99875 - Genomics and Biotechnologies Applied to Annual Crops

Learning outcomes

At the end of the course the student is aware: in Module 1, of the basics of molecular biology and genomics applied to selection with advanced methodologies such as the use of genomic sequence information and the use of cutting-edge molecular techniques for: 1. the characterization, management and use/enhancement of genetic diversity 2. the identification of genetic diversity useful for the purposes of selection (direct and reverse genetics) 3. The process of isolating the causal genes of the phenotypes. In Module 2, of molecular biology and biotechnology applications for: 1. The analysis of gene expression, proteomics and metabolomics. 2. biotechnological applications for the manipulation of gene transcription (defence, production of biostimulants and growth regulators) 3. in vitro culture techniques, transgenesis and genomic editing. At the end of the course the student knows and can critically analyze the benefits and risks deriving from the cultivation and use of vegetable GMOs.

Course contents

Concepts to know as they are useful for the full understanding of the lessons of both modules:

Classical or Mendelian genetics. Structure of DNA and RNA, organization of chromatin. Significant components of genomes (coding portion, gene content of a genome, structure of genes, Transposable elements Regulatory elements. Transcription and Translation of genes and their regulation. Morgan's chromosome theory, genetic mapping, forward and reverse genetic techniques
Inheritance of quantitative factors, polygenic Population genetics.

 

Module 1. Prof. Maccaferri, Applied genomics

Lesson 1. Introduction to genomics applied to genetic improvement. Definition of Genomics and Biotechnology. Genetic improvement 4.0 and integration of genomics components to answer the fundamental questions of modern genetic improvement. (Shared lesson Salvi and Maccaferri)

Lesson 2. Origin of native genetic variability. Genomic (auto and allo-polyploidy), chromosomal and gene or point mutations. Genetic diversity generated at meiosis and crossing over. Genetic diversity generated by the activity of transposable elements. Biological impact on transcript and protein functionality. Impact on qualitative (strong mutations) and quantitative (weak mutations) traits. Neutral, deleterious and positive mutations. Natural selection (positive, negative or purifying, diversifying). Effects on genetic diversity. Production of new species. Mutation models. Infinite site and Infinite allele model and effects on genetic diversity. Ancestral variant and derived variant.

Lesson 3. Genes and gene networks for traits of agronomic interest and for adaptation. Network of vernalization, photoperiod and response to cold and nitrogen. Disease resistance.

Lesson 4. Genome analysis. DNA and RNA sequencing. Short and long read techniques, parallel and single molecule techniques. Genome assembly. Structure and evolution of genomes. Annotation of functional elements of genomes (coding portion and transposable elements). Genomic databases and expression databases. Multi-alignment of sequences. BLAST (Basic Local Alignment Search Tool). Concept of homology, synteny and collinearity. Use of model species information. Translational genomics.

Lesson 5. The structure and organization of native genetic diversity. Estimation of genetic diversity in cultivated plants and concept of genetic erosion. Concept of working collection and core collection. Estimation of genetic and phylogenetic relationships between individuals and species. Population structure estimation using molecular markers (population structure). Genetic diversity in the centers of origin. evolutionary factors. Domestication. Fundamental genes for domestication. domestication syndrome. Effects of domestication on genetic diversity (Bottleneck Effect). Genetic structure of natural populations of autogamous and allogamous species. Linkage disequilibrium in autogamous and allogamous species. Relationship between recombination rate, number of historical meiosis, and linkage disequilibrium. Single bi-allelic mutations and organization of gene-level variants into gene haplotypes. Genomic or "long-range" haplotypes. Sequencing of multiple genomes of a species (pangenomes) and haplotype databases.

Lesson 6. Insights on the mapping of genes responsible for native variability (association or GWAS, and QTL analysis).

Lesson 7. Using molecular techniques to assist and increase efficiency in pre-breeding and breeding procedures with insights into Molecular Marker Assisted Breeding, Molecular Marker Assisted Backcrossing Genomic selection (GS) based on genomic prediction of breeding value.

 

Module 2. Prof. Salvi, Applied Biotechnology

Lesson 1. Advanced techniques for the study of gene expression, regulation and gene interaction. One- and two-hybrid systems, use of reporter genes, single-cell transcriptomics, spatial transcriptomics. Molecular approaches for the study of epigenetic processes. Molecular basis of heterosis with examples in cultivated plants.

Lesson 2. Advanced techniques for gene cloning and modification. Types of cloning vectors and their uses. Carriers Gateways. Gibson protocol. Gene synthesis. Isothermal amplification of DNA and its applications in plant genomics.

Lesson 3. Insights on NBT/gene editing. TALEN and ZFN. The evolution of CRISPR-CAS: base editing and prime editing. Other techniques (VIGS, and more). Synthesis and use of oligonucleotides in agriculture. Updates on regulations concerning agricultural applications of plants produced through NBT.

Lesson 4. Molecular farming and biotechnology for non-food agricultural plants. Plants as biofactories of molecules with high added value (recombinant proteins, vaccines, antibodies, biopolymers). Biotech techniques for energy production (biomass crops), for carbon capture.

Lesson 5. Applications of synthetic biology and biotechnology aimed at soilless agriculture, vertical farming and Cell Agriculture.

Readings/Bibliography

The slides of the lessons provided by the teachers on the VIRTUAL platform are an important basis for structuring the study in a logical sequence and focusing the insights on the most important topics. Therefore, please use them as a necessary but certainly not sufficient trace. The slides must be accompanied by the study of textbooks. The teachers will indicate the pages/chapters of the books to be studied.
Fundamental textbooks:

GENETICA AGRARIA (Russell, Wolfe, Hertz, Starr, McMillan, 2016, EdiSES publisher). The book is concise, highly schematic and provides chapters on even the most advanced topics of genomics and biotechnology, accompanied by intuitive diagrams.

MIGLIORAMENTO GENETICO DELLE PIANTE AGRARIE (F. Lorenzetti et al. 2017, Edagricole, Milan). The book is very detailed, comprehensive but long-winded. Many topics are covered excellently, but it is necessary to select the parts of interest to focus the study, based on the lessons.

"Review" type articles in English, provided by the teachers, written by specialists in the sector who provide an updated point on relevant topics of the course, also accompanied by videos

Office hours

See the website of Silvio Salvi

See the website of Marco Maccaferri