72709 - Advanced Genomic in Animal Production

Academic Year 2019/2020

  • Moduli: Luca Fontanesi (Modulo 1) Paolo Zambonelli (Modulo 2)
  • Teaching Mode: Traditional lectures (Modulo 1) Traditional lectures (Modulo 2)
  • Campus: Bologna
  • Corso: Second cycle degree programme (LM) in Animal Biotechnology (cod. 8522)

Learning outcomes

The student knows high-throughput technologies to identify genes involved in production and reproduction traits in livestock species. The student knows methodologies for structural and functional genomics. The student knows the most important bioinformatics resources in this sector.

Course contents

Module 1: Applied Animal Genomics
The module is based on lectures (20 hours) and lab activities (4 hours) according to the following program:


1) Foundational concepts in genomics

2) Livestock production systems - genomics and animal domestication

3) Next generation sequencing

4) Livestock genomes: structure and variability

5) High throughput genotyping platforms

6) Major genes, QTL and candidate gene analyses

7) Genome Wide Association Studies

8) Foundational concepts in animal breeding, genomic selection

9) Animal biodiversity

10) Genomics and animal product authenticity

11) Analysis of relevant literature, case studies

 


Module 2: Transcriptomics and elements of bioinformatics

This module is divided in two teaching units: the first theoretical and the second of practice.

Contents of the first teaching unit (16 hours).

1.     Internet bibliographic survey

2.     Encode project: the functional organization of genomes

3.     Structure of a coding gene and mechanisms regulating gene expression

4.     Regulation of gene expression mediated by microRNAs and other short RNAs

5.     High-throughput techniques to establish gene expression

6.     Examples of gene transcription influencing the production in livestock species

The knowledge acquired at the end of the first teaching unit are the functional organization of genes and genomes, the mechanisms regulating gene expression and the high- throughput methods used to quantify the gene expression level .

Contents of the second teaching unit (8 hours).

7.     Databases of genomes of livestock species

8.     Databases of genes and genomic regions associated to  productive traits of economic importance in the livestock field

9.     Alignment and other bioinformatics analyses of DNA sequences

The knowledge acquired at the end of the second teaching unit are the capacity to manage the main databases and software useful for the study of genomes of livestock species.


Readings/Bibliography

Module 1

  • Notes from the lectures, scientific articles provided by the professor during the course, ppt presentations given during the course.
  • Molecular and Quantitative Animal Genetics. H. Khatib, Ed. Wiley, 2014
  • Genetica Animale. Applicazioni Zootecniche e Veterinarie. G. Pagnacco, ed. Zanichelli, 2016.

Module 2

  • Slides of the lessons and other teaching material (articles, web pages) suggested during the lectures

  • Hartl, Jones. Genetica. Analisi di geni e genomi. EDISES Napoli

  • Brown TA, Genomi, EDISES, Napoli

  • Lesk Arthur M. Introduzione alla Genomica. Zanichelli, Bologna
  • Pascarella Stefano, Paiardini Alessandro, Bioinformatica. Zanichelli, Bologna

The slides will be given by e-mail to the students during the teaching period or in other period, always upon request by e-mail to the teacher.


Teaching methods

Module 1 is based on lectures (20 hours) and lab activities (4 hours) in a lab with next generation sequencers.

Module 2 is divided into 2 teaching units: the first is based on lectures for a total of 16 hours; the second includes 8 hours of practice in the bioinformatics lab.

Assessment methods

The course is divided in two modules:
1) Applied Animal Genomics
2) Transcriptomics and Elements of Bioinformatics
The evaluation of the integrated course takes into account the level of knowledge acquired by the student for both modules.

Module 1

For module 1 is evaluated the level of knowledge acquired for the following points:

Structural genomics in livestock with concepts of population genetics and genomics

High throughput  technologies for analysing complex genomes

Applications of genomics to the  animal breeding sector.

Use if databases to analyze livestock genomes

The student may prepare a written (text or slides) short thesis developing one of the topic of the course that will be discussed during the exam. The student have to demonstrate that he/she has acquired all basic and relevant concepts needed to prepare the short thesis.


Module 2

For module 2 is evaluated the level of knowledge acquired for the following points:

Gene structure and regulation of activity

Functional organization of genes and genomes

Techniques used to assess gene expression

Use of databases and software to analyze livestock genomes

The student may prepare a short thesis using slides developing one of the topic of the course that will be discussed during the exam.

 

Teaching tools

PC, video projector, blackboard, scientific articles.

Office hours

See the website of Luca Fontanesi

See the website of Paolo Zambonelli

SDGs

Zero hunger Responsible consumption and production Climate Action Life on land

This teaching activity contributes to the achievement of the Sustainable Development Goals of the UN 2030 Agenda.