DESAIN MULTIPLEX PRIMER SECARA IN SILICO BERBASIS GEN CHD (Chromodomain Helicase DNA-Binding) UNTUK PENENTUAN JENIS KELAMIN BURUNG

    Tsani Khofifah, - and Any Aryani, - and Diah Kusumawaty, - (2025) DESAIN MULTIPLEX PRIMER SECARA IN SILICO BERBASIS GEN CHD (Chromodomain Helicase DNA-Binding) UNTUK PENENTUAN JENIS KELAMIN BURUNG. S1 thesis, Universitas Pendidikan Indonesia.

    Abstract

    Penentuan jenis kelamin burung berperan penting dalam berbagai bidang, salah satunya dalam bidang konservasi. Lebih dari 50% spesies burung tidak menunjukkan dimorfisme seksual yang jelas, sehingga penentuan jenis kelamin menjadi sedikit lebih sulit. Metode konvensional seperti laparoskopi bersifat invasif, sehingga pendekatan molekuler berbasis PCR menjadi alternatif yang lebih akurat. Tetapi, primer yang tersedia sebelumnya masih memiliki keterbatasan dalam mengamplifikasi beberapa spesies burung. Penelitian ini bertujuan merancang multiplex primer baru berbasis gen CHD (Chromodomain Helicase DNA-Binding) untuk identifikasi jenis kelamin burung dan melihat prediksi panjang amplikon PCR secara in silico. Sebanyak 30 data sekuen Gen CHDW (betina) dan CHDZ (jantan) dari tiga familia burung (Accipitridae, Ardeidae, Psittacidae) dianalisis melalui Multiple Sequence Alignment (MSA), perancangan primer menggunakan perangkat lunak FastPCR, PCR in silico melalui PCR test, efektivitas primer melalui Primer-BLAST, dan multiplex PCR in silico melalui PrimerPooler. Pada penelitian ini, dihasilkan 12 pasang kandidat primer yang kemudian dihasilkan sepasang primer spesifik gen CHDW: 1:F_1-22; 1:R_336-356 dan sepasang primer spesifik gen CHDZ: 1:F_225-247; 1:R_325-346 dengan prediksi panjang amplikon 308–344 bp dan 122 bp. Uji kecocokan menunjukkan efektivitas primer pada 18 dari 30 spesies burung yang diuji, dengan hasil validasi PrimerPooler menunjukkan tidak adanya interaksi antar primer yang signifikan (ΔG = 0,0). Hasil ini menunjukkan potensi tinggi dari desain multiplex primer untuk identifikasi jenis kelamin burung secara efisien. Kata Kunci: Burung, gen CHD, penentuan jenis kelamin, in silico, multiplex primer Determining the sex of birds plays an important role in various fields, one of which is conservation. More than 50% of bird species do not show clear sexual dimorphism, making sex determination a little more difficult. Conventional methods such as laparoscopy are invasive, so PCR-based molecular approaches are a more accurate alternative. However, previously available primers still have limitations in amplifying some bird spesies. This study aims to design new multiplex primers based on the CHD gene (Chromodomain Helicase DNA-Binding) for bird sex identification and to predict PCR amplicon lengths in silico. A total of 30 sequence data of the CHDW gene (female) and CHDZ gene (male) from three bird families (Accipitridae, Ardeidae, Psittacidae) were analyzed using Multiple Sequence Alignment (MSA), primer design using the FastPCR software, in silico PCR via PCR test, primer effectiveness via Primer-BLAST, and in silico multiplex PCR via PrimerPooler. In this study, 12 pairs of candidate primers were generated, resulting in a pair of CHDW gene-specific primers: 1:F_1-22; 1:R_336-356 and a pair of CHDZ gene-specific primers: 1:F_225-247; 1:R_325-346 with predicted amplicon lengths of 308–344 bp and 122 bp. The compatibility test showed the effectiveness of the primers in 18 of the 30 bird species tested, with PrimerPooler validation results indicating no significant interaction between primers (ΔG = 0.0). These results demonstrate the high potential of multiplex primer design for efficient bird sex identification. Keywords: Birds, CHD gene, in silico, multiplex primers, sex determination

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    Official URL: https://repository.upi.edu/
    Item Type: Thesis (S1)
    Additional Information: https://scholar.google.com/citations?hl=en&user=U0qf-m0AAAAJ ID SINTA Dosen Pembimbing: Any Aryani: 6038233 Diah Kusumawaty: 6005459
    Uncontrolled Keywords: Desain multiplex primer, In silico, Gen CHD (Chromodomain Helicase DNA-Binding), Penentuan jenis kelamin burung Multiplex primer design, In silico, CHD gene (Chromodomain Helicase DNA-Binding), Bird sex determination
    Subjects: Q Science > Q Science (General)
    Q Science > QH Natural history
    Q Science > QL Zoology
    S Agriculture > SF Animal culture
    Divisions: Fakultas Pendidikan Matematika dan Ilmu Pengetahuan Alam > Program Studi Biologi - S1
    Depositing User: Tsani Khofifah
    Date Deposited: 02 Sep 2025 02:47
    Last Modified: 02 Sep 2025 02:47
    URI: http://repository.upi.edu/id/eprint/136932

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