Analisis Keragaman Genetik Dua Puluh Dua Aksesi Durian (Durio zibethinus L.) Berbasis Penanda Molekuler IRAP (Inter-Retrotransposon Amplified Polymorphism)

Galih Malvin Alfuada, Agus Budi Setiawan, S.P., M.Sc., Ph.D; Widhi Dyah Sawitri, S.Si., M.Agr., Ph.D

2026 | Skripsi | AGRONOMI

Durian (Durio zibethinus L.) merupakan komoditas buah tropis bernilai ekonomi tinggi yang berpotensi menghasilkan varietas dengan karakteristik unik. Penelitian ini bertujuan untuk menentukan keragaman genetik, struktur populasi, dan hubungan kekerabatan antar dua puluh dua aksesi durian dari populasi komersil dan landrace menggunakan penanda molekuler IRAP (Inter-Retrotransposon Amplified Polymorphism). Eksplorasi sampel dilakukan di Kabupaten Magelang, Kulonprogo, dan Sleman, dilanjutkan dengan analisis molekuler di Laboratorium Genetika dan Pemuliaan Tanaman, Universitas Gadjah Mada, pada Oktober 2025–April 2026. Parameter yang dianalisis meliputi efektivitas penanda (PIC, EMR, RP), persentase lokus polimorfik, keragaman alel (Na, Ne), indeks Shannon (I), heterozigositas harapan (He), koordinat utama (PCoA), dan analisis varians molekuler (AMOVA). Hasil AMOVA menunjukkan komponen keragaman genetik didominasi oleh variasi di dalam populasi (within populations) sebesar 97%, sedangkan keragaman antar-populasi (between populations) hanya 3% (PhiPT = 0,027; P = 0,001). Rendahnya diferensiasi antar-populasi ini diindikasikan oleh tingginya aliran gen (Nm = 8.99). Populasi Komersial mencatatkan tingkat keragaman tertinggi (He = 0,085 ± 0,003), diikuti Populasi Landrace (He = 0,076 ± 0,004). Analisis spasial PCoA dan dendrogram menunjukkan tingginya kedekatan genetik yang saling tumpang tindih (overlap) pada sebagian besar varietas, kecuali Aksesi Sitokong yang memisah tegas sebagai outgroup akibat ketiadaan insersi retrotransposon. Karakteristik genomik yang berbeda pada outgroup ini berpotensi besar untuk dimanfaatkan sebagai tetua donor dalam program hibridisasi untuk memaksimalkan efek heterosis dan memperluas basis genetik durian.

Durian (Durio zibethinus L.) is a tropical fruit commodity with high economic value that has the potential to produce varieties with unique characteristics. This study aimed to determine the genetic diversity, population structure, and kinship relationships between twenty-two durian accessions from commercial and landrace populations using the molecular marker IRAP (Inter-Retrotransposon Amplified Polymorphism). Sample exploration was carried out in Magelang, Kulonprogo, and Sleman Regencies, followed by molecular analysis at the Laboratory of Genetics and Plant Breeding, Universitas Gadjah Mada, in October 2025–April 2026. The parameters analyzed included marker effectiveness (PIC, EMR, RP), percentage of polymorphic locus, allele diversity (Na, Ne), Shannon index (I), expected heterozygosity (He), primary coordinates (PCoA), and molecular variance analysis (AMOVA). The results of AMOVA showed that the genetic diversity component was dominated by variation within populations by 97%, while the diversity between populations was only 3% (PhiPT = 0.027; P = 0.001). This low differentiation between populations is indicated by the high flow of genes (Nm = 8.99). The Commercial Population recorded the highest level of diversity (He = 0.085 ± 0.003), followed by the Landrace Population (He = 0.076 ± 0.004). Spatial analysis of PCoA and dendrograms showed high levels of overlapping genetic proximity in most varieties, except for the Sitokong Accession which separated firmly as an outgroup due to the absence of retrotransposon insertion. The different genomic characteristics of this outgroup have great potential to be utilized as donor elders in hybridization programs to maximize the effects of heterosis and expand the genetic base of durian.

Kata Kunci : molekuler, IRAP, durian, keragaman, genetik