66632 - Genetics Applied to Plant Biotechnologyenetic

Course Unit Page

SDGs

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

Zero hunger Responsible consumption and production Climate Action Life on land

Academic Year 2020/2021

Learning outcomes

At the end of the course the student acquires knowledge about the molecular basis/platforms required for the study of the structure and function of plant genomes. Particular attention will be devoted to applications for major crops of agricultural interest, especially cereals. The student will acquire the knowledge required to map and clone Mendelian and quantitative loci (QTL) of interest for genetic improvement. The student will learn also the main methods used to obtain transgenic plants. The student will learn how different genomic platforms and genetic engineering can be used for academic studies and for application purposes. The applications will mainly refer to the variety fingerprinting, mapping & cloning, marker-assisted selection (MAS) and obtaining GM plant and how these methods are integrated in breeding programs.

Course contents

A) Prerequisites

Students who enter this course must have a good knowledge of basic genetics and molecular genetics as well as good knowledge of the fundamentals of basic cellular biology and physiology of plants. These prerequisites are provided by the basic courses taught during the first and second year of the course.

B) Teaching Units

1. Introduction to the course.

This lecture will present a quick overview of the main topics of the course with an emphasis on applied aspects and their socio-economic implications (Total teaching unit 2 hours)

Knowledge obtained in the teaching unit 1

The student learns the main issues related to plant biotechnology and their socio-economic impact.

2. Genome structure in plants(Total of the teaching unit: 4 hours)

The student acquires the basic knowledge on the structure of plant genomes with regard to size, functionality, relations between euchromatin and heterochromatin, the role of transposons, synteny and microcolinearity. The course will also present evolutionary aspects that allow one to better interpret the existing synteny between different species.

Knowledge obtained in the teaching unit 2

Knowledge on genome structure in plants and the role of euchromatin and eterochromatin
Evolutionary aspects of genomes and synteny.

3. Molecular markers (Total of the teaching unit: 4 hours)

The student acquires the basic concepts for the analysis of DNA polymorphisms by RFLP markers, RAPD, SSR, AFLP and SNP. The course will also examine the advantages and disadvantages of each class of markers and the costs related to their use.

Knowledge acquired through teaching unit 3

Knowledge of the main featiures of the different classes of markers
Critical analysis of advantages and disadvantages of the main classes of molecular markers.

4. Experimental populations for mapping of Mendelian and quantitative characters and QTL analysis and its applications(Total of the teaching unit: 8 hours)

Experimental populations for mapping of Mendelian and quantitative loci. RIL, IL and DH populations, concept of QTL and analytical methods to identify QTLs: single-marker method and interval method. Advantages and disadvantages of the QTL. Marker assisted selection. Assisted backcrossing with markers and its advantages over the traditional method.

Knowledge obtained in the teaching unit 4

Knowledge on how to assemble experimental populations for mapping genes and QTLs.
Knowledge on how to map genes and QTLs.
Applications of molecular markers: marker-assisted selection and marker-assisted backcrossing.

5. Analysis of genetic variability through molecular markers and domestication of crops(Total of the teaching unit: 3 hours)

Analysis of biodiversity through molecular markers. Methods of statistical analysis to determine the molecular basis of genetic distance. Effect of domestication on genetic variability. Heterosis and molecular studies on the causes of heterosis.

Knowledge obtained in the teaching unit 5

Knowledge of how to use molecular markers to study biodiversity
Knowledge about the processes of domestication and consequences for the genetic variability
Heterosis and molecular basis of heterosis

6. Association mapping(Total of the teaching unit: 2 hours)

Concept of linkage disequilibrium. Association mapping at the level of the entire genome. Populations suitable for association mapping. Advantages and disadvantages of association mapping.

Knowledge obtained in the teaching unit 6

The student learns the methods to carry out association mapping
The student learns to critically analyze the advantages and disadvantages of association mapping in plants of agricultural interest

7. Sequencing of genomes and trascrptomes and TILLING (Total of the teaching unit: 4 hours)

Sequencing methods. Sequencing plant genomes. Sequencing polyploid species. Interpretation of results. Resequencing of genomes. Applications of sequencing data. Analysis of the transcriptome. Methods to quantify the transcripts. TILLING of mutant collections.

Knowledge obtained in the teaching unit 7

Knowledge on sequencing methods and issues related to the sequencing of the polyploid species.
Analysis of the transcriptome and quantification of transcripts.
Knowledge of the TILLING method

8. Genetic engineering(Total of the teaching unit: 5 hours)

Realization of plasmid constructs. Genetic engineering of plants withAgrobacterium tumefaciensand the biolistic method. New methods of genetic engineering. Marker genes and reporter genes. Applications of genetic engineering in agriculture. Socio-economic considerations on GM plants.

Knowledge obtained in the teaching unit 8

The student becomes familiar with the general aspects related to the genetic modification of plants and the use of genetically modified organisms in agriculture.
The student acquires tools and information for a critical assessment of GMOs of plant origin.

9. Contents of the laboratory teaching unit (Total of the teaching unit: 30 hours)

Genomic DNA extraction from herbaceous species
Obtaining molecular profiles to characterize the genetic variability present in natural and artificial populations of herbaceous species
Obtaining genetic maps and their use to identify loci that control Mendelian and quantitative (QTL) characters
Bioinformatics analysis for the study of plant genomes and synteny relationships between species phylogenetically close

Readings/Bibliography

Miglioramento genetico delle piante agrarie, by F. Lorenzetti - E. Albertini - L. Frusciante - D. Rosellini - L. Russi - R. Tuberosa - F. Veronesi, Libri EDAGRICOLE. additional details at http://goo.gl/CwecXc

Teaching methods

The course will analyze the main issues related to the molecular analysis of the genomes of species of agricultural interest and related applications. The course will also analyze the socio-economic and technical issues related to genetically modified crops (GMOs). During the lessons the students will be consulted on specific topics in order to verify the level of preliminary knowledge especially in the field of classical genetics and molecular genetics.

Assessment methods

The course evaluation takes into account the level of knowledge and skills acquired by the student in relation to what was presented in the course. The knowledge and skills taught in this course are assessed through an oral exam, lasting about 30 minutes. In particular, four questions will be formulated relating to the basic aspects developed in the teaching units in which the course is articulated, as well as applicative aspects.

Teaching tools

For lectures, overhead projector, PC and projector will be used. For practical exercises, no specific tool is needed

Office hours

See the website of Roberto Tuberosa