Animal genomic

Duration

28h Th, 10h Mon. WS

Number of credits

Lecturer

Michel Georges

Language(s) of instruction

French language

Organisation and examination

Teaching in the second semester

Schedule

Schedule online

Units courses prerequisite and corequisite

Prerequisite or corequisite units are presented within each program

Learning unit contents

I. Course title
Essential genomics for veterinarians and the animal sciences
II. Table of content
Chapter 1: Reference genomes
1.1 Basic anatomy of animal genomes
1.2 Generating reference genome sequences 
1.3 Annotating reference genome sequences
Chapter 2: Indivdual genomes 
2.1 Genetic polymorphisms
2.2 Origins of genetic polymorphism
2.3 Linkage disequilibrium and haplotype blocks
2.4 Interrogating genetic variation
2.5 Genomic reconstruction of our evolutionary history
2.6 Animal domestication 
Chapter 3: Individual phenomes
3.1 Neutral vs functional variants - germline vs somatic mutations
3.2 Monogenic traits
3.3 Oligogenic traits
3.4 Polygenic traits
3.5 Somatic versus germline mutations: cancer
Chapter 4: Geneticx dissection of the functional circuitry
4.1 Forward genetic dissection of the causative circuitry
4.2 Reverse genetic dissection of the causative circuitry
Chapter 5: Applied animal genomics
5.1 Individual identification and parentage control 
5.2 Managing genetic defects
5.3 Genomic selection
5.4 Conservation of animal biodiversity
5.5 Editing livestock genomes
5.6 New applications of genomic technology

Learning outcomes of the learning unit

At the end of this course, the student will be familiarized with:
1. The organisation and main features of the animal genome, sequencing technologies and methods used for the annotation of reference genomes. 2. Basic concepts in population and evolutionary genomics including the different types of genetic variants, the origins of genetic polymorphism, the notion of linkage disequilibrium and haplotype blocks, the pmain genotyping methods, the methods used for the reconstruction of our evolutionary history and of animal domestication. 3. Basic concepts in factorial and quantitative genomics including the distinction between mono-, oligo- and polygenic traits, the molecular basis of dominance and recessivity, the different types of epistatic intercations, the notion of heritabilioty and its estimation, the concepts of kinship and inbreeding coefficients. The student will understand the relative contribution of germline and somatic mutations/variants in the development of cancers. 4. The disctinction between forward and reverse genetic apporoaches, positional cloning, GWAS, cis- and trans-eQTL, stem cells and organoids, model organisms, gene editing techniques including CRISPR/Cas9, and the approches used to identify causative genes and variants. The students will be aware of the major mono- and oligogenic traits in domestic animals. 5. The main applications of genomics in veterinary medicine and animal science including individual identification and parentage control, management of inherited defects, genomic selection, conservation of domestic biodiversity, editing of livestock genomes, and other innovative applications.

Prerequisite knowledge and skills

1. Basic knowledge in molecular biology of the gene (structure of DNA/RNA/proteins, reoplication, transcription, translation, mitosis, meiosis) and mendelian genetics (Mendel's laws, dominance, recessivity, linkage)
2. Basic knowledge in probability and statistics (mean, variance, covariance, correlation).

Planned learning activities and teaching methods

Given the COVID19 pandemci, the course are organized remotely.
For thezir studies, the student have at their disposal:
1. Lecture notes (+:_ 175 pages) covering the entire course with text and figures, written in English.
2. Ten powerpoint presentations (2 per chapter) with audio comments in French for each slide.  The slides correspond largely to the figures in the text book.
Lecture notes and slides can be downloaded from the eCampus webpage or the webpage of the Unit of Animal Genomics (https://www.gigauag.uliege.be/cms/c_4766333/en/gigauag-teaching). Maje sure that you download the latest version of the material (realease data provided).
The modus operandi was agreed with the students.  Students study one cours per week for a total of ten courses/weeks (two courses per chapter). They can post questions on the discxussion foruml provided by eCampus. The teacher organizes one one-hour Q&A session per week in visio conference on eCampus.  The correspnding sessions are recorded and made available to the students.  
The practicals will be organized by visio conference using eCampus.  the students will receive questions of the same kind as the ones that they will have during the exmination in order to be well prepared. The teacher wil be availble to address any question that may arise from the questionnaire.   
 

Mode of delivery (face to face, distance learning, hybrid learning)

remoite (see above)

Organisational adjustments related to the current health context

(see above)

Recommended or required readings

(see above)

Assessment methods and criteria

Below you will find information on the evaluation methods planned for in-person and remote exams as well as those planned for hybrid sessions. Depending on how the health crisis evolves, the chosen method will be communicated to you no later than one month before the start of the exam session.

Any session :

- In-person

written exam ( multiple-choice questionnaire )

- Remote

written exam ( multiple-choice questionnaire )

- If evaluation in "hybrid"

preferred remote


Additional information:

Written exam comprising +/- 30 MCQ.

Work placement(s)

not applicable

Organizational remarks

Contacts

Items online