B1827 - Biotechnologies Applied to Breeding of Annual Crops

Learning outcomes

At the end of the course the student has a solid knowledge of the biology and structure of the plant genome and its characterizing elements including the nature and diffusion of mobile elements, polyploidy and the chloroplast genome. The student knows the genomic and biotechnological techniques aimed at dissecting the structure of the plant genome, identifying genes and studying their expression and function. Furthermore, the student knows the theoretical and practical aspects related to the main selection methodologies of cultivated plants, useful for promoting more sustainable agricultural systems; knows the principles of quantitative and population genetics, the methods of genetic improvement including crossing, selection, and genomic and biotechnological methods, including genome editing; knows the methods of studying genetic diversity for the evaluation, protection and use of genetic resources.

Course contents

Module 1 (Silvio Salvi)

Introductions to the genomes of cultivated plants: structure of the eukaryotic chromosome, nucleosome, telomere and centromere, structure of the genome, evolution of genomes. Genomes of the mitochondrion and chloroplast. Polyploidy in plants and in phylogeny. Haploidy and importance in genetic improvement. Concepts of forward and reverse genetics. Gene cloning: meaning and main methods with emphasis on plants of agricultural interest. Positional cloning. Cloning by insertion mutagenesis. BSA (for mapping by sequencing see module 2). TILLING and other reverse genetics techniques. Types of tagging (transposon and T-tagging, etc). Discussion of scientific articles regarding forward and reverse genetics. Quantitative genetics for applied genetics and breeding (Quantitative traits and components of phenotypic, genetic and environmental variance. Heritability). General approaches for the identification of genes underlying quantitative traits. Discussion of scientific articles on QTL analysis. Practical exercise on QTL analysis with data collection in the field, data processing, QTL analysis with software in a computer laboratory. Genetic engineering in plants. Biological bases and use of Agrobacterium. Examples of GMO cultivars of cultivated species. Cis-genesis. Definition and techniques of Genome Editing. Editing methods based on CRISPR-CAS. Critical analysis of the potential of editing in Italian agriculture. Case studies: biotechnological applications for a more productive, sustainable agriculture (tolerance to biotic and abiotic stress, reduction of chemical and energy inputs), and for the improvement of the nutritional profile – e.g. golden rice, for biomass production and for circular economy. Circular genomics.

Module 2 (Cristian Forestan)

Plant genome sequencing: general strategies. Sequencing techniques (Sanger, Next-Generation-Sequencing, long-read and single-molecule); assembly, anchoring and annotation of genomes. Genomics to support mapping and cloning. SNP-array. Mapping-by-sequencing. Genomic browsers and functional databases. Main genomic projects of cultivated plants. Transposable elements: biology, evolution and mechanisms of production of genetic variability. DNA methylation and mechanisms of epigenetic regulation and techniques for the analysis of the epigenome. Analysis of the transcriptome and regulation of gene expression: transcriptomic analyses from microarrays to RNA-seq, up to single-cell transcriptomics and spatial transcriptomics. Use of transcriptomics to study gene function. Time-course experiments. Co-expression networks. Identification of the master switches of a pathway. Techniques for the identification of binding sites of transcription factors. Gene expression database. Other –omics: proteome analysis and metabolomics. Integration of omics for understanding systems biology.

Module 3 (Marco Maccaferri)

Genetic structure of autogamous and allogamous plant populations. Neutral model. Hardy-Weinberg law and insights into population genetics. Main types of selection: purifying, positive, diversifying. Linkage disequilibrium. Gene haplotypes and long-range haplotypes. Methods for measuring genetic diversity in populations.
Plant genetic resources; germplasm collections. Genetic structure of natural and artificial populations and methods of analysis and improvement of the same. Methods of collection and conservation and molecular and phenotypic characterization of plant genetic resources.
Pre-breeding and the role of biodiversity in genetic improvement programs. Collections formed through molecular marker-assisted introgressions and the concept of “linkage drag”.
Process of domestication of cultivated plants and genetic consequences. Domestication syndrome and its molecular bases. Main genes involved in domestication. Concept of selective sweep and their identification in populations.
Examples of useful genes and alleles / mutations used in genetic improvement. The genes of N. Strampelli and N. Borlaugh. Main regulatory genes and gene networks of developmental processes and response to abiotic stress. Multiallelic series genes, self-incompatibility locus S and disease resistance loci.
Association mapping analysis or GWAS in populations, germplasm collections, variety panels.
Analysis of differences between populations for mapping and populations for breeding. Additional techniques for genetic improvement: recombination modifications, the Ph gene in cereals. Molecular basis of heterosis. Mutagenesis. Synthesis of synthetic polyploids using germplasm accessions. Synthesis of new species through polyploidy induction and accelerated domestication. Introduction to genetic improvement in the agri-food and agro-industrial supply chain for increasing primary plant production, improving the healthiness of food products and the sustainability of agricultural systems. Main critical factors for planning a breeding project. Main applications of marker-assisted selection (MAS) and genomic selection (GS). Selection for multiple traits and for adaptation to different environmental conditions.

Readings/Bibliography

Lorenzetti, Albertini, Frusciante, Rosellini, Russi, Tuberosa, Veronesi. 2018. Miglioramento genetico delle piante agrarie. EDAGRICOLE.

Scientific articles and handouts provided by teachers during class.

Teaching methods

Lectures and exercises in biotechnology laboratory, computer laboratory and greenhouse.

Assessment methods

The learning assessment and evaluation will consist of a single final oral exam, with all instructors participating. Two questions will be asked for each module, designed to test knowledge of the topics covered in the program and the ability to correctly apply genetic and biotechnological tools and procedures in the breeding of annual plants. The exam lasts approximately 30 minutes.

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

Lectures will be held in classrooms equipped with projectors for presentations (e.g., PowerPoint). The slides and other teaching materials will be made available on Virtuale. Where available, links to specialized websites for further study suggested by the instructors will be provided. Practical exercises will be conducted in laboratories equipped for molecular biology and biotechnology activities, in greenhouse or in experimental fields, and in computer labs (with individual seats per student). Industry experts (e.g., seed and nursery sector professionals; doctoral students and/or researchers from foreign laboratories, etc.) will be invited to supplement and complement the training and foster contact between students and the world of postgraduate work and research.

Office hours

See the website of Silvio Salvi

See the website of Cristian Forestan

See the website of Marco Maccaferri