Characteristics and organization

This Master is an official Master of the Spanish university system within the framework of the European Space for Higher Education. This Master has a clear international character and it has been on offer since 1982, its contents being updated and revised for each new edition.

Duration, mode and study regime

The Master has a duration of two years (120 ECTS) and is delivered on a face-to-face mode, full time basis. The Master begins every second year, so candidates may only register every two years.

The credit system follows the European Credit Transfer System (ECTS), where one credit equals 25 workload hours (including lectures, practical work, tutorials, preparing and sitting examinations, and personal and group work). The total workload hours per academic year is 1500.

In order to access the second part of the Master, it is necessary to have passed the first one and submit the required protocols for the tutored training activities constituting the second part (Practicum and Master’s final work) duly endorsed by the tutors. The period between registration to the first part of the Master and the Master of Science awarding date may not exceed four years. In exceptional, and duly justified cases, special exemptions may be granted.

Scientific direction and academic co-ordination

The Master scientific direction is performed by Prof. Ignacio Romagosa (University of Lleida, Agrotecnio, Spain).

The Master programme avails of a technical coordinator (Dr. Ramzi Belkhodja) belonging to the CIHEAM Zaragoza staff, who is in charge of supervising all those aspects related to the Master development and daily follow-up of the programme. The coordinator deals with the students’ suggestions and claims, acting as liaison between them, the scientific directors, the lecturers, the CIHEAM Zaragoza administration and the UdL/UPM-CBGP/Agrotecnio/CIHEAM Zaragoza Studies Commission of the Master.

Lecturers are assigned a time devoted to tutorials and clarification of doubts during their lecturing period. In the case of guest lecturers, CIHEAM Zaragoza facilitates anytime the contact between them and the students throughout the programme, even when they are no longer present physically.

To accomplish the project on the design of a plant breeding programme, students are assigned tutors who supervise the development of the work, and advise them in the search for information and in the choice of methodology to be applied to the proposed programme.

Students, if they request so, are assessed by the scientific director of the Master, the technical co-ordinator and the UdL/UPM-CBGP/Agrotecnio/CIHEAM Zaragoza Studies Commission of the Master on the election of the Practicum and the research work to be carried out during the second part of the Master, as well as on the election of the Practicum tutor, the research project director and the most adequate institutions for these activities. The Master’s organizing institutions also propose topics related to their research activities or other topics of interest previously arranged with a collaborating institution.

While carrying out the Practicum and the research work, each student has the guidance and advice of the Practicum tutor and the research project director, who must be a doctor of acknowledged prestige in the topic chosen.

Competences of this Degree

General competences

• 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.
• GC4 Making decisions and generating new ideas and knowledge in complex systems.
• GC5 Learning and working autonomously, responding to unforeseen situations and re-aiming a strategy if necessary.
• GC6 Team-working and promoting exchange and collaboration attitudes with other students, researchers and professionals.
• GC7 Communicating reasoning and conclusions both to a general audience and to a specialized public.
• GC8 Writing presentations and synthesis, preparing and presenting oral communications, and defending them in public.

Specific competences

• 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.
• SC3 Assessing the importance of genetic resources as variability sources in breeding programmes, and commanding the appropriate processes for their collection, conservation, evaluation and use.
• SC4 Understanding and using quantitative tools to solve biological, mathematical and statistical problems.
• SC5 Designing, planning and analyzing statistical and agricultural experiments with methodological thoroughness, assuming the limitations of the experimental approach.
• SC6 Distinguishing and assessing the molecular marker types most used in genetic studies, and making and comparing genetic maps, as well as detecting QTLs.
• SC7 Assessing the relevant methods and techniques that contribute to greater efficiency in the processes of selection and development of new varieties, particularly molecular techniques aimed at the development of marker-assisted selection programmes.
• SC8 Assessing the advantages and drawbacks of using different strategies and methodologies for improving tolerance/resistance to stress conditions from the perspective of improving the productivity, safety and quality of crops, ensuring the sustainability of agricultural systems.
• SC9 Integrating the knowledge of plant physiology, biochemistry and pathology in a plant breeding programme.
• SC10 Planning, developing and assessing specific programmes for breeding in different situations and environments, considering the available materials, the objectives set and the agronomic, environmental and socioeconomic constraints.
• SC11 Having a good command of the national and international legislation concerning the registration of new varieties and the protection of the intellectual property rights and, in particular, breeder's rights and patents.
• SC12 Assessing and comparing the processes of obtaining certified seeds and plants, and seed processing. Knowing the functioning of the seed marketing sector, as the final part of the breeding process.
• SC13 Assuming the responsibility of planning and carrying out, under the supervision of a tutor, but in a manner that must be largely autonomous, a work of initiation to research in the field of plant genetics and breeding.

Transversal competences

• TC CIHEAM Zaragoza Engaging in a multidisciplinary and multicultural environment.
• TC1UdL Achieving correction both in oral and written communication.
• TC2UdL Mastering a foreign language.
• TC3UdL Mastering information and communication technologies.
• TC4UdL Respecting the fundamental rights of equality between men and women, the promotion of Human Rights and the values of a culture of peace and democratic principles.

Syllabus

The programme of the Master is structured in two parts. The first part (60 ECTS) is professionally oriented and comprises lectures, practicals, personal and group work and study, and technical visits. This part is delivered by UdL, UPM-CBGP and Agrotecnio lecturers and guest lecturers of acknowledged experience from international institutions and universities, research centres and companies from different countries. The second part (60 ECTS) focuses on initiation to research, applying discerningly the knowledge, skills and competences acquired in the first part of the Master to the tackling of real issues related to plant genetics, genomics and breeding. This part of the Master is carried out at UdL, UPM-CBGP and Agrotecnio or other prestigious universities, research centres or companies, generally in Spain or the student’s country of origin, under the supervision of a Practicum tutor and a research project director, who must be a PhD with experience and reputation in the research topic.

To see each Unit programme in detail, please refer to the section Syllabus and Study guide.

First part of the programme

Unit 1. Agricultural systems and plant breeding (4.5 ECTS)
The Unit presents the historical evolution of plant breeding and makes the student understand and analyse the different elements and conditions that must be considered when designing a breeding programme, highlighting the role played by innovation.The Unit introduces also the agronomical, physiological and environmental context of plant breeding, and its contents are applied transversally in various of the following units. In this part, the Unit first presents the agricultural systems, the use of resources and the different production systems and cultivation technologies, then providing a vision on the importance of digitalization and the use of big data in agriculture. Subsequently, the Unit discusses the physiological determinants of crop production in the context of breeding, focusing on the genotypic effect, as well as the relationships climate change/agriculture, presenting options to adapt agriculture to the effects of climate change and to mitigate the impact of agriculture on climate change. Finally, the Unit deals with the use of crop models, presenting examples applied to plant breeding.

Unit 2. Plant genetics (6 ECTS)
The Unit presents the principles of plant genetics and its contents are of greatest importance to understand the following Units.The Unit presents the different plant reproduction systems, the evolution in the domestication of crop plants, the genetic structure of plant populations and the basis of quantitative genetics. The study of genetic diversity is the main core of the Unit, considering the different tools and methodologies that make possible its detection and assessment as well as the identification and validation of the genes responsible for traits of breeding importance.

Unit 3. Structural and functional genomics (3 ECTS)
The Unit complements the previous one, deepening the study of genomic structure and function using current and cutting-edge methodologies.The Unit first presents the bases and technologies of plant genome sequencing and assembly that allow the characterization and location of genes in the genome. The advantages of using pangenomes to improve the identification of variants from sequence data and genes associated with key traits are then presented. Subsequently, the Unit deals with how transcriptomics helps to measure gene expression and to discover relativeness among genotypes. Finally, the use of other omic technologies is introduced.

Unit 4. Introduction to data science for plant breeding (7.5 ECTS)
The Unit gathers the main statistical tools and methods used in the analysis of genotypic and phenotypic performance of plant material in breeding programmes.The first part of this Unit presents an introduction to the scripting languages. Then the unit deals with the design and analysis of individual experiments, and linear regression and correlation analysis. After an introduction to multivariate methods, the Unit deals with the statistical principles, objectives and methods for Genotype x Environment interaction (GxE) analysis. Finally, main elements of the selection theory are presented. The different parts of the Unit combine tutorials and practicals. Open-access software R studio is used throughout the different subjects of the Unit.

Unit 5. Bioinformatics (3 ECTS)
The Unit complements Unit 4, presenting bioinformatics resources in depth, first dealing with the available databases, software tools and methods, to subsequently analysing data filtering, imputation phasing, formatting and exportation. Then the Unit deals with genome sequencing, alignment and mapping, and genome comparison.

Unit 6. Breeding methods and variety development (12 ECTS)
This unit describes and analyzes different methods for the development of pure lines, populations’ improvement, hybrids development and clonal selection, assessing their advantages and constraints in relation with the general and specific objectives of the breeding programme. Germplasm diversity and development is being introduced with an emphasis in plant genetic resources, germplasm management and mutation breeding. Finally, the unit deals with commercial seed and plant production as the ultimate purpose of agricultural breeding programmes, and the legal aspects considering variety registration, variety protection and essentially derived varieties with FAO treaty and farmers rights and Nagoya protocol as an example of access and benefit-sharing. The Unit focuses on several special methods and techniques used in plant breeding programmes such as, in vitro techniques, double haploids and juvenility management. The unit analyses also 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.

Unit 7. Marker enable prediction and selection (6 ECTS)
This unit reviews different tools for linkage mapping and GWAS. First, the Unit studies different genetic concepts relate with alleles inheritance such as Identity by descent (IBD) and Identity by state (IBS) and their application in QTL mapping. Genetic distance and population structure is being introduced as a commonly caused by selection, mutation and drift in quantitative genetics.  Secondly, of the unit is devoted to QTL (Quantitative Trait Loci) detection and QTL validation, QTL mapping and GWAS. The last part of the unit is about evaluation of selection strategies based on different types of selection in plant breeding. This unit treats also genomic prediction and selection as extensions of QTL mapping and marker assisted selection. The initial part of the unit deals with these background principles for genomic prediction as well as with QTL mapping, GWAS, multiple regression and selecting genetic predictors. The main body of the Unit is then consist in theory and practice of genomic prediction and selection with special attention to different genomic prediction models (ridge, GBLUP, Lasso) and the construction of training and test set for genome enable prediction. 

Unit 8. Phenomics and analysis of amics data (3 ECTS)
This Unit introduces infrastructure needed for field and indoor platform phenomics. Then specific experimental designs and corresponding mixed models treated in detail together with spatial and longitudinal modelling. Statistical and machine learning techniques presented for pre-processing of phenomic data. Methodologies for the identification of the genetic basis of new phenotypic traits demonstrated. Finally, phenomic traits integrated in prediction models for yield. Examples and exercises used real data from phenotyping platforms and field experiments. 

Unit 9. Applied breeding programmes (9 ECTS)
The Units introduces breeding crops in a climate change framework. The first part of the unit is devoted to, in particular to breeding for cereal resistance/tolerance to drought and heat tolerance. As a previous stage to their handling, the physiological bases for determining development, growth and yield are studied, in order to enhance indirect selection for improving yield under stress. Resistance and/or tolerance mechanisms, adaptive traits and selection methods used are studied. The second part of the unit deals with tolerance and resistance to biotic stress. Pest biology and the nature, sources and manipulation of resistance are tackled, as well as the factors influencing its expression. The aspects of breeding that are specific to pest resistance and the importance of the use of resistant plants as part of sustainable integrated pest management programmes are highlighted. This second part also deals with breeding for resistance to fungi, bacteria, virus and nematodes. Plant/pathogen interaction and the different resistance mechanisms are reviewed, paying special attention to their assessment and the selection methods to obtain resistant cultivars. The third part of the unit covers crop quality components, as well as the factors influencing it. The approaches to improve crop quality are reviewed considering conventional breeding and other methodologies that can increase the efficiency of breeding processes. The last part of the unit is to study different autogamous, allogamous and vegetatively propagated species, their reproductive characteristics, the sources of variation and the breeding objectives and methodology, reviewing current breeding programmes where traditional breeding is combined with the use of biotechnology tools. Finally, the unit deals with case studies such as are cereals (wheat, maize and barely), vegetables and fruit trees.

Unit 10. Individual projects: design of plant breeding programme (6 ECTS)
Throughout the first part of the Master, students carry out an individual project of a breeding programme, on a plant species of their choice applied to specific environmental and socio-economic conditions, normally those of their country of origin. This project allows students to: (i) apply the principles and methodology presented during the course; (ii) gain experience in finding technical and scientific information, as well as in the selective treatment of such information; (iii) make a critical assessment of different breeding alternatives; (iv) learn how to define and integrate the different components of a breeding programme; and (v) acquire experience in the preparation and presentation of oral communications and their public defence.

Second part of the programme

Unit 11. Introduction to research (30 ECTS)
This Unit is divided into two subjects. The first one, "Soft skills" (6 ECTS) provides skills in writing, composition and review of technical and scientific texts, and for the establishment and use of bibliographic reference databases, preparation of interviews, writing and presenting CVs, group work and handling of different cultures and  Management of projects and programmes. The second subject "Practicum on Plant Breeding" provides the background knowledge, skills, and attitudes necessary for the planning and realization of research or professional projects in a given topic within the Master speciality. The Practicum topic is chosen according to the educational and professional interest of the student, and can take place in various universities, research centres and companies collaborating in this part of the programme. It is a practical professional stage in which the student, under the supervision of a tutor, works and learns autonomously and benefits from being included in a working team. Training focuses on understanding the scientific-technical objectives of the research or work carried out by the host team on the topic chosen for the Practicum, on the handling of the instrumentation and equipment used by such team, on the identification of sources of knowledge relevant to the topic and on the effective planning of work.

Unit 12. Master’s final work (Master Thesis) (30 ECTS)
Represents the application of the training received to the production of an original research project on a specific topic, within the scope in which the student has performed the Unit "Introduction to research", and whose results are potentially publishable. The student is provided with training and supervision to master the application of techniques and methods selected for the research and for becoming able to objectively assess the significance of the results and conclusions obtained. Likewise, the student is endowed with the necessary training in order to produce a written document on the project carried out, and submit and orally defend the research results before a jury.

Schedule

First part of the Master (first academic year)

It usually starts at the end of September and finishes at the beginning of June. This part takes place during morning and afternoon, with two periods of vacation: Christmas (3 weeks) and Easter (2 weeks). The exact dates are determined each year according to the annual planning of the academic year and are announced in advance.

Unit 1 to Unit 6 are developed sequentially, in the first semester. Units 7 to 9 are also developed sequentially in the second semester. Unit 10, "Individual projects: design of plant breeding programme", entails the application of the training received in the different subjects of the first academic year, so it takes place over the two semesters. To see the specific timetable for each Unit, please refer to the section Syllabus and Study guide.

Second part of the Master (second academic year)

The subject "Soft skills" takes place in two weeks during the first and the second semester. The Practicum on Plant Breeding and the Master’s final work (Master Thesis) are developed during the third and fourth semesters, amounting in total a maximum duration of 10 months. The Practicum usually begins in early September, although, depending on the Protocol established or the convenience of the tutor and the host institution, the starting date may be delayed or slightly brought forward, prior acceptance of the UdL/UPM-CBGP/Agrotecnio/CIHEAM Zaragoza Studies Commission of the Master. Since this part of the programme [Practicum and Master’s final work (Master Thesis)] occurs in the collaborating institutions (universities, research centres or companies), the working schedule and holiday calendar is adapted to the specific requirements of such institutions.

Languages

English is the working languages of the Master. To see specific requisites for language knowledge, please refer to the section Access, admission and scholarships. Before the beginning of the first part of the Master, an intensive Spanish language course is organized from July to September for CIHEAM Zaragoza scholarships holders and other students who wish to improve their Spanish language. For information about the students that must follow the Spanish language course please refer to the section Access, admission and scholarships. For more details about the course, consult the epigraph "Spanish language course", under the section Practical information for the students.

In the first part of the programme, the lectures of Units 1 to 9 are delivered in English. The handouts provided by the lecturers will be in English. The exams can be taken either in Spanish, English or French. In Unit 10, students may write the design project of a plant breeding programme and perform the oral presentation and defence of the Unit in Spanish, English or French.

In the second part of the programme, within the Practicum of Unit 11, tutored training is in English. The periodical reports are in English. The oral exam before the Jury may also be taken in Spanish or English. In Unit 12, the Thesis document and oral presentation are preferably in English.

Lecturers of the first part of the Master

The quality of the lecturers guarantees high-level training and constant updating of topics. The diversity of their origin, both geographical and institutional, contributes to the dynamism of the courses and enables the students to contrast different theories, methods and results.

In the Master’s last edition, 83 lecturers from 13 different countries have participated, coming from:

Universities: Germany: University of Göttingen, Technical Univ. Munich and Hohenheim; Italy: Università di Bologna; Spain: Universitat de Barcelona, Universidad de Córdoba, Universidad de León, Universitat de Lleida, Universidad de Málaga, Universidad Politécnica de Madrid; The Netherlands: Wageningen UR; US: Oregon Statate University; Switzerlands: University of ETH.

Research Centers: France: Institut National de la Recherche pour l'Agriculture, L'Alimentation et l'Environnement (INRAe); Italy: Centro di ricerca per le produzioni foraggere e lattiero-casearie (CREA-FLC); Spain: Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA-GA), Consejo Superior de Investigaciones Científicas (CSIC), Centre de Recerca en Agrigenòmica (CRAG), Instituto de Ciencias de la Vid y del Vino (ICVV); UK: National Institute of Agricultural Botany, The James Hutton Institute, EBIO, EMSEMBL

Enterprises and other private bodies: Bayer, BASF, Corteva, Eurecat, Sequencia Biotech., Ramiro Arnedo, Syngenta.

International Organizations: CBD-UN, Community Plant Variety Office (office in France), FAO, CIHEAM Zaragoza (office in Spain), ICARDA

To see in detail who are the lecturers providing training in every Unit, please refer to the section Syllabus and Study guide.

Master’s final work (Master Thesis)

Choice of topic for the Master Thesis

The choice of topic corresponds to the students themselves, according to their interest of training. If students so require, they receive advice on the choice of the most appropriate director and institution to carry out the desired project. Likewise the organizing institutions propose topics related to the activities of cooperative research co-ordinated by them or other topics of interest previously agreed with collaborating institution. The topic for the Thesis will belong to the area within which the student has developed the Practicum for the Unit "Introduction to research".

Centres where Theses are carried out

The work is carried out in renowned institutions (universities, research centres or companies) generally in Spain or in the student's country of origin, under the scientific supervision of a doctor of renowned prestige. The student, with the support of the director, should inform the UdL/UPM-CBGP/Agrotecnio/CIHEAM Zaragoza Studies Commission of the Master periodically on the development and progress of the work.

The collaboration established with numerous prestigious institutions in the different specialities of the Master for carrying out the Thesis is critical in the success of the programme. The students develop their training within a framework of team research, counting on excellent resources and expert advice. The experience gained during this period is not simply an acquisition of knowledge and practical skills, but also fully introduces the students into professional reality.

Pre-requisites

In order to develop this Unit, the student must have passed the first part of the Master and submit a research protocol supported by a director. The Protocol should be examined by an evaluation committee formed by the UdL/UPM-CBGP/Agrotecnio/CIHEAM Zaragoza Studies Commission and lecturers of the Master, who will consider:

• The characteristics of the research to be performed: (i) coherence and viability of the project; and (ii) concordance between the chosen theme and the candidate’s previous training, the foreseeable professional insertion and the training or productive demands in the student’s country of origin
• The scientific guarantees and the suitability of the director and the institution where the project is to be carried out

In the course of the second semester of the first academic year, CIHEAM Zaragoza publishes the basis for the presentation of protocols and scholarship applications for the second part of the programme.

Topics for the Master Thesis

The topic choice for the Master Thesis is very wide. Some of the topics chosen most frequently are the following:

• Applications of genomics and other current technologies to variability characterization and crop breeding (markers/QTL analysis, genetic transformation, gene expression, mapping)
• Study of quality traits
• Resistance to pests and diseases
• Physiological factors related to crop yield
• Variety behaviour in specific environments

Some examples of Master Thesis

Some of the theses carried out in recent years can be found below, as an indication of the variety of themes, directors and institutions involved in this training activity:

Title: Towards the engineering of the saffron biosynthetic pathway in rice (2020)
Author: María Lobato, Biotecnologa, Spain
Venue: Departamento de Producción Vegetal y Ciencias Forestales, Escuela Técnica Superior de Ingeniería Agraria, Universitat de Lleida, Spain
Thesis Directors: Paul  Christou and Derry Álvarez

Title: Targeted meiotic DNA double strand break induction using the CRISPR/Cas9 system analysed via single pollen genotyping (2020)
Author: Reena Dubey, Agronomist, India
Venue: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
Thesis Directors: Stefan Heckmann

Title: Characterization of the genetic resistance to aggressive strains of Cucumber mosaic virus (CMV) in melon (2020)
Author: Chaymae Benkirane, Agronomist, Morocco
Venue: Centro de Investigación en Agrigenómica (CRAG), IRTA-CSIC-UAB, Barcelona, Spain
Thesis Directors: Ana Montserrat Martín-Hernandez

Title: Caracterización y mapeo fino de QTLs implicados en la domesticación de melón (Cucumis melo L.) [Characterization and fine-mapping of QTLs involved in melon (Cucumis melo L.) domestication] (2018)
Author: Chyamaa Riahi Agronomist, Tunisia
Centre where Thesis was carried out: Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC/Universidad Politécnica de Valencia, Spain
Thesis Directors: Antonio Monforte and María José Gonzalo

Title: Rachis fragility in F1 crosses between barley lines with alternative mutations (2018)
Author: Miriam Fernández, Agronomist, Spain
Centre where Thesis was carried out: Departamento de Genética y Producción Vegetal, Estación Experimental de Aula Dei, CSIC, Zaragoza, Spain
Thesis Directors: Ana M. Casas and Ernesto Igartua

Title: Evaluation of a Pisum spp. germplasm for resistance to Fusarium oxysporum f. sp. pisi Schlecht and Orobanche crenata Forsk (2018)
Author:Wohor Zakaria Osman, Biologist, Ghana
Centre where Thesis was carried out: Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas (IAS-CSIC), Córdoba, Spain
Thesis Directors: Diego Rubiales and Nicolas Rispail

Title: Saturation of the chromosome I region containing the gene controlling low vicine and convicine content in faba bean (Vicia faba L.) seeds (2016)
Author: Fatema Alzahraa Bakro, Biologist, Syria
Centre where Thesis was carried out: Área de Mejora y Biotecnología, Centro “Alameda del Obispo”, Instituto de Investigación y Formación Agraria y Pesquera (IFAPA), Spain
Thesis Directors: Ana M. Torres and Natalia Gutiérrez

Title: Effects on resistance of mixed infections involving the crinivirus Cucurbit yellow stunting disorder virus (CYSDV) and the potyvirus Watermelon mosaic virus (WMV) in cucurbit crops: characterization of responses to WMV in selected melon accessions (2016)
Author: Bader Arouisse, Agronomist, Morocco
Centre where Thesis was carried out: Centro de Investigación en Agrigenómica (CRAG), IRTA-CSIC-UAB-UB, Bellaterra, Barcelona, Spain
Thesis Directors: Juan José López-Moya and Ana Beatriz Moreno

Title: Firmness QTL analysis in sweet cherry (2016)
Author: Francisco Balas, Biologist, Spain
Centre where Thesis was carried out: Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria del Gobierno de Aragón (CITA), Zaragoza, Spain
Thesis Director: Ana Wunsch

Master indicators

Geographical origin of lecturers and students

Academic indicators