Evaluasi Distribusi Alel SMII2 pada Tiga Populasi Kelapa Sawit menggunakan Genotyping CAPS (Cleaved Amplified Polymorphic Sequence)

Abstract

Pertumbuhan tinggi batang kelapa sawit yang cepat (45–75 cm/tahun) mempersulit pemanenan dan memperpendek umur ekonomis tanaman, sehingga pengembangan varietas dwarf menjadi prioritas program pemuliaan modern. Penelitian ini bertujuan mengevaluasi distribusi alel dwarf pada lokus SMII2 menggunakan Genotyping CAPS (Cleaved Amplified Polymorphic Sequence) terhadap 500 individu, terdiri atas populasi Elaeis guineensis hasil pemuliaan (n = 183) dan tipe liar (n = 192), hibrida interspesifik E. oleifera × E. guineensis (n = 125), serta tiga individu E. oleifera sebagai kontrol. Kualitas DNA hasil ekstraksi sampel memenuhi standar Genotyping (rasio A260/A280 1,83–2,04; A260/A230 1,91–2,02) dengan keberhasilan amplifikasi PCR 100%. Pemotongan amplikon 460 bp dengan enzim AvaII menghasilkan tiga genotype kodominan: homozigot reference (aa; 460 bp), heterozigot (Aa; 460/272/188 bp), dan homozigot alternate (AA; 272/188 bp). Seluruh individu E. guineensis, baik populasi pemuliaan maupun tipe liar, bergenotype aa (frekuensi alel A = 0,00); seluruh hibrida interspesifik bergenotype Aa (frekuensi A = 0,50); dan kontrol E. oleifera bergenotype AA (frekuensi A = 1,00). Validasi lima tahap, meliputi replikasi teknis lintas batch, kontrol positif dan kontrol spesies, Sanger sequencing , dan analisis BLAST, mengonfirmasi hasil Genotyping yang konsisten, reprodusibel, dan akurat. Lokus SMII2 mampu membedakan alel dwarf interspecific namun tidak dapat membedakan variasi intraspecific dalam E. guineensis, dan berpotensi dimanfaatkan sebagai alat pelacak introgresi alel dwarf dalam program marker-assisted backcross.

Rapid trunk height growth in oil palm (45–75 cm/year) complicates harvesting and shortens plantation economic lifespan, making dwarf variety development a priority in modern breeding programs. This study aimed to evaluate dwarf allele distribution at the SMII2 locus using CAPS (Cleaved Amplified Polymorphic Sequence) Genotyping across 500 individuals, comprising Elaeis guineensis breeding (n = 183) and wild-type (n = 192) populations, interspecific hybrids of E. oleifera × E. guineensis (n = 125), and three pure E. oleifera individuals as controls. The DNA quality of extracted samples met Genotyping standards (A260/A280 ratio 1.83–2.04; A260/A230 ratio 1.91–2.02), with 100% PCR amplification success. Digestion of the 460 bp amplicon with AvaII resolved three codominant genotype classes: homozygous reference (aa; 460 bp), heterozygous (Aa; 460/272/188 bp), and homozygous alternate (AA; 272/188 bp). All E. guineensis individuals, from both breeding and wild-type populations, exhibited the aa genotype (allele A frequency = 0.00); all interspecific hybrids exhibited the Aa genotype (allele A frequency = 0.50); and E. oleifera controls exhibited the AA genotype (allele A frequency = 1.00). Five-step validation, including technical replications across batches, positive and species controls, Sanger sequencing , and BLAST analysis, confirmed consistent, reproducible, and accurate Genotyping. The SMII2 locus differentiates dwarf palm but is strictly interspecific, unable to discriminate intraspecific samples, and holds potential as a tracking tool for dwarf allele introgression in marker-assisted backcross breeding programs.