BIODIVERSITY STUDIES BY APPLICATIONS OF GENOME ANALYSES

Single discipline educational activity

Course Sheet

Academic Year of enrolment:

2020/2021

Type of Course:

Elective Course

Optional/Mandatory:

Optional

Degree:

Master's Degree Programme in AGRICULTURAL SYSTEMS

Disciplinary Sector:

Agrarian Genetics

Language:

Italian

Credits:

Programme Year:

Professor and Collaborators:

RODRIGUEZ Monica

Obligatory attendance:

Yes

Minimum hours of attendance:

Hours of classroom activity:

Prerequisites:

It is suggested, but not compulsory, that the students who want to attend the course have previously attended a course in Agricultural Genetics

AF code:

A000368

Assessment Methods

Verification of learning:

The exam will be subdivided into two parts. The first part (supported by a slide presentation) will aim at evaluating the student's skills in presenting a recent study on one of the subjects of the course. The second part (based on oral questions) will aim at evaluating the student's skills and knowledge acquired during the course.

Teaching period

First semester

Objectives

Achieve the basic knowledge on biodiversity and understand the importance of its conservation and exploitation, with a focus on agricultural species. Learn which tools are availble to perform biodiversity studies at phenotypic and molecular level by attending lectures and participating to practicle bioinformatic activities (computer based excercises). Most common genomic analyses, development of molecular markers and analyses of data obtained by means of next-generation sequencing techniques will be the focus of the lessons of the course. Simulated and real genomic data will be analysed

Contents

Lecture and practical activity (1 CFU)
Introduction to biodiversity and agro-biodiversity. Genetic resources, wild and cultivated species. Domestication and genetic erosion. Centres of crop diversity. Sampling and characterization of crop genetic resources. Conservation tools: in situ and ex situ conservation. Bases on genetic structure of populations. Diversity within and between populations.
Molecular tools for genetic diversity studies. Practical activities (using students PC) on molecular data analyses.
Lecture and practical activity (1 CFU)
Study of agro-biodiversity by means of phenotypic traits. Mendelian and quantitative traits. Effects of the environment on quantitative traits. Quantifying environmental and genetic variation. Heritability.
How to choose the phenotypic traits to characterise a crop species. How to collect phenotypic data. Examples of field trial designs.
Lecture and practical activity (1 CFU)
Basic concepts on crop genomes. Online bibliographic research and use of online available dataset. Tools for genomic analyses (sequencing and exploitation of public databases). Study of crop diversity by means of genomic data.
Development of molecular markers (eg. SSRs and SNPs derived from Next Generation Sequencing approaches). Genome browsing. Sequence analysis and genome comparison.
Lecture and practical activity (1 CFU)
Bases of genetic map contruction and QTL mapping. Association mapping based on genome-wide markers and phenotypic data (Genome Wide Association studies, GWAS).
An example of GWAS using real data.

Recommended Bibliography

Text:
Genetica Agraria. Russell, Wolfe, Hertz, Starr, McMillan
Miglioramento genetico delle piante agrarie. AA Lorenzetti, Albertini, Frusciante, Rosellini, Russi, Tuberosa, Veronesi.
Scientific papers and reviews regarding the main subjects of the course, video (e.g. TED talks) and other teaching materials to be defined with students.

Methods of Provision

Conventional

Teaching Methods

Slide presentation; practical activities: personal computer required. If required, the lessons might be registered and make these available online.

Contacts/More Information

During the course practical sessions will be held which require personal computers. The students are therefore recommended to bring their own laptop and to have basic informatics skills.
If needed by foreign students, the teacher is available to held the lessons and the examinations in English, as well as to provide the educational materials/programs and any further help in English.

BIODIVERSITY STUDIES BY APPLICATIONS OF GENOME ANALYSES

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Course year: 2

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BIODIVERSITY STUDIES BY APPLICATIONS OF GENOME ANALYSES