93966 - Genetics and Biotechnology for Resilient Crops

Academic Year 2021/2022

  • Teaching Mode: Traditional lectures
  • Campus: Bologna
  • Corso: Second cycle degree programme (LM) in Precise and Sustainable Agriculture (cod. 5705)

Learning outcomes

At course completion, the student possesses knowledge on: the potential of biotechnology based genetic improvement to develop resilient cultivars suitable for sustainable agricultural systems; the molecular genetic control of the main features of agronomic interest including the response to abiotic and biotic stresses, the efficient use of water and nutrients, and host-pathogen interaction; genetic improvement methods that integrate assisted selection, phenotyping high-throughput, genetic engineering and genomic editing. In particular, the student possesses the skills to: participate in the management of genetic improvement programs aimed at varietal development in seed and nursery companies; evaluate and incorporate the appropriate biotechnological tools into genetic improvement programs; recognize and manage the positive aspects and critical issues of varietal innovation in agricultural systems, considering the entire production chain.

Course contents

Knowledge and skills to be achieved

At the end of the course the student will acquire knowledge on principles of Agricultural Genetics, Plant Breeding, Breeding for sustainable agriculture, notions of Genomics and Biotechnology applied to plant breeding.

Students will know the basis of main selective methods for self-pollinating, allogamous and vegetative propagation herbaceous plants, the genetic structure of the cultivated varieties. The students will know how to apply the basis of Mendelian Genetics, Quantitative genetics, population genetics, genomics and biotechnology to practical professional and research applications. Among those: the management, conservation, characterization and use of Plant Genetic resources, either stored in Gene Banks or in open environment contexts; conduction of plant breeding programs as professional plant breeder or researcher; plant varietal choice decisions in specific agricultural systems and environments, particularly as integrated into high value agro-food value chains that target sustainable, high value products and that make use of precision agriculture and identity-preserved productions.

CONTENTS

A) PREREQUISITES

The student who accesses this course must have a good knowledge of the fundamentals of mathematics, chemistry, plant biology, agronomy, crop biology and physiology, plant pathology as well as a knowledge of the fundamentals of statistical analysis (sample, mean, variance and standard deviation). These prerequisites are provided either by the basic courses delivered during the bachelor and during the first year of the course.

Most importantly, students must have already a clear and good knowledge of the fundamentals of Agricultural Genetics. These prerequisites are provided by the courses of the three-year degrees of class L-25 - AGRICULTURAL AND FOREST SCIENCES AND TECHNOLOGIES and by the courses of the first year, first cycle, of the master's degree course in Agricultural Sciences and Technologies.

It is highly recommended to resume the AGRICULTURAL GENETICS course to fully understand, acquire and retain the information material that will be provided with this course in time.

B) TEACHING UNITS

The course is divided into the following units.

1. Introduction to genetic improvement in the agri-food and agro-industrial chain (4 hours).

Introduction to genetic improvement in the agri-food and agro-industrial chains. Objectives of breeding. History of Plant Breeding. Contribution of genetic improvement to the increase and sustainability of primary plant production and to the improvement of the healthiness of plant food products. Main critical factors for planning a genetic improvement project according to the objective to be achieved and the biology of the species. Impact of Genomics and biotechnology applied to modern plant breeding

Contribution of genetic improvement to the increase and sustainability of primary plant production and to the improvement of the healthiness of plant food products. Main critical factors for planning a genetic improvement project according to the objective to be achieved and the biology of the species.

2. Reproductive systems, authogamy, plant breeding and natural populations. (3 hours). Mendelian concepts in plant breeding. Mendelian postulates. Genotype and phenotype. Predicting genotype and phenotype. Progeny test. Multiple alleles, pleiotropy. Haploidy and double haploids. Allogamy. Hybrid vigour. Artificial hybridization. Population generation and population types for breeding. Wide crosses. Clonal propagation. In vitro culture.

3. Molecular marker technology I. (2 hours). sequencing, cloning and genomics as fundamental tools for advanced plant breeding and biotechnology. Main technologies for identifying sequence polymorphisms and develop DNA marker assays useful in varietal characterization, germplasm and for genetic improvement. Critical evaluation of advantages and limitations. Sequencing of DNA and RNA techniques. Next generation sequencing. RNAseq. Gene networks. Genomics and available databases.

4. Molecular marker technology II. (3 hours). Use of molecular markers for genetic diversity estimate in germplasm and for genetic improvement = marker assisted selection. Critical evaluation of advantages and limitations. Sequencing of DNA and RNA techniques. Next generation sequencing. RNAseq. Gene networks. Genomics and available databases.

5. Introduction to population genetics I. (2 hours). Allele and genotype frequencies in populations. Hardy-Weinberg equilibrium - Diploid equilibrium - and perturbating factors. Gametic equilibrium or haploid equilibrium. Linkage disequilibrium concept. Random mating and inbreeding and their effects on allogamous and authogamous crops. Population improvements and relevance of crossing, artificial crossing, and inbreeding to facilitate selection

6. Introduction to population genetics II. (3 hours). Genetic basis of quantitative traits and components of the phenotypic variance: genetic and environmental variance. Estimation of heritability in a broad and narrow sense. Use of heritability in predicting the response to selection and its limits. Selection for multiple characters and for adaptation to different environmental conditions.Decision making in breeding. Selection methods. Gene action and plant breeding. Variance. Heritability concept. Breeding trial experimental design for single and multiple environment assessment. Response to selection. Recurrent selection.

7. Germplasm for breeding. (2 hours). Plant genetic resources; germplasm collections and their managements. Principles underlying the genetic structure of natural and artificial populations and their methods of analysis. Methods of collection and conservation of plant genetic resources. Role of biodiversity in genetic improvement programs. Molecular methods to estimate population genetic structure. Empirical and molecular methods to estimate genetic relationships among individuals / accessions.

8. Plant domestication (two hours). implication for plant breeding and modern molecular concepts. Recent concept of Fast domestication. Polyploidy. (one hour)

9. Breeding objectives. (3 hours). Ideotype concept. Plant architecture. Deconvolution of complex trait to increase the heritability and to improve the dissection of the inheritance. proxy trait concept. Breeding for yield in relation to the environment. Target population environment concept. Breeding for quality traits in relation to the environment.

10. Breeding for self-pollinated species. (2 hours) Genealogical selection method ("pedigree"). Variants and modifications including single seed descent, bulk method, double haploids, speed breeding. Breeding for cross pollinated species. (1 hour). Hybrid cultivars. Heterosis and adaptation to environment. Combinatory objectives of hybrid cultivars.

11. Molecular Breeding I. (2 hours) Mapping of genes and mapping of QTL. How to do. Linkage mapping in artificial populations. Genome-Wide Association mapping in cultivated or natural germplasm collections/panels bas. Definition of the locus space, gene content, candidate genes and causal gene, causal mutation and quantitative trait nucleotide. The three steps leading to the causal gene isolation.

12. Molecular Breeding II. (3 hours) Marker assisted selection. Concept and practice by simple markers and haplotype markers. Concept of identification and selection for the perfect marker obtained from the causative nucleotide. Breeding-by-design. Backcross and backcross assisted breeding. Concept of introgression breeding with molecular marker. Negative Concept of linkage drag and how to control it with molecular markers.

13. Mutagenesis. (2 hours). Methodologies. Mutagenesis based on forward- and reverse genetics concepts.

14. Transgenesis (2 hours). Definition. Transgene construct components. Ballistic and Agrobaterium transformation methods. Transgenics for resilience to abiotic stresses and resistance to plant diseases and pests. Transgenic cassettes. Gene editing. Cisgenesis. (1 hour). Introduction to Editing techniques and induced modifications. Implications for the product registration and cultivations. Examples of editing for resistance to diseases and for fast domestication.

15. High-throughput phenotyping (1 hour). Hand-held instruments and remote sensing. Phenomobiles and Drones. RGB, multispectral and hyperspectral imaging. Vegetation indexes. Genetic basis and selection for adaptation to environments. (1 hour) Inheritance of phenologycal traits. Developmental master switch. The developmental regulation and gene network. Vernalization and photoperiod sensitivity genes. Earliness per se. Senescence master switches (NAC genes). Useful alleles discovered by breeders and selected for various environments. Epistasys associated to phenology regulators. (2 hours)

16. Genetic basis and Breeding for resilience to abiotic stresses. (2 hours) Molecular and physiological response to drought, cold, heat. Master regulators of the response. Signaling transduction pathways. Hormonal regulation.

17. Breeding for resistance to disease and insect pests (3 hours). Genetic basis and Breeding for resistance to pathogens and viruses: PTI and ETI. Small secreted proteins. Molecular and physiological response. Master regulators of the response. Signaling transduction pathways. Salycilic acid and jasmonate signal transduction pathways. Discrimination between biotrophic, emi-biotrophic and necrotrophic pathogens and relative host-response strategies. Seedling and adult plant resistances. Major loci and quantitative resistances and effects of resistance durability.

18. Relevance of Root system architecture, biology, functionality and genetics in sustainable agriculture. (2 hours). Genetics of nutrient and water sensing and uptake. Genetics of root system architecture. Genetics of Root-microbiome and fungal interactions (cost-beneficial balance). Microbiome for healthy soils.

Exercises / direct experience

E1. Plant genetics applications in the field of genetic improvement. Domestication and breeding effects. (4 hours). Genetic and phenotypic variation. (video collections previously prepared)

E2. Molecular Markers Laboratory (4 hours). Expertise in the identification of DNA molecular markers that can be used for varietal identification and selection. Either in person in the lab (difficult considering the current COVID situation) or video collection previously prepared

E3. Computer Exercises on QTL mapping, population structure and GWAS using molecular marker-based genotypic data and phenotypes from real experiments, using dedicated softwares. Analysis of genetic and phenotypic data for the determination of the structure of the populations and for the mapping of QTL (6 hours) Basic knowledge of methods for the analysis of the genetic structure of populations, of genetic relationships in the germplasm, for the mapping of loci and the conduction of MAS

E4. Genetic resources and loci for the improvement of disease resistance in wheat. (video collections)

SEMINARS Towards the end of the course the teaching lessons will be complemented by at least two seminars with breeders from cereal and horticulture seed companies. This will help students to be exposed to a direct interaction with breeders and to have a more direct perception of the aspects related to the selection in a seed company.

The teacher and post-doctoral from the Genetics andGenomics area have also prepared video taken directly from the fields (in spring time) regarding the principal topics of the course, using wheat as a reference

Readings/Bibliography

Texts / Bibliography

For basic concepts of Agricultural Genetics to be reviewed / refreshed:

  1. Essential iGenetics by Peter J. Russell. Benjamin-Cummings Publishing Company
  2. Genetica Agraria (Peter J. Russell, Wolfe, Hertz, Starr, McMillan), EdiSES editor, 2016. (In Italian, however wery well done)
  3. Genetics. 3rd Edition (Monroe W. Strickberger)
  4. Introduction to Genetic analysis 12th edition (Anthony Griffiths; John Doebley; Catherine Peichel; David A. Wassarman)

The reference texts of the course:

  1. Principles of Plant Genetics and Breeding, 2nd Edition George Acquaah. ISBN: 978-0-470-66475-9 October 2012 Wiley-Blackwell 760 Pages. This is the reference course text book for the first part of the course. The more specific second part of the course will be complemented by specific reviews provided directly through VIRTUALE
  2. The text book is necessarily Complemented by Didactic material provided by Virtuale:

    - Schemes and slides presented in class

    - Review manuscripts on specific topics

    For More specific text books, highly recommended for broadening your personal view or to deepening some chapters:

  3. Essentials of Plant Breeding, Rex Bernardo, Stemma Press, 260 pages, ISBN 978-0-9720724-2-7. Highly recommended, one of the best plant breeding books in general and especially for the first part of the course. Available only at https://bernardo-group.org/books-and-software/
  4. Plant Biotechnology and Agriculture Prospects for the 21st Century

    Arie Altman and Paul Michael Hasegawa Academic Press

    Hardcover ISBN: 9780123814661

    eBook ISBN: 978012381467

  5. Plant, Genes and Agriculture Sustainability through Biotechnology. Maarten J. Chrispeels and Paul Gepts. Oxford University Press Academic
  6. Plants, Biotechnology and agriculture, Denis Murphy, CABI Publishing

    Additional relevant Books

  7. Principles of Plant Breeding, Robert Waine Allard, 1960-1999 John Wiley & Sons Inc; Subsequent edition (26 aprile 1999)
  8. Breeding field crops, John Milton Poehlman, Springer (freely available)

Teaching methods

The basis of the course is provided by direct lessons based on power-point presentations.

The course is divided into lessons and practical works. The practical exercises are centered on the analysis of molecular markers and to general and practical aspects of plant breeding in general and breeding for resilience to abiotic stresses / resistance to diseases.

In addition, in the second part of the course, the lessons will be complemented by seminars from plant breeders and researchers in the field

Discussion groups (two to four-five students working together), case-study examinations and preparation of short seminars on the topics will be used to deepen technical topical topics related to the subject of study.

Teacher/student weekly direct meetings for open discussion and lesson revision will be opened in free student hours, preferably the day after lessons.

Assessment methods

The assessment test is carried out through a final oral exam. There are three to four main questions related to three main and different topics addressed during the course. Additional specific questions will be addressed according to student knowledge and response. Questions are aimed at ascertaining the knowledge relating to the basic and applicative aspects developed during the lesson and practice hours. The duration of the test is about 30 minutes.

Teaching tools

Teaching support tools

  • power-point slides, discussion of scientific manuscripts, direct observations in the molecular lab, botanic garden, field
  • Bibliographic material available at the University Library System and provided on the VIRTUALE platform.
  • Blog / forum for teacher-student communications on the IOL platform, accessible only to students of the course.
  • Weekly direct meetings with the professor and post-docs of the group.

Office hours

See the website of Marco Maccaferri

SDGs

Responsible consumption and production Climate Action Life on land

This teaching activity contributes to the achievement of the Sustainable Development Goals of the UN 2030 Agenda.