Tsaqif, Muhammad (2026) Penentuan Marka Genetik yang Berasosiasi dengan Weedy Rice Menggunakan Generalized Linear Mixed Model (GLMM) dalam Genome-Wide Association Study (GWAS). Other thesis, Institut Teknologi Sepuluh Nopember.
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Abstract
Fenotipe warna kulit biji (merah dan putih) merupakan salah satu ciri utama fenomena de-domestikasi pada weedy rice yang menjadi ancaman serius bagi produktivitas pertanian global karena sifatnya yang sangat kompetitif terhadap padi budidaya. Penelitian ini bertujuan untuk menentukan marka genetik berupa single nucleotide polymorphism (SNP) yang berasosiasi dengan warna kulit biji pada padi (Oryza sativa), khususnya pada subspesies indica. Mengingat sifat fenotipe yang kategorikal biner, penelitian ini menerapkan metode genome-wide association study (GWAS) dengan pendekatan generalized linear mixed model (GLMM) menggunakan fungsi link logit untuk mengatasi keterbatasan model linier standar dalam menangani data non-normal. Analisis dilakukan terhadap 864 individu padi yang berasal dari basis data 3,000 Rice Genomes Project (3K RGP) dengan total 143.589 SNP yang telah lolos kontrol kualitas ketat, yaitu call rate ≥90% dan minor allele frequency (MAF) ≥0,05. Hasil analisis menunjukkan adanya stratifikasi populasi yang kuat yang membagi sampel menjadi empat kelompok utama (Ind1A, Ind1B, Ind2, dan Ind3) berdasarkan asal geografisnya. Implementasi GLMM dengan menyertakan 65 komponen utama (PCA) sebagai efek tetap dan genetic relationship matrix (GRM) sebagai efek acak terbukti efektif mengontrol inflasi statistik akibat hubungan kekerabatan antar individu. Melalui pengujian berganda dengan koreksi Bonferroni (P<3,48×10^(-7)), diidentifikasi sebanyak 52 SNP yang berasosiasi signifikan dengan warna kulit biji. Lokus utama ditemukan secara spesifik pada kromosom 7 yang berkaitan erat dengan gen Rc (pengatur utama jalur biosintesis pigmen). Analisis linkage disequilibrium (LD) mengonfirmasi bahwa SNP-SNP signifikan tersebut berada dalam blok LD lokal yang mencerminkan sinyal genetik yang sama pada Kromosom 7. Temuan ini memberikan validasi metodologis penggunaan GLMM untuk sifat biner dan memberikan wawasan penting bagi strategi pemuliaan padi yang lebih presisi dalam mengidentifikasi karakter de-domestikasi.
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The seed coat color phenotype (red and white) is a primary characteristic of the de-domestication phenomenon in weedy rice, which negatively impacts global agricultural productivity. This study aims to identify genetic markers in the form of Single Nucleotide Polymorphisms (SNPs) associated with seed coat color in rice (Oryza sativa), specifically within the indica subspecies. Given the binary categorical nature of the phenotype, this research employs the Genome-Wide Association Study (GWAS) method using a Generalized Linear Mixed Model (GLMM) approach with a logit link function. The analysis was conducted on 864 rice individuals from the 3,000 Rice Genomes Project (3K RGP) database, involving a total of 143,589 SNPs that passed strict quality control criteria, specifically a call rate ≥90% and Minor Allele Frequency (MAF) ≥0.05. The results indicate strong population stratification, dividing the samples into four main groups (Ind1A, Ind1B, Ind2, and Ind3) based on geographic origin. The implementation of GLMM, incorporating the 65 Principal Components (PCA) as fixed effects and a Genetic Relationship Matrix (GRM) as a random effect, proved effective in controlling statistical inflation. Through multiple testing with Bonferroni correction (P<3.48×10^(-7)), 52 SNPs were identified as significantly associated with seed coat color. A major effect locus was specifically found on Chromosome 7 (position 6,067,855 bp), which is closely related to the Rc gene (the master regulator of the proanthocyanidin pigment biosynthesis pathway). Linkage Disequilibrium (LD) analysis confirmed that these significant SNPs reside within local LD blocks, reflecting high recombination rates in the population. These findings provide methodological validation for the use of GLMM in binary traits and contribute to more precise rice breeding strategies for identifying de-domestication characters.
| Item Type: | Thesis (Other) |
|---|---|
| Uncontrolled Keywords: | De-domestikasi, Generalized Linear Mixed Model, Genome-Wide Association Study, Padi Indica, Warna Kulit Biji, De-domestication, Generalized Linear Mixed Model, Genome-Wide Association Study, Indica Rice, Seed Coat Color |
| Subjects: | S Agriculture > SB Plant culture > SB191.R5 Rice farming |
| Divisions: | Faculty of Science and Data Analytics (SCIENTICS) > Statistics > 49201-(S1) Undergraduate Thesis |
| Depositing User: | Muhammad Tsaqif |
| Date Deposited: | 30 Jan 2026 01:21 |
| Last Modified: | 30 Jan 2026 01:21 |
| URI: | http://repository.its.ac.id/id/eprint/131037 |
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