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Information
| Unit | INSTITUTE OF NATURAL AND APPLIED SCIENCES |
| ZOOTECHNICS (PhD) | |
| Code | ZO682 |
| Name | Genom Analyses in Farm Animals |
| Term | 2025-2026 Academic Year |
| Term | Fall |
| Duration (T+A) | 3-0 (T-A) (17 Week) |
| ECTS | 6 ECTS |
| National Credit | 3 National Credit |
| Teaching Language | Türkçe |
| Level | Doktora Dersi |
| Type | Normal |
| Mode of study | Yüz Yüze Öğretim |
| Catalog Information Coordinator | Doç. Dr. Mervan BAYRAKTAR |
| Course Instructor |
The current term course schedule has not been prepared yet.
|
Course Goal / Objective
This PhD-level course aims to equip animal-science researchers with advanced skills to generate, process, and interpret livestock genomic data. Starting from modern sequencing platforms, students will build a holistic workflow encompassing bioinformatic analysis, genome-wide association mapping, detection of selection signatures, and functional annotation. Graduates will be able to integrate genomic insights into sustainable livestock-production strategies and address ethical considerations surrounding the use of genomic technologies.
Course Content
“Genomic Analyses in Farm Animals” is a PhD-level course designed to provide animal-science researchers with an integrated framework for generating, processing, and interpreting livestock genomic data. Beginning with the gene-to-phenotype continuum, the course traces the evolution of genomic research and reinforces key concepts in genome organization and architecture. Students explore state-of-the-art sequencing technologies, learn to navigate major public databases, and master next-generation sequencing (NGS) pipelines in depth. Through hands-on sessions, they practice read filtering, alignment, variant calling, and quality-control steps using core bioinformatics tools. Advanced statistical modules introduce genome-wide association studies (GWAS) and selection-signature detection, enabling students to pinpoint loci underlying economically important traits. Subsequent weeks focus on biological interpretation via gene-enrichment and pathway analyses, culminating in discussions on ethical, economic, and environmental implications of applying genomics to sustainable livestock production. By combining lectures, laboratory workshops, and literature-based seminars, the course equips participants to design and manage independent genomic research projects with scientific rigor and real-world relevance.
Course Precondition
Scanning the internet for course-related resources
Resources
Mondal, S., & Singh, R. L. (Eds.). (2020). Advances in animal genomics. Academic Press.
Notes
Mondal, S., & Singh, R. L. (Eds.). (2020). Advances in animal genomics. Academic Press.
Course Learning Outcomes
| Order | Course Learning Outcomes |
|---|---|
| LO01 | It can analyze livestock next-generation sequencing (NGS) data end-to-end, from quality control to variant calling. |
| LO02 | Design and execute genome-wide association studies (GWAS) and selection-signature analyses to identify loci of economic importance. |
| LO03 | Perform gene-enrichment and pathway analyses with bioinformatic tools and provide biologically meaningful interpretations of the results. |
| LO04 | Evaluate ethical, environmental, and economic dimensions when integrating genomic data into sustainable livestock-breeding programs. |
Relation with Program Learning Outcome
| Order | Type | Program Learning Outcomes | Level |
|---|---|---|---|
| PLO01 | Bilgi - Kuramsal, Olgusal | After undergraduate education, increases knowledge in one of the fields of animal breeding and breeding, feeds and animal nutrition, biometrics and genetics. | 2 |
| PLO02 | Bilgi - Kuramsal, Olgusal | Understands the interaction between different disciplines | 3 |
| PLO03 | Bilgi - Kuramsal, Olgusal | Gains the ability to develop strategic approaches and produce regional, national or international solutions for the field of animal science | |
| PLO04 | Bilgi - Kuramsal, Olgusal | Gains the ability to develop knowledge with scientific methods by using the data in animal science, and to use this knowledge with the awareness of scientific, social and ethical responsibility. | |
| PLO05 | Bilgi - Kuramsal, Olgusal | Gains the ability to use and develop information technologies with computer software and hardware knowledge required by the field of animal science. | |
| PLO06 | Bilgi - Kuramsal, Olgusal | Gains the ability to convey their own studies or current developments in the field of animal science to groups in the field or other fields of science, verbally and visually. | |
| PLO07 | Bilgi - Kuramsal, Olgusal | Gains the ability to evaluate the quality processes of animal products | 3 |
| PLO08 | Bilgi - Kuramsal, Olgusal | Gains the ability to keep animal production dynamic in accordance with changing economic and social conditions. | |
| PLO09 | Bilgi - Kuramsal, Olgusal | Gains the ability to follow national and international current issues, to follow developments in lifelong learning, science and technology, to constantly renew themselves and to transfer innovations to animal production. | 2 |
| PLO10 | Bilgi - Kuramsal, Olgusal | Hayvansal ürünler ile insan sağlığı ve toplum refahı arasındaki ilişkiyi özümser |
Week Plan
| Week | Topic | Preparation | Methods |
|---|---|---|---|
| 1 | Introduction | Scanning the internet for course-related resources | Öğretim Yöntemleri: Anlatım, Tartışma |
| 2 | From Gene to Genomic Studies | Scanning the internet for course-related resources | Öğretim Yöntemleri: Anlatım, Tartışma |
| 3 | Overview of Genomic Analyses | Scanning the internet for course-related resources | Öğretim Yöntemleri: Anlatım, Tartışma |
| 4 | Genome Organization and Architecture | Scanning the internet for course-related resources | Öğretim Yöntemleri: Anlatım, Tartışma |
| 5 | Sequencing Technologies | Scanning the internet for course-related resources | Öğretim Yöntemleri: Anlatım, Tartışma |
| 6 | Animal Data Banks | Scanning the internet for course-related resources | Öğretim Yöntemleri: Anlatım, Tartışma |
| 7 | NGS Workflows and Core Bioinformatics Tools I | Scanning the internet for course-related resources | Öğretim Yöntemleri: Anlatım, Tartışma |
| 8 | Mid-Term Exam | Scanning the internet for course-related resources | Ölçme Yöntemleri: Yazılı Sınav, Sözlü Sınav, Ödev |
| 9 | NGS Workflows and Core Bioinformatics Tools II | Scanning the internet for course-related resources | Öğretim Yöntemleri: Anlatım, Tartışma |
| 10 | Genome-Wide Association Studies (GWAS) I | Scanning the internet for course-related resources | Öğretim Yöntemleri: Anlatım, Tartışma |
| 11 | Genome-Wide Association Studies (GWAS) II | Scanning the internet for course-related resources | Öğretim Yöntemleri: Anlatım, Tartışma |
| 12 | Selection Signature Analysis I | Scanning the internet for course-related resources | Öğretim Yöntemleri: Anlatım, Tartışma |
| 13 | Selection Signature Analysis II | Scanning the internet for course-related resources | Öğretim Yöntemleri: Anlatım, Tartışma |
| 14 | Gene Enrichment & Pathway Analysis | Scanning the internet for course-related resources | Öğretim Yöntemleri: Anlatım, Tartışma |
| 15 | Genomic Ethics & Future Perspectives for Sustainable Livestock Production | Scanning the internet for course-related resources | Öğretim Yöntemleri: Anlatım, Tartışma |
| 16 | Term Exams | Scanning the internet for course-related resources | Ölçme Yöntemleri: Yazılı Sınav, Sözlü Sınav, Ödev |
| 17 | Term Exams | Scanning the internet for course-related resources | Ölçme Yöntemleri: Yazılı Sınav, Sözlü Sınav, Ödev |
Student Workload - ECTS
| Works | Number | Time (Hour) | Workload (Hour) |
|---|---|---|---|
| Course Related Works | |||
| Class Time (Exam weeks are excluded) | 14 | 3 | 42 |
| Out of Class Study (Preliminary Work, Practice) | 14 | 5 | 70 |
| Assesment Related Works | |||
| Homeworks, Projects, Others | 0 | 0 | 0 |
| Mid-term Exams (Written, Oral, etc.) | 1 | 15 | 15 |
| Final Exam | 1 | 30 | 30 |
| Total Workload (Hour) | 157 | ||
| Total Workload / 25 (h) | 6,28 | ||
| ECTS | 6 ECTS | ||