dari segi ekologi dan ekonomi di dalam negeri maupun secara global. Salacca menghadapi kendala pada pendeskripsian spesies, pencatatan varietas baru, perbanyakan vegetatif, serta penentuan jenis kelamin bibit tanaman. Informasi keragaman genetik berperan penting dalam proses identifikasi marka molekuler yang efektif untuk DNA barcoding. DNA barcoding genom kloroplas seperti dari wilayah rbcL dan matK secara luas digunakan untuk identifikasi spesies yang dapat memaksimalkan pemanfaatan Salacca. Penelitian ini bertujuan mengeksplorasi variasi genetik runutan nukleotida gen matK parsial yang bervariasi tinggi pada empat spesies Salacca. Penelitian dilaksanakan pada bulan April hingga Desember 2024 di Laboratorium Biologi Molekuler Tumbuhan, Departemen Agronomi dan Hortikultura, Fakultas Pertanian, IPB University. Amplifikasi fragmen matK dengan primer spesifik gen dilakukan pada 4 spesies Salacca sebelum Sanger sequencing. Multiple Sequence Alignment menggunakan software Geneious Prime untuk mengidentifikasi Single Nucleotide Polymorphisms (SNP) mengungkap variasi genetik. Terdapat temuan 14 situs SNP yang menunjukkan tipe haplotipe yang berbeda dari keempat spesies. Analisis filogenetik menunjukkan kedekatan kekerabatan spesies Salacca yang digunakan dengan 28 aksesi spesies lain dari famili Arecaceae melalui clade yang terbentuk. Penemuan tersebut menekankan potensi wilayah matK dalam meningkatkan studi keragaman genetik, analisis filogenetik, serta upaya konservasi untuk spesies Salacca. Kata kunci: marka molekuler, primer spesifik gen, salak mawar, Sanger sequencing, SNP.

ABSTRACT KAYLA MAR’ATI SHOLIHAH. Diversity of Partial matK Gene Nucleotide Sequences from Four Salacca Species. Supervised by SUDARSONO and AWANG MAHARIJAYA. Salacca belongs to the Arecaceae family which has the potential to develop more significantly in terms of ecology and economy, domestically and globally. Salacca faces problems in describing species, recording new varieties, vegetative propagation, and determining the sex of plant seedlings. Information on genetic diversity plays an important role in the process of identifying effective molecular markers for DNA barcoding. DNA barcoding of the chloroplast genome such as from the rbcL and matK regions is widely used to identify species that can maximize the utilization of Salacca. This study aims to explore genetic variation of highly variable partial matK gene nucleotide sequences in four Salacca species. The study was conducted from April to December 2024 at the Plant Molecular Biology Laboratory, Department of Agronomy and Horticulture, Faculty of Agriculture, IPB University. Amplification of matK fragment with gene-specific primers was performed in 4 Salacca species before Sanger sequencing. Multiple Sequence Alignment using Geneious Prime software to identify Single Nucleotide Polymorphisms (SNPs) revealed genetic variation. There were 14 SNP sites found that showed different haplotype between the four species. Phylogenetic analysis revealed genetic relationship closeness of the Salacca species used with 28 accessions of other species from Arecaceae family through the formed clade. The findings underscore the potential of matK regions in advancing genetic diversity studies, phylogenetic analyses, and conservation efforts for Salacca species. Keywords: gene-specific primer, molecular marker, Sanger sequencing, salak mawar, SNP.