Section 1 Molecular taxonomy.
- Applications of molecular taxonomy from agri-food security to biodiversity and biomonitoring;
- Principles and methods of molecular taxonomy;
- DNA extraction from agri-food and other environmental matrices;
- DNA barcoding and metabarcoding: from single organism to communities;
- NGS sequences platform used in metabarcoding;
- Single marker vs multiple markers, PCR-free gene capture approaches;
- Reference databases and ad-hoc built databases;
- Workshops will be conducted on experimental design, primer selection and library preparation,
basic skills on bash environments, analyses of NGS data and taxonomy assignment
Section 2- Genomics.
- Techniques and approaches in genome, exome and epigenome sequencing;
- Strategies for plant genome analysis and assembly;
- Plant genome structure, synteny and evolution;
- Applications of genomics in plant breeding;
- Workshops will be conducted on sequence analysis and alignments; design of experiments in plant genomics;
Section 3 Functional genomics.
- Techniques and approaches in RNA analysis and modulation;
- Strategies for genome modification;
- Integration of high throughput /content techniques (omics) and data analysis;
- Workshops will be conducted on gene targeting; RNA expression analysis and integrated omics to modulate biological functions.
Prerequisites for admission
PLEASE CHECK THE SYLLABUS PROVIDED IN THE MOODLE PAGE OF THE COURSE!!!
The student can take full advantage of the teachings if some background is known about molecular biology, molecular genetics (molecular markers and their use), organic chemistry, and biochemistry.
These topics, for example, are a useful wealth of knowledge: Plant cell, haploid-diploid development cycle of higher plants, mitosis and meiosis
Chemical composition and structure of DNA, the Watson and Crick model, DNA replication, gene structure of a eukaryote, transcription, translation, genetic code, expression regulation, dogma of molecular biology
Mutations, molecular basis of mutations, point mutations, IN / DEL, gene mutations, chromosomal.
Polyploidy, auto and allopolyploidy. Causes and mechanisms of origin, advantages of polyploidy. Importance in domestication, diffusion.
Mendel, theory and practice of Classical Mendelian Genetics, inheritance of simple characters, Mendel's three laws, Chi2 test
Chromosomal theory of inheritance
Dominance, semi-dominance (partial dominance), co-dominance. Meaning in allogamic and autogamous species. Genetic load in genetic species and purifying selection in autogamous species. Allard hypothesis
Gene interaction or epistasis and pleiotropy.
Gene association and recombination, crossing over, recombination, calculation of map distances between loci, genetic maps, linkage.
Transition from gene markers to molecular markers. Genetic and molecular markers, concepts, types (RFLP, SSR, SNP, IN / DEL) and their use, PCR, genome sequencing, genomic databases, outline of Next Generation Sequencing
Gene haplotypes at the causal loci of natural gene variability and haplotypes with diagnostic molecular markers.
Quantitative or complex traits, normal distribution: multifactorial hypothesis, genetic control of quantitative traits. QTL: loci for quantitative characters.
Basics of the genetic improvement of autogamous and allogamic plants and selection assisted by molecular markers.
The slides (in English) will be timely provided during the course and will include explanatory text; additionally, papers and books abstracts will be posted on the Ariel website of the course. Suggested text books:-Genomes (T.A. Brown, 2018); Molecular Plant Taxonomy - Methods and Protocols. Ed. Pascale Besse. Humana Press, 2014.-Environmental DNA for biodiversity research and monitoring. P. Taberlet, A. Bonin, L. Zinger, E. Coissac. Oxford University Press, 2018; Bioinformatics and Functional Genomics, 3rd Edition Jonathan Pevsner ISBN: 978-1-118-58178-0 October 2015 Wiley-Blackwell 1168 Pages