General information on the Unit
Contact hours: 72.5 (36 lectures, 36.5 practicals)
Personal work hours: 52.5
Venue: Mediterranean Agronomic Institute of Zaragoza, laboratories of the Department of Genetics and Plant Production and of the Department of Pomology of the Experimental Station of Aula Dei of CSIC, and laboratory of the Department of Molecular Biology of the Aula Dei Scientific and Technological Park.
- Developed during the first academic year of the Master, in the middle of the first semester.
- The assessment of this Unit consists in a written exam and the assessment of problem and exercise solving 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 deals with different types of molecular markers and their applications. Then, their use in the estimation of genetic diversity and distances is studied, as well as linkage map creation. Another part of the unit is devoted to QTL (Quantitative Trait Loci) detection and QTL validation. Finally the principles of marker-assisted selection are introduced. In the laboratory practicals, students acquire experience in DNA extraction and in marker analysis methodology. Practicals are also carried out on building genetic maps and using QTL mapping in the analysis of complex quantitative traits through the use of specific software programs.
- SC1 Mastering the basics and principles of modern plant breeding, including new quantitative and molecular tools like genomics and, in general, the knowledge and application of '-omics' technologies.
- SC2 Identifying and assessing phenotypic and genetic variability and determining the components of variation.
- SC4 Understanding and using quantitative tools to solve biological, mathematical and statistical problems.
- SC6 Distinguishing and assessing the molecular marker types most used in genetic studies, and making and comparing genetic maps, as well as detecting QTLs.
- GC1 Integrating scientific and technical knowledge and applying them discerningly.
- GC5 Learning and working autonomously, responding to unforeseen situations and re-aiming a strategy if necessary.
The student, at the end of the learning of this Unit:
- Is familiar with the different types of molecular markers most used in genetic studies and has experience in the construction and comparison of genetic maps.
- Understands the main applications of molecular markers in genetic studies and breeding programmes.
- Has practical experience in DNA extraction and in the use of markers.
- Has practical experience in the use of computer software for the construction of genetic maps.
- Knows how to use instruments for QTL classical and advanced analysis to locate and identify complex traits of interest in breeding.
- Molecular marker types
- Estimating genetic diversity and distances
- Linkage maps
- QTL detection (Quantitative Trait Loci)
- Biparental crosses
- Assotiation genetics
- Multiparental populations
- QTL validation
- Advanced backcrosses
- Near isogenic lines
- Fine mapping and positional cloning
- Principles of marker-assisted selection
Learning activity 1: Lectures combined with examples
Percentage of contact: 49%
Learning activity 2: Session of joint discussion of selected publications. Reading of a series of scientific papers of different levels to analyse and interpret genetic diversity results. Students work in groups and each group debates their conclusions with the lecturer and the other groups.
Percentage of contact: 100%
Learning activity 3: Practical sessions of solving exercises and problems
a) Calculation of genetic diversity matrices, factorial analysis and building phylogenetic trees using specific software.
b) Study on linkage and recombination. The exercises are carried out manually, with EXCEL software and using specific packages for the construction of genetic maps
c) QTL mapping using specific software.
In the three cases the exercises are carried out in pairs.
Hours: 20 (a: 4; b: 4: c: 12)
Percentage of contact: 60% (a: 50%; b: 100%; c: 50%)
Learning activity 4: Practical sessions in the lab
a) DNA extraction and genotyping using basic molecular markers. The practicals are carried out in the laboratory of the Department of Genetics and Plant Production and the laboratory of the Department of Pomology of the Experimental Station of Aula Dei of CSIC.
b) RNA extraction and detection of genetic expression using Real-Time PCR. The practicals are carried out in the laboratory of the Department of Molecular Biology of the Aula Dei Scientific and Technological Park.
In both practicals the students work in pairs and prepare a report including the results.
Hours: 27 (a: 16; b: 11)
Percentage of contact: 75% (a: 75%; b: 75%)
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 in Bellaterra, Barcelona (visit illustrating both Units 4 and 5).
Percentage of contact: 75%
Assessment system 1: Written exam developed from questions provided by the different lecturers of the Unit. The exam is a multiple choice test. The exam assesses the content of lectures as well as the understanding of exercise b, of the discussion of selected publications and of the processes observed during the technical visit.
Each correct answer is scored 1, each incorrect answer is penalized as –(1/no. of options). The final score is the sum of all scores divided by the number of questions
Weighting: 50% of the final score of the Unit.
Assessment system 2: Global assessment of the exercises and problems a and c by the lecturers 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: 20% of the final score of the Unit
Assessment system 3: Global assessment of the report on the laboratory practicals by the lecturers 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: 30% of the final score of the Unit
Pere ARÚS, CRAG, Barcelona (Spain)
Ana CASAS, CSIC-EEAD, Zaragoza (Spain)
Ángel FERNÁNDEZ MARTÍ, Fundación PCTAD, Zaragoza (Spain)
Jordi GARCIA-MAS, CRAG, Barcelona (Spain)
Yolanda GOGORCENA, CSIC-EEAD, Zaragoza (Spain)
Silvio SALVI, Univ. Bologna (Italy)