GENOMICS AND MOLECULAR MARKERS
Learning outcomes of the course unit
Genome sequencing has generated a huge amount of data which have revolutionized the research approach. the 'omic' concept has been applied to all field of genetic research with the aim to study the whole genome at structural and functional level. the objective of the course is to provide the knowledge of the basic principle of the new approaches in the field of biological and genetic analysis. Practical activities are not foreseen, however the students will have the opportunity to apply some of the approaches previously discussed, during the stage period. The case studies can be considered an opportunity to train the students in the critical analysis of research approaches.
Course contents summary
The course is organized in two groups of lectures. The first group is focalized on “Molecular markers” and will give an overview of the most popular molecular markers used for DNA analysis. Protocols and associated problems will be described. Case studies will be described and discussed in order to give some examples of the main applications of molecular markers (genetic mapping, fingerprinting, marker-assisted selection, association mapping, locating and cloning genes for important traits, forensic sciences, positional cloning of disease genes). The second group of lectures will regard genomic analysis, in order to provide the knowledge about the characteristics of a genome in different types of organisms. The main steps of genomic analysis will be discussed (genetic mapping, physical mapping, genome sequencing, and annotation)
Case studies will be discussed about genomic characterization in model organisms. The discussion of case studies will allow the students to understand how molecular markers can be useful in genomic analysis.
Molecular markers: definition and classification; Molecular markers based on restriction and hybridisation techniques; Molecular markers based on PCR; Markers based on sequencing.
Analysis of genetic variability and gene flow; genotyping and DNA fingerprinting; segregation models and development of association maps; Mapping strategies: NIL (near isogenic lines) and BSA (bulk segregant analysis); QTL mapping; Marker Assisted Selection (MAS) for qualitative and quantitative traits in crops; Map-based cloning; Linkage disequilibrium (LD); Genomics and proteomics techniques for food safety
Genome sequencing projects of model organisms.
Cloning vectors; Genomic and cDNA libraries; restriction maps; Southern blot hybridization (SBH); In situ hybridization
Genetic maps, physical maps. Sequencing methodologies: classical and NGS (Next Generation Sequencing). Genome annotation through bioinformatics. Gene expression analysis: RT-PCR, mRNA profiling.
Libri di testo
Brown TA, “Genomi” Edises (cap 1-9)
Greg Gibson and Spencer V. Muse,"Indroduzione alla Genomica" - Zanichelli (cap. 1,2,5)
Lewin B, et al. “ Il gene” Zanichelli (seconda edizione compatta 2011) ( cap. 4, 5, 23)
Barcaccia, Falcinelli "Genetica e Genomica" vol III cap 17,18 Cap 20 (come approfondimento)
-Wang D.G, Fan J.B., Siao C.J., Berno A., Young P., Sapolsky R., Ghandour G., Perkins N., Winchester E., Spencer J., Kruglyak L., Stein L., Hsie L., Topaloglou T., Hubbell E., Robinson E., Mittmann M., Morris M.S., Shen N., Kilburn D., Rioux J., Nusbaum C., Rozen S., Hudson T.J., Lipshutz R., Chee M., Lander E.S. Large-scale identification, mapping, and genotypimg of single-nucleotide polymorphisms in the human genome. Science. 1998, 280: 1077-1082
-Rafalski A. Applications of single nucleotide polymorphisms in crop genetics. Current Opinion in Plant Biology. 2002, 5:94-100
-Morgante, M., and A.M. Olivieri. PCR-amplified microsatellites as markers in plant genetics. Plant J. 1993, 3:175-182.
-Hunt D.J., Parkes H.C., Lumley I.D. Identification of the Species of Origin of Raw and Cooked Meat Products Using Oligonucleotides Probes. Food Chem. 1997, 60: 437-442
-Gupta P.K., Roy J.K., Prasad M. Single nucleotide polymorphisms: a new paradigm for molecular marker technology and DNA polymorphism detection with emphasis on their use in plants. Curr.Sci. 2001, 80: 524-535
-Andersen J.R. and Lübberstedt T. Functional markers in plants. Trends in Plant Science. 2003, 8 (11): 554-560
The course is organized in lectures, some practical activities in will regard the use of genomic database and literature database. This activity is instrumental for the preparation of the final exam.
Assessment methods and criteria
The learning ability will be verified with an oral examination based on: i) discussion of a scientific topic, chose by the student, taken from scientific literature; ii) general questions about the topics treated within the course. In this way the teacher will be able to evaluate the learning ability in general and the ability to apply the knowledge acquired to the understanding of the research approaches utilized in the genomic field.