General information on the Unit
Contact hours: 73 (42 lectures, 31 practicals)
Personal work hours: 77
Venue: Mediterranean Agronomic Institute of Zaragoza, laboratory of the Department of Genetics and Plant Production and laboratory of the Department of Pomology of the Experimental Station of Aula Dei of CSIC.
- Developed during the first academic year of the Master, at the end of the first semester.
- The assessment of this Unit consists in a unique exam at the end of the first semester.
Requisites and permanence
There are no previous requisites
Combination of theoretical and practical classes, individual and group study and work, and technical visits.
Lecturers may deliver the course in Spanish or in English. In the second case, simultaneous interpretation into Spanish is provided. The documents supplied by the lecturers may also be written in Spanish or in English.
Presentation of the Unit and context within the syllabus
The unit reviews different genomic technologies, showing how these tools influence plant breeding strategies and provide new alternatives in the selection of complex traits. First, an introduction to the use of bioinformatics and database management is provided. A second part of the unit is devoted to genome sequencing and resequencing, as well as to comparative genomics. Through practical exercises, the students acquire experience in accessing different gene databases, comparing them and finding useful information, as well as providing hands-on experience of comparative map displays. Mutagenesis and TILLING are special tools used to generate and detect new allele forms for basic research and applied plant breeding. Finally, the unit analyses genome editing and the different stages of plant transformation processes, reviewing the control of gene expression and the molecular analysis of regenerated plants. The breeding interest of transgenic organisms and the modified traits are assessed. Special attention is paid to risk assessment, legislation and social implications of utilizing transgenic plants.
- SC1 Mastering the basis and principles of modern plant breeding, including new quantitative and molecular tools like genomics, and the knowledge and application of '-omics' technologies in general.
- SC4 Understanding and using quantitative tools to solve biological, mathematical and statistical problems.
- GC1 Integrating scientific and technical knowledge and applying them discerningly.
- GC2 Performing scientific and/or technical information searches and processing them selectively
- GC3 Analyzing results or strategies and elaborating conclusions which contribute to clarify the problems and to find possible solutions
The student, at the end of the learning of this Unit:
- Has gained experience in the use of different available genomic databases and computer software specific for genomic analysis.
- Appreciates the practical achievements that mutagenesis and TILLING have reached in the development of new varieties and materials of interest for genetic studies, and knows the methods for the induction of artificial mutations and the molecular bases of the changes produced.
- Has a deep insight in the implementation of genetic transformation for the obtaining of transgenic varieties resistant to certain biotic and abiotic stresses, to get high quality varieties, particularly nutritious, and molecules of industrial or pharmaceutical use.
- Assesses the advantages and disadvantages of the application of genetic transformation from a technical and socio-economic perspective.
- Is capable of integrating genomic advances in conventional breeding programs in order to achieve specific objectives and increase programme efficiency.
- Genome databases and bioinformatics
- Genome sequencing and resequencing
- Comparative genomics
- Mutagenesis and TILLING
- Genome editing
- Applied plant biotechnology
Learning activity 1: Lectures combined with case studies
Percentage of contact: 42%
Learning activity 2: Practical sessions of solving exercises and problems
The aim of the practicals is to explore the tools for genome sequencing and the databases of plant genomes, to compare genomes and to get started in the use of BLAST, ENSEMBL, etc., as well as in other transcriptomics and gene expression tools. The students work in pairs in the computer room to have access to the bioinformatics software available in internet.
Percentage of contact: 80%
Learning activity 3: Work in groups
The students work in groups of 4-5 members and, tutored by the lecturer, they analyze literature related to the issues of production and use of transgenic plants. Each group produces an oral presentation in class. The results of each group are discussed with the lecturer and the other groups.
Percentage of contact: 65%
Learning activity 4: Practical sessions in the lab
The practicals are carried out in the laboratory of the Department of Genetics and Plant Production and in the laboratory of the Department of Pomology of the Experimental Station of Aula Dei of CSIC.
(1) Detection of transgenic Bt maize, through real-time PCR
(2) Assessment of in vivo resistance to the borer, observing survival throughout time of Sesamia nonagrioides larvae released in two- to three-week-old maize seedlings. Students are provided with a specific plant, and they must justify whether it is a transgenic plant or its original, susceptible to the borer
Percentage of contact: 50%
Learning activity 5: Technical visit to a research centre in the field, such as the Centre de Recerca en Agrigenòmica (CRAG) of the CSIC-IRTA-UAB-UB in the Campus Central de la Universidad Autónoma de Barcelona en Bellaterra, Barcelona (visit illustrating both Units 4 and 5).
Percentage of contact: 75%
Assessment system 1: Written exam composed of questions provided by the different lecturers of the Unit, with free access to the PC, for solving practical exercises, similar to those carried out during the practical sessions. The exam is a combination of multiple choice questions with other concrete ones requiring a short development. The exam assesses both the content of lectures and the understanding of the practicals and the processes observed during the technical visit.
In the written exam, the questions which are not multiple choice are marked according to the technical and conceptual precision of the answer, and to the reasoning approach, and the exercises according to the understanding of the methodology and the validity of the results.
Weighting: 80% of the final score of the Unit
Assessment system 2: Global assessment of the exercises and problem solving by the lecturer in charge. The understanding of the methodology and the quality of the results obtained will be assessed. The score is the same for both members of the pair.
Weighting: 10% of the final score of the Unit
Assessment system 3: Assessment of the work in groups by the lecturer in charge. The assessment is based on the presentation and defence of the work. The clarity of the presentation and the quality of the reasoning provided in the defence will be assessed. The score is the same for all members of the group.
Weighting: 10% of the final score of the Unit
Carlos ALONSO, CSIC-CNB, Madrid (Spain)
Teresa CAPELL, UdL, Lleida (Spain)
Paul CHRISTOU, UdL-ICREA, Lleida (Spain)
Ángel FERNÁNDEZ MARTÍ, UC Davis (US) / CITA-GA, Zaragoza (Spain)
Jordi GARCIA-MAS, CRAG, Barcelona (Spain)
David MARSHALL, The James Hutton Institute, Dundee (UK)