95956 - High-Throughput Technologies for Sustainable Animal Breeding

Learning outcomes

At the end of the course, students know the main technologies and applications of large-scale phenotyping and genotyping to enhance the efficiency and sustainability of animal breeding programs. Students know the main phenomics and genomics platforms and their application for sustainable livestock production, and how to design breeding programs in a circular economy perspective.

Course contents

SPECIFIC PREREQUISITES FOR THIS COURSE:

To better understand the topics covered in this course, students are advised to have already acquired knowledge in the following areas: basic statistics, biochemistry, and animal production.

SPECIFIC CONTENTS:

The syllabus is structured as follows:

Lectures:

• Introduction (4 hours): The domestication of livestock species, topics associated to animal production. The student is expected to define animal production system and what are the main drivers of genetic variation.
• Collection of information (4 hours): Phenotypes recorded in animal breeding. Herdbook and marker information. The student is expected to know the main characteristics of a trait to be potentially included in breeding programs, and the importance of herdbook and genetic markers in a breeding perspective.
• Phenomics (4 hours): Definition and platforms for large-scale recording of animal traits in a breeding perspective. The student is expected to know the importance of the collection of a phenotype on a large-scale and at a cost-effective.
• Genomics (4 hours): Genome mapping and sequencing. The SNP-chip technology. Association studies: candidate gene approach and genome-wide association studies. The student is expected to know the main platforms for genotyping and how to quantify the association between genotype and animal characteristics.
• Animal model (8 hours): Definition and components of the animal model. Variance components and genetic parameter estimation: heritability, repeatability, genetic correlations. Genetic and genomic relationship matrices: A, G and H. The student is expected the sources of variation contributing to the phenotypic variability of trait and the importance of genetic parameters estimation for selective breeding.
• Genomic selection (4 hours): The concept of breeding value. Estimation of animal genetic and genomic breeding value. Genetic and genomic methods for breeding value estimation. Application of genomic selection. The student is expected to learn how to estimate animal genetic and genomic breeding value, including multiple steps and one step methods.
• Evaluation of a breeding program (4 hours): The response to selection and the genetic gain. Quantification of the genetic trend and monitoring the rate of inbreeding using genomic data in a population under genetic selection. The student is expected to be able to evaluate the effectiveness of a breeding program and to propose mating strategies to optimize the rate of genetic gain.

Laboratory and Practical Sessions:

• Python hands-on (8 hours)
• Visits/Seminars (8 hours)
• Student Journal Club (8 hours)

Readings/Bibliography

The teaching materials for this course are available on the Virtuale Learning Environment (https://virtuale.unibo.it/?lang=en).

Suggested textbooks:

• Molecular and Quantitative Animal Genetics. H. Khatib, Ed. Wiley, 2014
• Genomes 4. T.A. Brown, Ed. Garland Science, 2017

Supplementary reading:

• Linear Models for the Prediction of Animal Breeding Values. R.A. Mrode, Ed. Cabi, 2014
• Scientific articles and readings provided on Virtuale

Teaching methods

The course includes both theoretical lectures and practical sessions.

Considering the types of activities and teaching methods adopted, attendance for this course requires the successful completion of Modules 1 and 2 via e-learning, and Module 3 on health and safety training in study environments. Information about the schedule and access to Module 3 is available in the dedicated section of the Degree Program website.

Participation in practical and laboratory sessions requires wearing a lab coat and appropriate footwear. Suitable personal protective equipment (PPE), such as disposable latex gloves, will be provided as needed.

Assessment methods

The assessment for the Monodisciplinary Course “High-throughput Technologies for Sustainable Animal Breeding” consists of a written exam using EOL platform (https://eol.unibo.it/?lang=en), with both multiple-choice and open questions. Multiple-choice questions are 10 and each correct answer is evaluated +1 point, 0 for each wrong or missing answer. Open questions are 10 and each correct answer is evaluated +2, 0 for each wrong or missing question. Student Journal Club presentations are evaluated up to 5 bonus points on the final evaluation.

A minimum score of 18/30 is required to pass the exam.

Negative results are not graded numerically but recorded as “withdrawn” or “failed” in the electronic transcript on AlmaEsami, and do not affect the student’s academic record.

Grades for individual parts and the final grade will be published on the Virtuale Learning Environment (https://virtuale.unibo.it/?lang=en) by the designated course contact within 5 working days of the exam.

Students may reject the final grade 1 time, by informing the course examiner via email within 5 working days.

The designated course contact for this course is Prof. Giulio Visentin.

Students can register for exams through the AlmaEsami platform (http://almaesami.unibo.it/). Exams are scheduled during the designated periods in the academic calendar. Additional sessions are available for students beyond the standard program duration.

Students with learning disorders and/or temporary or permanent disabilities: please, contact the office responsible (https://site.unibo.it/studenti-con-disabilita-e-dsa/en/for-students) as soon as possible so that they can propose acceptable adjustments. The request for adaptation must be submitted in advance (15 days before the exam date) to the lecturer, who will assess the appropriateness of the adjustments, taking into account the teaching objectives.

Teaching tools

The lessons are delivered with the support of audiovisual systems, including PowerPoint presentations, a video projector, and the Teams platform. In case of difficulty in understanding the course content, the instructor is available for clarification meetings, which must be scheduled via email.

Office hours

See the website of Giulio Visentin