Athaurrakhman, Daniyal Wiraharja (2025) Pemetaan Quantitative Trait Loci Menggunakan Metode-Metode Interval Mapping (Studi Kasus: Asosiasi Genetik pada Resistensi Capsicum Annuum terhadap Virus Gemini). Other thesis, Institut Teknologi Sepuluh Nopember.
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Abstract
Pemetaan Quantitative Trait Loci (QTL) adalah salah satu cara dalam pemuliaan tanaman untuk mengetahui lokus yang berasosiasi dengan suatu sifat fenotipe tertentu dan menentukan Single Nucleotide Polymorphism (SNP) mana yang berkontribusi. Pemetaan QTL bisa dilakukan dengan pemetaan interval marka molekuler, di antaranya metode pemetaan interval standar (SIM), regresi Haley-Knott, dan pemetaan interval komposit (CIM). Penting untuk dilakukan analisis pemetaan QTL dengan metode tersebut, terutama untuk tanaman Capsicum annuum atau cabai, karena produksi cabai rentan dan fluktuatif karena penyakit yang disebabkan oleh virus Gemini (Geminiviridae). Oleh sebab itu, pemetaan QTL diharapkan mampu mengidentifikasi lokasi lokus dan SNP yang memiliki hubungan dengan resistensi cabai menghadapi virus Gemini, sehingga didapatkan varietas cabai yang tahan lama dan mengurangi risiko gagal panen karena virus tersebut. Sebanyak 341 individu Capsicum annuum menjadi sampel dengan 49 SNP dari 12 kromosom, dengan nilai AUDPC yang berasal dari pengamatan kondisi fisik setiap individu selama 12 minggu. Proses ekstraksi, bioinformatika hingga genotyping dalam laboratorium dilakukan sebagai langkah awal analisis. Kemudian, estimasi peta genetik dilakukan terlebih dahulu, sebelum ketiga metode dilaksanakan. Dalam kasus ini, metode regresi Haley-Knott terbukti lebih baik dalam pemetaan QTL ketahanan Capsicum annuum terhadap virus Gemini, dengan berhasil mengidentifikasi dua penanda SNP (H1 dan H2) yang memiliki asosiasi sangat tinggi (nilai LOD 21,663 dan 56,014) dengan akurasi masing-masing 80,93% dan 91,78%. Validasi lebih lanjut menunjukkan individu dengan genotipe 1/1 dan 1/2 pada kedua SNP tersebut cenderung rentan, mengindikasikan peran krusial kedua penanda ini dalam respons ketahanan tanaman.
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Quantitative Trait Loci (QTL) mapping is a method in plant breeding used to identify loci associated with a specific phenotypic trait and to determine which Single Nucleotide Polymorphisms (SNPs) contribute to it. QTL mapping can be performed using molecular marker interval mapping, including standard interval mapping (SIM), Haley-Knott regression, and composite interval mapping (CIM). Conducting QTL mapping analysis using these methods is crucial, particularly for Capsicum annuum (chili pepper), as its production is susceptible to fluctuations due to diseases caused by the Gemini virus (Geminiviridae). Therefore, QTL mapping is expected to identify the location of loci and SNPs associated with chili pepper resistance to the Gemini virus, aiming to develop durable, resistant chili varieties and reduce the risk of crop failure. A total of 341 Capsicum annuum individuals were sampled, with 49 SNPs from 12 chromosomes, and AUDPC (Area Under the Disease Progress Curve) values derived from a 12-week observation of each individual's physical condition. The initial steps involved laboratory procedures such as extraction, bioinformatics, and genotyping. Subsequently, a genetic map was estimated before the three mapping methods were implemented. In this case, the Haley-Knott regression method proved to be superior for QTL mapping of Capsicum annuum resistance to the Gemini virus. It successfully identified two SNP markers (H1 and H2) with very high associations (LOD scores of 21.663 and 56.014) and accuracies of 80.93% and 91.78%, respectively. Further validation indicated that individuals with genotypes 1/1 and 1/2 at both SNP loci tended to be susceptible, highlighting the crucial role of these two markers in the plant's resistance response.
| Item Type: | Thesis (Other) |
|---|---|
| Uncontrolled Keywords: | Pemetaan Interval Standar, Pemetaan QTL, Pendekatan Haley-Knott, Haley-Knott Approach, QTL Mapping, Standard Interval Mapping |
| Subjects: | Q Science > QA Mathematics > QA274.2 Stochastic analysis Q Science > QA Mathematics > QA401 Mathematical models. Q Science > QH Biology > QH426 Genetics |
| Divisions: | Faculty of Science and Data Analytics (SCIENTICS) > Statistics > 49201-(S1) Undergraduate Thesis |
| Depositing User: | Daniyal Wiraharja Athaurrakhman |
| Date Deposited: | 25 Jul 2025 02:07 |
| Last Modified: | 25 Jul 2025 02:07 |
| URI: | http://repository.its.ac.id/id/eprint/120777 |
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