MSc Plant Sciences Specialization F: Plant Breeding (Distance Learning) Wageningen University Course Descriptions (DRAFT )

Transcription

1 MSc Plant Sciences Specialization F: Plant Breeding (Distance Learning) Wageningen University Course Descriptions (DRAFT )

2 PBR22803 Principles of Plant Breeding (Distance Learning) Teaching methods: 0.5 DT; 0.5 DG; 2.0 DEL Contact person: R.E. Niks (niks001) Lecturer(s): R.E. Niks (niks001) Examiner(s): R.E. Niks (niks001) This course introduces students to key principles of plant breeding. Different subjects are the importance of the mode of reproduction of crops and the genetic consequences for selection. Various selection methods are discussed. For an effective selection programme it is imperative to distinguish genotype from phenotype, since only the genotypic differences are relevant to genetically improve the crop. - understand the advantages and limitations of plant breeding selection programmes - understand the role of mode of reproduction of plants on the genetic composition of crops - analyse genetic segregations - analyse observations to separate genetic and non-genetic components of variation - know the methods and perspectives of modifying genome numbers (ploidy levels) and DNA sequences Activities: The course consists of a number of e-learning modules that explain and illustrate the principles, and give numerous exercises to the student to test his understanding. Feedback on correct and wrong answers is given. Group assignments, self-tests and discussions are other activities in this course. Literature: Recommended: G. Acquaah, Principles of Plant Genetics and Breeding, 2nd Edition Wiley-Blackwell 2

3 PBR23303 Learning) Plant Pathology and Disease Epidemiology (Distance Teaching methods: 0.5 DKC; 1.0 DT; 1.0 DG; 0.5 DEL Contact person: Jan van Kan (kan001) Lecturer(s): Jan van Kan (kan001) Wopke van der Werf (werf001) Examiner(s): Jan van Kan (kan001) Wopke van der Werf (werf001) The course focuses on the interactions of plants with attackers (viruses, micro-organisms, nematodes, insects, parasitic plants), and beneficial organisms (symbiotic bacteria and fungi), as well as on interactions between beneficial organisms and pathogens and their hosts at different integration levels, from molecules to ecosystems. - summarize molecular and physiological principles of interactions between plants and attackers; - discuss the complexity of defence mechanisms that plants possess to (directly or indirectly) counteract attackers; - compare different strategies and biochemical tools used by attackers to invade plants and reproduce - explain how symbiotic organisms interact with plants without triggering defence responses; - understand that the trophic lifestyle of an attacker is related to the way in which it uses its genetic toolbox - describe case studies of plant disease epidemics in time and space (field, regional, and continental scale) - apply key concepts in the population biology of plant diseases, such exponential growth, logistic growth, life tables, relative rate of increase, and net reproductive ratio - describe the effect of host genetics, crop diversity and landscape diversity on the rate of spread and population increase of plant diseases and pests - understand and apply basic probability models for sampling distributions of plant disease - formulate concepts for integrated management of plant disease on the basis of insight in epidemiology Activities: Reading study material, video clips, self-assessments, participation in role-playing game Literature: Available through the course website 3

4 PBR31803 Genetics (Distance Learning) Teaching methods: 0.5 DKC; 1.5 DT; 0.5 DG; 0.5 IS Contact person: Herman van Eck Lecturer(s): Herman van Eck and other lecturers Examiner(s): Herman van Eck This course gives an overview of the role of genetics in life sciences and the structural basis of genetics. Following on this basis a series of more advanced topics is addressed, including extensions and exceptions to single locus Mendelian inheritance, transposable elements and genome size, population genetics and evolution, complex traits, genetic diversity, biosystematics, phylogenetics, and genome evolution. - analyse questions and problems on all aspects of Mendelian genetics, including deviations from standard segregation ratios; - apply quantitative and population genetics concepts to infer the effects of selection, non-random mating, mutation, genetic drift on forward genetic screens - describe the relation between genes, chromosomes and DNA and the concept of genome structure; - understand evolutionary concepts explaining the origin of biological complexity, and processes shaping the genome, such as horizontal gene transfer, genome duplications, hybridisations, transposition; - apply quantitative and biosystematic approaches to evaluate genetic structure and diversity of populations, as well as phylogenetic analyses Activities: Topics will be introduced and taught using knowledge clips (DKC). Students will read the textbook supplemented with scientific articles (IS). In depth study of the topic is facilitated using Distance Tutorials (DT) using Feedbackfruits and Peer to peer on line discussion. Literature: Textbook Griffiths, An Introduction to Genetic Analysis 11 th edition, and scientific papers 4

5 PBR23803 Plant Biotechnology (Distance Learning) Teaching methods: 0.7 DKC; 0.5 DT; 0.7 DG; 0.2 DEL; 0.9 IS Contact person: Christian Bachem (Bache001) Lecturer(s): Christian Bachem (Bache001), and other lecturers Examiner(s): Christian Bachem (Bache001) Assumed knowledge: Basic molecular biology and plant biochemistry Plant biotechnology is a discipline that connects the new insights into genes and their products with the end product that is destined for the market. As with other technological disciplines, plant biotechnology comprises a mixture of many other scientific areas of biological sciences such as molecular biology, biochemistry, physiology and genetics. In this course we will present information on the basics of classical plant biotechnology through to advanced methods for modifying and improving plants and plant products. This will be done using knowledge clips, exercises and study of a set textbook. In addition the participants will have the opportunity to apply the knowledge gained during the course and use their own creativity in the form of an group assignment that will run throughout the course. Another main feature of the course will be to analyse and assess the implications of this new technology for wider society. The assignment will form a central part of the course and will be submitted in the form of a written report and a presentation the latter will be reviewed and evaluated by fellow students. The presentations and debates will form part of practical week at the WUR campus. 1. Understand the scientific and technological components of what is and is not Plant Biotechnology 2. Understand the molecular biological basis of the key technologies comprising Plant biotechnology 3. Analyse literature an apply the findings to a biotechnological problem 4. Critically review the position of Plant Biotechnology in relation to society 5. Conceive, plan, write and present a project proposal for a plant biotechnological product Activities: 1. Read the assigned chapters in the book 2. Watch the knowledge clips and additional learning material 3. Carry out on-line assignments 4. Peer to peer on line discussion 5. Plan and execute a project assignment 6. Prepare presentation and written report 7. Debate the placement of plant biotechnology in to societal and cultural contexts. Literature: Textbook: Plant Biotechnology, Slater, Scott & Fowler 2 nd ed. OUP. Additional academic literature (PDFs) provided by tutor. 5

6 PBR32303 Wageningen Weeks Part 1 (Distance Learning) Teaching methods: 1.8 P; 0.8 T; 0.4 EO; Contact person: Guusje Bonnema (bonne001) Lecturer(s): Guusje Bonnema, Richard Visser and other lecturers Examiner(s): Guusje Bonnema, Richard Visser During this two week practical, students of the Distance Learning Specialization come to Wageningen and will meet each other and Wageningen University staff for the first time. This practical period builds on the courses PBR (Principles of plant breeding), PBR (genetics) and PBR (Plant Biotechnology) and the Skills that are an integral part of this Distance Learning MSc. In the one day excursion we will visit two plant breeding companies. This will be a vegetable breeding company, with application of genomics and Marker assisted selection in breeding programs of many of their crops; special attention is given to their seed quality management. In addition, an ornamental breeding company or crop breeding (potato) company will be visited, with different breeding strategies. For the Skills training, students will have an interactive training and will present their Plant biotechnology assignment and have a debate on societal issues related to plant breeding. The practicals are designed to increase insight in genetic and breeding principles (heritability, epistasis, genetic diversity, segregation ratio s) and train skills in plant biotechnology research. - apply relevant laboratory techniques for assessing gene expression in transformed plants; - make crosses in a diverse range of plants; - understand the concepts genetic diversity, heritability and epistasis by phenotyping and genotyping plant populations and fitting the outcome to genetic models; - develop self-awareness of personal qualities and skills; - present a group assignment using Powerpoint; - participate in a debate about the (im)possibilities of plant biotechnology from a societal and a technical point of view - receive feedback from peers and supervisors, and skilfully provide feedback for your fellow students Activities: Excursion to two breeding companies and a technology lab; Practical experiments to apply knowledge from the courses Principles in Plant Breeding, Genetics and Plant Biotechnology aimed to improve research skills and practical skills, and deepen the understanding of theoretical concepts; Practical assignments to train communication and personal skills; doing tests, give presentations, participate in debates, reflect on own behaviour and that of your co-students and group Literature: Available through the course website. 6

7 MAT25303 Advanced Statistics for DL (Distance Learning) Teaching methods: 1.3 DKC; 1.0 DT; 0.4 DG; 0.3 DEL Contact person: Gerrit Gort Lecturer(s): Gerrit Gort, Bas Engel, Evert-Jan Bakker, Elly Korendijk Examiner(s): Gerrit Gort Bas Engel Assumed knowledge: Basic Statistics Statistical design and analysis of data using R; statistical methods for analysis comprise simple and multiple regression, one-way and two-way analysis of variance (with and without interaction), analysis of covariance, chisquare tests for contingency tables, logistic regression. - comprehend basic ideas of statistical inference, experimental design and data collection, such as random sampling, randomisation and blocking, for experimental and observational studies - determine an appropriate statistical model and associated statistical inference procedure, given the description of the experiment and research question, for continuous data (in the context of linear regression, analysis of (co)variance) and discrete data (in the context of goodness-of-fit and contingency tables for categorical data and logistic regression for binary data and proportions) - carry out the analysis, for a given problem, using the statistical program R, check model assumptions, interpret results, and formulate conclusions in terms of the actual problem Activities: Study knowledge clips with theoretical assignments, practical assignments and case studies using R, reporting on results. Literature: Ott, RL, Longnecker M (2010) An introduction to statistical methods and data analysis (6 th edition), Brooks/Cole ISBN ; ISBN ; BIB/

8 PBR32803 Markers in Genetics and Plant Breeding (Distance Learning) Teaching methods: 0.2 DKC; 0.5 DT; 0.5 DG; 1.8 DEL Contact person: Chris Maliepaard Lecturer(s): Rients Niks, Jan-Kees Goud, Chris Maliepaard Examiner(s): Chris Maliepaard, Rients Niks, Jan-Kees Goud Assumed knowledge: Principles of Plant Breeding, Genetics, Statistics In this course, the students will be made familiar with the use of molecular markers in genetic research and plant breeding, the estimation of genetic distance based on marker genotype frequencies in different types of segregating populations, the construction of linkage maps, the analysis of quantitative trait loci (QTLs) and the discovery and application of markers in research and for selection in breeding programs, both for qualitative and quantitative traits. - understand the concept of genetic markers in genetic research and breeding - understand the use of polymorphic markers in segregating populations - use sequence information for discovery of single-nucleotide polymorphisms (SNPs) and understand how these can be used as molecular markers for genetic mapping, QTL analysis and marker-aided selection - analyse genetic segregations, including cases where genetic linkage occurs - infer linkage/non-linkage and to calculate genetic distance from genotype frequencies in a segregating population - use software to construct a genetic map from marker genotyping data in a segregating population and interpret the result - distinguish and contrast genetic and physical maps - map a gene involved in a qualitative trait in a mapping population - Understand the concept of QTL analysis using a genotyped mapping population, a linkage map for that population and a quantitative phenotypic trait scored in the population - distinguish and contrast QTL mapping procedures based on single marker analyses, interval mapping, composite interval mapping - perform QTL analyses using QTL mapping software and interpret the results - understand the principles of bulked-segregant analysis and selective genotyping - understand the application of molecular markers in indirect selection for phenotypic traits in breeding programs Activities: Study an E-learning module, individual and group exercises, application of software Literature: Available through the course website 8

9 PBR33303 Quantitative and Population Genetics (Distance Learning) Teaching methods: 0.1 DKC; 0.5 DT; 0.4 DG; 2.0 DEL Contact person: Chris Maliepaard Lecturer(s): Chris Maliepaard, Bas Zwaan Examiner(s): Chris Maliepaard Assumed knowledge: Genetics, Statistics, both at MSc level In this course, students will learn concepts and applications of quantitative and population genetics. Applications will be taught in exercises within the context of Plant Breeding, using statistical analyses. Quantitative genetics part: - Comprehend and contrast the inheritance of qualitative vs. quantitative traits and the consequences for plant breeding. The inheritance of monogenic vs. polygenic traits and the relationship to qualitative and quantitative traits. - Comprehend the importance of quantitative traits in breeding and possibilities and consequences for selection over shorter and longer periods. - Comprehend the concepts of additivity, dominance, incomplete (partial) dominance and overdominance in single-locus and multi-locus genetic models. Comprehend the concept of epistasis and recognize different forms of two-locus epistasis - Comprehend how dominance and overdominance can be involved in the explanation of heterosis and consequences for breeding (choice pure line or hybrid cultivars, maintaining heterozygosity in OPV, inbreeding depression after sib mating or selfing). - Calculate midparent value, (net) additive effect, (net) dominance effect and (means based) dominance ratio from the means of a trait in basic generations such as BC1, F2, RILs, including parental generations P1 and P2 and F1. Interpret results in terms of consequences for breeding. - Comprehend the concepts of additive genetic variance, dominance genetic variance, dominance ratio and their expectations in different breeding generations /research populations. - Use quantitative genetics models and statistical methods to quantify additive genetic variance, dominance genetic variance, (variance based) dominance ratio in basic breeding and research populations. - Comprehend the concepts of genetic and environmental variance, narrow-sense and wide-sense heritability. Understand that heritability estimates are specific for certain traits in certain populations tested in certain environments with a certain experimental design but also have a wider interpretation outside those specific contexts. - Use quantitative genetics models and statistical methods to estimate variance components (genetic variance, environmental variance, variance associated with G*E interaction) and to estimate wide-sense and narrow-sense heritability. - Comprehend the concepts of Selection Differential, selection intensity, Response to selection, genetic correlation, indirect selection and Correlated Response to Selection, and the so-called breeders equation. Understand how the response to selection may vary according to the heritability, the selection intensity, the type of material, the stage at which the trait can be evaluated (before/after flowering!). Understand indirect selection in terms of these concepts. Understand the relevance of response to selection in terms of progress per time unit for selectable traits in a breeding program. Understand the relationship between quantitative genetic theory of indirect selection and applications in indirect selection, notably in markerassisted selection of quantitative traits and/or genomic selection on breeding values of quantitative traits. - Calculate response to selection and correlated response to selection, given a heritability estimate, intensity of selection, selection differential. 9

10 - Apply quantitative genetics theory and methodology to compare expected effectiveness of different possible breeding strategies (e.g. breeding hybrid vs. pure line cultivar) under given assumptions and limitations. Population genetics part: To be filled in. Activities: Knowledge clips, individual and group exercises, online discussion, E-learning modules Literature: Kearsey and Pooni Chapters 1 4.3, 15.5 to 15.8; Moose et al. 2004; Visscher et al

11 PBR31802 Breeding for Quality (Distance Learning) Teaching methods: 0.5 DKC; 0.8 DT; 0.2 DG; 0.5 IS Contact person: Dr. AG Bovy Lecturer(s): Dr. AG Bovy; Dr. L. Trindade Examiner(s): Dr. L. Trindade Assumed knowledge: Genetics, principles of plant breeding, molecular markers, mapping populations Traditionally, producer traits such as yield and disease resistance have been the primary breeding targets in many crops. In current agriculture, however, consumer-driven quality traits, such as flavour colour and nutritional value have become increasingly important and the same holds for the production of specific plant compounds which can be used as sources for bio-based applications. Breeding for Quality is directed at improving whole fruit/vegetable characteristics and plant compounds, where flavour, colour, texture, absence of antinutritional factors or allergens, and shelf-life are important breeding objectives. Breeding for Quality also comprises the efficient production of all kinds of compounds, which are used as ingredients by the food, pharmaceutical, chemical, textile, paper, etc. industries. Examples of such compounds are: carbohydrates (starch, fructans, cellulose), proteins (wheat gluten, pea storage proteins), vegetable fats/oils (rape seed oil, cocoa fat), and secondary metabolites like flavours, fragrances, and phytoestrogenic molecules. In breeding programs, the existing genetic variation is exploited to increase the yield of (or enrich mixtures in) the target compounds. For this, it is necessary to understand the metabolic routes leading to the synthesis of the desired compound, and to have knowledge on how these compounds can be determined in the plant material - explain the major characteristics of various quality traits; - define appropriate selection strategies for specific target traits; - apply relevant analytic and statistical screening techniques for trait evaluation; - use this knowledge to develop breeding strategies for improved resistance, tolerance and quality Activities: Study knowledge clips with theoretical assignments, group activities, individual assignments and literature Literature: Available through the course website 11

12 PBR32302 Breeding for Abiotic Stress Tolerance (Distance Learning) Teaching methods: 0.3 DKC; 1.7 DEL Contact person: Gerard van der Linden Lecturer(s): Gerard van der Linden Examiner(s): Gerard van der Linden Abiotic stress is the stress imposed on plants by the non-living environment. Abiotic stress is responsible for huge yield losses in crops around the world. In this course we will assess the impact that abiotic stresses (drought, salinity, nutrient deficiency) have on agricultural production, and provide you with knowledge and tools for successful breeding for abiotic stress tolerance. The following questions will be addressed: - What can agriculture do to minimize yield losses now and in a future where the climate changes, and input will be further restricted? - What are the requirements for successful breeding for abiotic stress tolerance? - How does a plant respond to abiotic stress, and which physiological and molecular mechanisms are important? - Which traits contribute to stress tolerance, how can these be measured and used for selection? How do modern genomics techniques contribute to abiotic stress tolerance breeding? After successful completion of this course students are expected to: - have acquired knowledge on how agriculture, crops and individual plants are affected by abiotic stress - have learned about main mechanisms that help plants to cope with abiotic stress - know about tools that can be used to monitor and understand the response and tolerance of plants to different abiotic stresses - be able to integrate the above knowledge for the design of a sensible breeding strategy for the improvement of abiotic stress tolerance in target crops. Activities: Online lectures with video clips on specific subjects, short assignments Literature: Available through the course website 12

13 PBR32802 Breeding for Resistance (Distance Learning) Teaching methods: 0.1 DKC; 0.5 DT; 0.3 DG; 0.1 DEL; 1.0 IS Contact person: Vivianne Vleeshouwers (vlees001) Lecturer(s): Vivianne Vleeshouwers (vlees001), Rients Niks (niks001), Yuling Bai (yulin001) Examiner(s): Vivianne Vleeshouwers (vlees001) Assumed knowledge: DL-Principles of Plant Breeding, DL-Plant Pathology Biotic stress factors are among the main limitations for producing high quality and high quantities of vegetal products. Resistance breeding focuses at the use of genetic resources for improving plant defence against these stress factors. Biotic stress factors include pathogens and pests that infect or feed on crop plants. The present course deals with defence mechanisms and strategies that protect host plants against pests and pathogens, inheritance of resistance genes, and durable effectiveness of resistance genes. Explain the major characteristics of various resistance traits Discuss the various aspects of plant-pathogen interaction using the correct terminology Use the knowledge of plant-pathogen interaction to develop breeding strategies for improved and durably effective resistance Choose the most appropriate screening and selection methods to develop cultivars with effective resistance to pathogens and pests Activities: Study the textbook Breeding Crops with Resistance to Diseases and Pests Make exercises, some corresponding to certain parts of the book and other on line Make peer review assignments Study e-learning modules on the (lack of) durability of resistance and partial resistance Literature: Niks RE, Parlevliet JE, Lindhout P, Bai Y (2011) Breeding crops with resistance to diseases and pests. Wageningen Academic Publishers:198pp 13

14 PBR33803 Germplasm and Seed Technology (Distance Learning) Teaching methods: 0.5 DKC; 0.5 DT; 0.3 DG; 0.5 DEL; 0.2 IP; 1.0 IS Contact person: Jan-Kees Goud (goud001) Lecturer(s): Jan-Kees Goud (goud001), Herman van Eck (eck001) and others Examiner(s): Jan-Kees Goud (goud001), Herman van Eck (eck001) Assumed knowledge: Principles of Plant Breeding This course introduces students to a number of important aspects of plant breeding, such as the process of domestication, germplasm development and the importance of gene banks. Also, important practical aspects on bringing a cultivar to the market are discussed, such as breeders rights and patents, and the design of seed and plant production programs. Attention to financial aspects of breeding programs will also be given. 1. explain the theory of domestication, the gene pool concept, and the process of germplasm development 2. explain the importance of gene banks and explain how they work 3. explain and discuss the principles of breeders rights and patents 4. understand how seed production programs are designed 5. evaluate planning and financial aspects of breeding programs. Activities: - Watch knowledge clips - Study e-modules - Hand-in assignments - Watch DVD/YouTube movie and answer questions - Interact with peers and supervisors in discussions Literature: Book chapter(s): Acquaah, G, 2012, Principles of plant Genetics and Breeding, 2 nd edition Article: Zamir, D. 2001, Nature Reviews Genetics 2(12):983 DVD/YouTube: Seed hunter 14

15 PBR34303 Genomics and Bioinformatics (Distance Learning) Teaching methods: 0.7 DKC; 0.5 DT; 0.7 DG; 0.2 DEL; 0.9 IS Contact person: Christian Bachem (Bache001) Lecturer(s): Christian Bachem (Bache001), Herman van Eck (Eck001) Examiner(s): Christian Bachem (Bache001), Herman van Eck (Eck001) Assumed knowledge: Basic knowledge of molecular biology and genetics Genomics is a new area of research that relates to holistic study of the genome a the gene, transcript, protein and metabolite levels. Due to the large amounts of data involved in this study computer tools are extensively used. During the course we will present basic concepts genomics and introduce students to the problems of dealing with and understanding these large datasets. We will discuss the basic architecture of the genome and the implications for genome evolution. We will also deal with the structural and functional aspects of genomics from gene through to metabolites. The course will help the students to analyse and understand the links and relationships between genes and their various products. The course will comprise information packages in the form of knowledge clips and these will be combined with a large number of exercises where the knowledge provided will be applied to practical bioinformatics problems. 1. Understand the organisation of plant genomes and how these evolved 2. Be able to explain the connections between gene, transcript, protein and metabolite 3. Have a basic understanding of the technologies that generate the various genomics data sets 4. Be able to analyse genomics data and retrieve biologically significant information from it 5. Gain an insight into the dependence and interactions between the different functional genomics levels 6. Have the ability to integrate information from genes to pathways to networks at an organism level 7. Understand and debate the potential role of genomics in a wider societal and cultural setting Activities: 1. Read and understand the set texts and literature provided in the course 2. Watch and study the knowledge clips and other learning material 3. Follow the computer tutorials 4. Carry out the exercises and report the results 5. Participate in on-line debates and discussions 7. Carry out and submit assignments Literature: Information will be primarily provided in the DL course material. Other information sources will be actively retrieved from the providers of internet tools that will be used throughout the course 15

16 PBR34803 Experimental Design and Data Analysis of Breeding Trials (Distance Learning) Teaching methods: 0.3 DKC; 1.5 DT; 0.5 DG; 0.7 DEL Contact person: Chris Maliepaard Lecturer(s): Chris Maliepaard, Gerrit Gort, Bas Engel, Marcos Malosetti Examiner(s): Chris Maliepaard Assumed knowledge: Statistics at MSc level In this course, students are taught principles of experimental design of trials and statistical analysis of trial data with a special emphasis to linear and generalized linear methods, mixed models, analysis of multi-environment trials using different statistical methods. - Comprehend statistical principles underlying experimental designs for breeding trials with respect to randomization, replication (including types of replicates and pseudo-replication), blocking, experimental units, the use of controls, orthogonality, balance and efficiency, power. - Comprehend the connections between these design principles and the models and model assumptions underlying statistical analyses, most importantly linear regression and analysis of variance (distributional assumptions, independence, equal variance; additivity or linearity of effects, single or multiple random error terms) - Apply these concepts when designing an experiment - Explain, distinguish and characterize the following experimental designs: completely randomized design (CRD), randomized complete block design (RCB), incomplete block designs (including resolvable designs: lattice designs and alpha designs, row-column designs) and split-plot designs. - Understand effects of missing values, data errors, outliers, uneven replication, confounding of effects, and violations of distributional assumptions and assumptions of equal variance and independence. - Understand statistical analysis methods, most notably single and multiple linear regression, one-way, twoway and multi-factorial analysis of variance including interactions, analysis of covariance, post-hoc pairwise comparisons with and without a multiple comparisons correction. - Understand, distinguish, and apply the concepts of standard deviation, standard error of a parameter of interest, standard error of the mean (SEM), standard error of a difference between means (SED) and least significant difference (LSD) and their relationship with the residual variance estimated from an Anova or regression analysis and with confidence intervals for parameters of interest (regression coefficients, means, differences between means) - Understand and explain R2 and adjusted R2 in the context of single and multiple regression analysis and Anova - Understand when generalized linear models (GLM) are more appropriate for data analysis than linear regression or Anova - Understand when linear mixed models (LMM) are more appropriate for data analysis than linear regression or Anova - Be able to perform different analyses using GLMs: logistic regression for binary data, threshold models for multinomial or ordinal data, loglinear regression for counts - Understand how and why distribution and link functions need to be specified in GLMs - Understand the difference between fixed terms and random terms in a mixed model analysis, both conceptually and in applications - Specify a linear mixed model in fixed and random terms for a data analysis with unbalanced designs 16

17 - Specify a linear mixed model in fixed and random terms for a data analysis with dependent observations - Comprehend and apply linear mixed models in different contexts: estimation of variance components (e.g. for heritability estimation), or quantify the relative importance of environmental and genetic contributions to the variation in multi-environment trials; analysis of split-plot trials; account for dependence/relatedness in full-sib and half-sib family analyses. - Use a linear mixed model for the estimation of variance components - Explain genotype by environment interaction as a concept in multi-environment trials in plant breeding and in statistical terms - Quantify, test and characterize genotype-by-environment interaction using different evaluation methods: analysis of variance, mixed models, Finlay-Wilkinson regression, AMMI and GGE biplot - Comprehend and discuss the concepts of stability, adaptability and (wide/specific) adaptation in plant breeding in the context of Finlay-Wilkinson regression - Understand the concepts underlying principal components analysis (PCA), including loadings and scores plots, biplots and the effects of centering/scaling on PCA - Perform a principal components analysis - Be able to interpret a PCA biplot in terms of (approximate) correlations among variables (from the angles of the loadings to the origin), in terms of distances among the objects (or clustering of separation of objects in the PC-space), and in terms of relating objects to variables (according to relative positions of the objects to the loadings vectors). - Estimate heritability of traits from estimates of variance components obtained from Anova and mixed models in genotype trials. Activities: Knowledge clips, individual and group exercises, E-learning modules Literature: Available through the course website 17

18 PBR35303 Wageningen Weeks Part 2 (Distance Learning) Teaching methods: 1.8 P; 0.8 T; 0.4 EO Contact person: Guusje Bonnema (bonne001) Lecturer(s): Guusje Bonnema, Richard Visser and other lecturers Examiner(s): Guusje Bonnema, Richard Visser Assumed knowledge: Theoretical knowledge from the courses preceding the stay in Wageningen. During this two week practical, students of the Distance Learning Specialization return to Wageningen to meet again with each other and with Wageningen University staff. This practical period builds on the theory of the preceding courses. The programme will include practicals, excursions, and plenary presentations and discussions of the group work related to the Continuous Course and the course Design of Plant Breeding programmes. - assess quality criteria, by evaluating biochemical properties (lab test) and taste (student panels) - assess influence of genotype and environment on biotic and abiotic stress responses - assess chlorophyll content and evaluate role in stress response - assess genetic variation and map QTL for traits - understand the concepts genetic diversity, heritability and epistasis by phenotyping and genotyping plant - present a plant breeding program using Powerpoint; - define questions and recommendations as a group to breeding programs presented by others - receive feedback from peers and supervisors, and skilfully provide feedback for your fellow students Activities: Excursion to breeding companies and/or a plant biotechnology lab Practical experiments to apply theoretical knowledge from the preceding courses of the programme, aimed to improve research skills and practical skills, and deepen the understanding of theoretical concepts Practical assignments to train communication and personal skills; give presentations, participate in debates, reflect on own behaviour and that of peers Literature: Available through the course website 18

19 PBR35803 Design of Plant Breeding Programmes (Distance Learning) Teaching methods: 0.5 DKC; 0.5 DT; 1.0 DG; 1.0 IP Contact person: Guusje Bonnema Lecturer(s): Guusje Bonnema and other lecturers Examiner(s): Guusje Bonnema Assumed knowledge: All preceding courses This course is closely connected to the project part of the Continuous Course (YEI61812), and focuses on the integration of knowledge on various aspects of plant breeding into a breeding programme for a specific crop. The theoretical and practical aspects of plant breeding are taken into account and combined with some economic, societal and environmental aspects. - integrate theoretical and practical knowledge in a design study for a breeding program; - understand structure and connections between breeding methods, techniques and breeding goals; - select parameters (parental choice, breeding strategy, population genetics, selection methods, traits of interest) that are crucial for successful practical breeding; - reflect on breeding methods and their presuppositions; question, adjust and estimate their implications; - set up a breeding programme for a specific crop (all along the chain from defining the specific breeding goal(s) until marketing the newly developed variety); - justify the choices made in the breeding program; - write a work plan and final report of the breeding program; - present the work plan and final breeding plan to peers Activities: Study knowledge clips on theoretical background, work on a group assignment to design a breeding program, reporting on plans and results Literature: Available through the course website 19

20 PBR36303 New Trends in Plant Breeding (Distance Learning) Teaching methods: 0.5 DKC; 0.5 DT; 0.5 DG; 0.5 IP; 1.0 IS Contact person: Jan-Kees Goud (goud001) Lecturer(s): Vivianne Vleeshouwers (vlees001), Luisa Trindade (trind001), Edith Lammerts van Bueren (lamme022), Olga Scholten (schol0), Robert van Loo (loo006), and Gerard van der Linden (linde027) Examiner(s): Jan-Kees Goud (goud001) Assumed knowledge: Principles of Plant Breeding, Breeding for Quality, Breeding for Tolerance, Breeding for Resistance, Plant Pathology This course aims at preparing students for a career in plant breeding industry or in science. Subjects treated are at a higher integrational level, not only taking into account plant breeding aspects, but regarding all aspects involved, such as environmental issues, products and chain issues, climate change and limiting resources. Subjects treated include new trends and technologies in plant breeding, such as effector-based plant breeding, bio-based economy, climate resilience, new crops, alternative cropping systems, breeding for low-input cropping systems, and breeding for symbiosis between plants and micro-organisms. 1. apply effector-based plant breeding for the selection of cultivars with resistance to plant pathogens 2. evaluate the challenges of the bio-based economy from the breeding perspective 3. assess morphological and physiological components relevant for the breeding of climate resilient plants 4. design breeding programs on alternative cropping systems, such as mixed cropping systems and low-input cropping systems 5. evaluate breeding possibilities in new crops 6. evaluate possibilities of breeding for symbiosis between plants and micro-organisms Activities: - Watch knowledge clips - Read articles - Hand-in assignments - Read scientific literature - Case study on novel breeding strategies, either focused on scientific research or on implementation in a commercial breeding program Literature: Available through the course website. In addition, students need to search for relevant literature as part of the case study. 20

21 YEI61812 Continuous Course (Distance Learning) Teaching methods: 3.0 DT; 9.0 DG Contact person: Anja Kuipers Lecturer(s): Guusje Bonnema, Truus van Woudenbergh, and others Examiner(s): Guusje Bonnema, Truus van Woudenbergh The continuous course has two major elements, skills building and a project. Skills building focuses on the following skills: 1. Online study and communication skills (e.g. ICT, active cooperation in groupwork, intercultural communication, giving and receiving feedback) 2. Academic skills (project management, information literacy, scientific writing, presentation skills, argumentation skills, reflective learning) The project relates to the content of the online specialisation itself, and also comprises training of specific contentrelated skills. For the online specialisation Plant Breeding the project focuses on translating principles of plant breeding into design, and on the synthesis and writing of a breeding programme that includes and connects all relevant aspects on a multidisciplinary level. The project of the online specialisation Epidemiology and Public Health focuses on intervention mapping, and writing a grant proposal. - perform a project in an international team; - determine the project aims, develop a project plan and formulate tasks on the basis of disciplinary knowledge and general academic skills and attitude; - contribute to the execution of the project at an academic level by retrieval, selection and analysis of information; - integrate relevant research-based information into scientifically correct written report, and present and defend conclusions and recommendations in a professional and well-argued way; - implement reflective learning by assessment of, and reflection on, personal functioning in a professional team; - give and receive feedback in writing and verbally, based on assessment of the contribution of other team members to team performance and execution of project tasks. Activities: Tutorials and assignments for development of skills. Team meetings, literature study, proposal and report writing, oral and online presentation Literature: Skills building: literature provided via Blackboard. Project: Specific literature available via Blackboard. In addition, students need to search for relevant project related literature