CD Skripsi

Segmentasi Genom Kopi Liberika Berdasarkan Perbedaan Genetik Varietas Menggunakan Hidden Markov Model

---

Liberica coffee is an economically valuable plantation commodity, yet identifying its varieties based on morphological characteristics before the age of two years remains challenging. This limitation hampers the efficiency of early-stage selection and the development of superior cultivars. The core issue lies in the inability of morphological methods to distinguish between the Lim 1 and Lim 2 varieties during early growth stages, thereby necessitating a more accurate genetic-based approach. This study implements a Hidden Markov Model (HMM) to perform genome segmentation and identify unique genomic regions that differentiate the two varieties. The analysis begins with preprocessing genotype data in VCF format, converting it into numerical representations, and constructing genomic windows using 1000 bp intervals. The HMM was then developed using four states selected through Bayesian Information Criterion (BIC) evaluation and trained using the mean_diff feature as an indicator of genetic variation between varieties. The segmentation results reveal that each state exhibits distinct levels of genetic divergence, with one state consistently showing the highest mean_diff values and representing the most informative genomic regions for varietal discrimination. Statistical evaluation using the t-test indicates significant differences between states, while visualizations such as boxplots, transition matrices, emission heatmaps, and linear genome tracks further support the conclusion that the model accurately captures structured patterns of genetic differentiation. The unique genomic regions identified in this study hold potential as molecular markers for Liberica coffee varietal identification. Overall, the HMM approach has proven effective in uncovering relevant genomic variation, thereby supporting faster and more accurate varietal identification and offering a framework for future genomic research.

Keywords: HMM, Genome, Liberica coffee, Lim 1 and Lim 2 varieties, VCF

---

Ketersediaan

Informasi Detail

Judul Seri

-

No. Panggil

2203135939

Penerbit

Pekanbaru : Universitas Riau – FMIPA – Sistem Informasi., 2025

Deskripsi Fisik

-

Bahasa

English

ISBN/ISSN

-

Klasifikasi

2203135939

Tipe Isi

-

Tipe Media

-

Tipe Pembawa

-

Edisi

-

Subjek

SISTEM INFORMASI

Info Detail Spesifik

-

Pernyataan Tanggungjawab

ayu

Versi lain/terkait

Lampiran Berkas

Komentar

---

Anda harus masuk sebelum memberikan komentar