05546 - Agricultural Genetics

Learning outcomes

This course gives the basis of Mendelian genetics, quantitative genetics, population genetics, and of the main biotechnological applications. The course gives also some example of plant breeding, to understand the economic importance of genetics and the relevance of the management genetic resources in sustainable agriculture.

Course contents

A) Prerequisites

For this course the student should have basic knowledge of the fundamentals of biology, mathematics and statistics. These skills are acquired in high school and in the basic courses given during the first year, first cycle, and with which it is coordinated.

B) Teaching units

1. Molecular basis of replication of genetic information and its expression (6 hours)

1.1. The genetic inheritance and the hereditary material.

1.1.1. DNA composition and replication.

1.1.2. Analysis of DNA: extraction, purification, electrophoresis, denaturation, restriction and ligation, PCR, sequencing.

1.2. The gene and its expression: RNA transcription of the message, genetic codification and translation of the message (with elements of protein synthesis).

1.3. Gene regulation and the central dogma of molecular biology.

Knowledge acquired in Unit 1

• The structure of the genetic material and how it is replicated (DNA) or transcribed (RNA).

• The principles on which they are based methods to the use of DNA for diagnostic, forensic or commercial purposes.

• The main aspects of the translation of genetic information and of gene regulation.

2. Transmission of hereditary material: Mendel's experiments, genetic association and genetic maps (8 hours) (integration with the course of biology: reproduction and morphological and functional aspects of mitosis and meiosis; integration with the statistics course: the Chi-square test).

2.1. Transmission of genetic material: basics of sexual reproduction and recombination, genetic aspects of mitosis and meiosis. Homozygosity and heterozygosity.

2.2. Mendel's experiments: dominance, segregation, independent segregation.

2.3. Likage: the recombination of linked genes (crossing-over), verification of the independence with Chi-square statistical test.

2.4. Construction of linkage maps and use of genetic markers. Two-point testcrosses; three-point testcrosses.

Knowledge acquired in Unit 2

• The inheritance of Mendelian traits.

• The role of sexual reproduction for obtaining recombinant genotypes.

• The procedures used for the construction of genetic maps.

3. The dynamic genome: the main modifications of genetic material and genetic engineering (10 hours)

3.1. Genomic and chromosomal mutations.

3.2. Importance of polyploids: evolutionary processes through polyploidy in plants (the particular case of the genus Triticum).

3.3. Genetic mutations and creation of new variability.

3.4. Mutagenesis: artificial mutation induction and its use in genetic improvement.

3.5. Elements of genetic engineering. Genetic transformation of plants with Agrobacterium tumefaciens and with the biolistic method.

Knowledge acquired in Unit 3

• The main modifications of the genetic material (mutations).

• The relationships between mutations and the occurrence of genetic variability.

• The general aspects related to the use of genetically modified organisms in agriculture.

4. Inheritance of quantitative traits (6 hours) (integration with the course statistics: mean and variance).

4.1. Generalities: Johannsen experiments, genotypic and phenotypic effects, the economic importance of quantitative traits.

4.2. Analysis of the components of the mean in case of multifactorial genetic determination, additive and dominance effects. Inbreeding and heterosis.

4.3. East experiments, components of the phenotypic variance, the contribution of environmental variability, heritability.

Knowledge acquired in Unit 4

• The mode of inheritance of quantitative traits.

• Understanding of how traits of agronomic and economic importance are determined by polygenes.

5. Population genetics (6 hours) (integration with the course of statistics: the Chi-square test).

5.1. The Hardy-Weimberg allelic and genotypic frequencies equilibrium and its verification with appropriate statistical tests (Chi-square)

5.2. Equilibrium of a population: mutation, migration, selection, random mating, population size (genetic drift).

5.3. Biodiversity intra-specific and evolution. Study of populations for germplasm conservation and enhancement of genetic resources. Theoretical aspects and management.

Knowledge acquired in Unit 5

• The population genetics and intermating.

• The factors affecting allelic and genotypic frequencies.

• The genetic basis of intra-specific biodiversity conservation and managements.

6. Evolution and plant breeding (6 hours)

6.1. Evolution and domestication of cultivated plants: history of plant breeding.

6.2. Genetic improvement in self-pollinated and cross-pollinated plants. Main genetic aspects of the management of genetic improvement programs.

6.3. Genetics in seed production and seeds marketing.

Knowledge acquired in Unit 6

• The main genetic aspects involved in artificial selection.

• The most relevant genetic aspects of seed marketing.

• The importance of intra-specific biodiversity and the main aspects of germplasm conservation management.

7. Practical classes (24 hours)

The practical classes are considered as integral part of each teaching units.

1) Activities carried out during the practical classes.

a) demonstrating simple DNA analysis,

b) observations and measurements of plant material specially developed for educational needs,

c) examination of data collected by the students or by simulated the teacher and simple statistical analysis,

d) critical analysis of simple bibliography, guided by the teacher but conducted by the student,

e) organization of team reports and presentation of short scientific seminars.

2) Tools used for the practical classes: (integration with the didactic field of DipSA and the experimental farm in Cadriano, where materials are bred in previous years for the establishment and maintenance of the original genetic material).

a) Plant material: maize and wheat genotypes chosen so as to highlight the most important genetic phenomena covered in the course. These materials are completely original and developed ad hoc over the years through controlled fertilization prevailingly by the teacher.

i) Plant material growth in the didactic field of DipSA. Maize genotypes – pure lines, their hybrid and F2 population resulting from it - are grown by the teacher from the beginning of August and are shedding at the beginning of the course in autumn semester (it is clarified the mere use for demonstration purposes, and the fact that the cultivation of corn does not happen normally in autumn). The plants are presented to the students and their growth is followed for the duration of the course, then they are analyzed and sacrificed after approximately 40 days and measured by the students in the verification of genetic events covered during the course (integration with the experimental farm in Cadriano)..

ii) Plant material grown in advance, and in particular ears of maize produced as a result of self-fertilization of hybrids made ad hoc for the students. Such hybrids are resulting from the cross of lines differing for two traits and are therefore used for the experimental verification of independent segregation (integration with the experimental farm in Cadriano).

b) Tools used in plant genomics and breeding laboratory: (integration with the research laboratory of plant genomics and breeding of DipSA).

i) simple tools for molecular analysis are brought into the classroom and explained to the students. The demonstration will be supported by the staff working in the genetics laboratory DipSA.

3) Subjects of the practical classes

a) Practical classes of Unit 1 (4 hours)

i) Demonstration of simple techniques of extraction of DNA and its analysis. For this purpose laboratory instruments are carried in the classroom and explained to students during a demonstration. Exercise carried out in co-presence with other researchers in the group of agricultural genetics DipSA (integration with the research laboratory of plant genomics and genetic improvement of DipSA).

ii) Demonstration of simple examples of the use of DNA analysis for diagnostic, forensic and for the protection of intellectual property

b) Practical classess of Unit 2 (6 hours)

i) Illustration of flowering and pollination in plants grown in the didactic field (integration with the didactic field at DipSA).

ii) Application of the statistical test Chi-square to the genetic material set up ad hoc for the study of the genetic linkage. Organization of the worki in teams, formulating hypotheses, experimental verification, drafting of a report to be completed as homework. This report is graded up to 1 point in the final evaluation.

iii) Use of statistical tests for the analysis of simulated data of genetic markers segregation. Construction of a simple linkage map.

c) Practical classes of Unit 3 (2 hours)

i) Possible applications of genetic engineering in agriculture with analysis of bibliographic information and discussion.

d) Practical classes of Unit 4 (4 hours)

i) Study of the consequences of self-fertilization on the media components with experimental data measured on maize plants grown in the didactic field (integration with the didactic field at DipSA).

ii) Study of the components of the phenotypic variance with experimental data measured in the corn plants grown in the field of teaching (integration required with the didactic field at DipSA).

e) Practical classess of Unit 5 (0 hours)

There are no practical classess

f) Practical classess of Unit 6 (8 hours)

i) Review of case-studies of plant breeding, analysis of simple bibliography guided by the teacher, also available in English. Preparation of seminars conducted by students, with presentation and discussion in the classroom, in Italian or English. (The seminar is graded up to 3 points in the final evaluation)

ii) Visit of the seed research analysis laboratory (LaRAS) of DipSA, upon availability (integration with the seed research analysis laboratory (LaRAS) of DipSA).

Knowledge acquired in Unit 7

• Familiarity with the results of diagnostic assays useful for forensic or commercial purposes.

• Ability to recognize the major genetic events in practice.

• Acquisition of scientific method in genetic research by means of statistical verification of data.

• Ability to autonomously acquire new information, using critical skills and source verification, partly in English.

• Acquisition of experience in team-working and in public communication of technical subjects.

Readings/Bibliography

F. Lorenzetti, S. Ceccarelli, D. Rosellini, F. Veronesi. Genetica agraria - Genetica e biotecnologie applicate all'agricoltura. Patron,

Bologna, 2011.

Additional readings:

M. Busconi e altri. Genetica agraria, EdiSES, Napoli, 2016

G. Barcaccia, M. Falcinelli. Genetica e genomica, Vol I genetica vegetale, Liguori Napoli, 2005; G. Barcaccia, M. Falcinelli. Genetica e genomica, Vol II miglioramento genetico, Liguori Napoli, 2005.

Notes from the course available on line.

Literature and notes in English will be provided upon request.

Teaching methods

The course consists of 36 hours of lectures and 24 hours of tutorials (practical classes).

The lectures are intended to illustrate the subject and to stimulate the involvement of students in order to assess the prior knowledge, the learning progresses and to promote a critical discussion of the topics covered.

The practical classes are held at the didactic field at DipSA, at other facilities of DipSA and in the classroom. The practical classes include: demonstrations of DNA analysis, observations and surveys of plant material specially developed, examination of data collected by the students or simulated by the teacher and simple statistical analysis, critical discussion of basic bibliography (also in English) conducted by the students, and preparation of reports and short seminars (also in English). The objectives of the practical classes are to make the students familiar with the results of diagnostic assays useful for forensic or commercial purposes, to develop the ability to practically recognize main genetic phenomena and to acquire the scientific method in genetic research by means of the statistical verification of data. Practical classes also aim to encourage the attitude to autonomously acquire new information, using critical skills and verification of sources, partly in English. Not last goal is to promote ability to team working and communicating technical reports.

Assessment methods

The exam can be taken in English, upon request.

The oral exam consists of three specific questions on the following subjects:

1) on basis of genetic information, its expression and Mendelian genetics,

2) major changes in the hereditary material and controlling quantitative traits,

3) population genetics and bases of genetic improvement.

Each question allows for a maximum of 10 points. To pass the exam the minimum score is 18, with at least 5 in each question. An excellent oral exam can allow to pass the exam with the highest score. The oral exam lasts usually about 30 minutes.

All students who achieve a score at least sufficient in the oral test, can also add the results of their practical activities (report and seminar), as specified in the program. This evaluation (for a maximum of 4 points) is added to that obtained in the interview.

Teaching tools

Personal computer and projector for classroom activities.

Original plant material specially developed at the University Experimental Farm (Cadriano) will be used in practical-application.

Scientific literature provived by the Sistema Bibiliografico di Ateneo.

Mailing list for teacher-student communication will be used, which is accessible to students of the course only, being password-protected (password will be distributed during classes or requested to the teacher).

Material: the material presented will be made available to the students in electronic format via Internet. Access to the material will be allowed to students belonging to the mailing list only.

Office hours

See the website of Elisabetta Frascaroli