Plant genomics and breeding

A.Y. 2019/2020
12
Max ECTS
112
Overall hours
SSD
AGR/07
Language
Italian
Learning objectives
The course will offer the students the main knowledge of genome structure, organization and evolution in model systems and in crops. The course will also provide a detailed description of the main mechanisms of regulation of gene expression and analyze principles and methodologies for forward and reverse genetic analysis. Furthermore the course will offer to the students the Essential of genetics improvement in plant breeding.
Expected learning outcomes
At the end of the course the students will have to know the different components and their distribution and organization within the plant genome. They will have acquired a good comprehension of the characteristics of the repetitive DNA sequences and their role in the evolution of single genes and genomes. They will also have acquired the notions regarding the different levels of regulation of gene expression and learned the principles of the use of phenotypic and molecular markers in the construction of genetic maps and in the study of genetic diversity. They will be able to identify the main characters, along with their molecular basis, of the processes of domestication and crop improvement. They will also have acquired some useful tools for the identification of genes and the study of gene function and expression in plants.
Course syllabus and organization

Unique edition

Responsible
Lesson period
First semester
Course syllabus
DU1 K06-48-A' - 'Plant genetics and genomics'
Genome architecture. Different components of the eukaryotic genome: single DNA sequences, single genes and gene families, repetitive DNA sequences, tandem and intersperse repeats. Genetic maps: visible phenotypic markers, DNA molecular markers and linkage analysis. Transposable elements (TE): class I and II elements, molecular and functional features; main TE families in maize, from their discovery to the study of their role in genome and gene evolution. Comparative analysis of plant genome structure and size, colinearity of genomes in cereal species. Orthologous and paralogous genes, evolution of gene families.
Gene expression. Different levels of regulation of gene expression. Regulation of transcription: cis-regulatory sequences and transcription factors; epigenetic changes, DNA methylation and histone modifications. Role of environmental (light, temperature) and internal (developmental stage, hormones) signals on gene expression. Variants of transcription factors and their role in the domestication process, examples in rice, maize and tomato. Regulation of gene expression and plant development: seed origin and domain differentiation.
Functional genomics. Forward genetics: mutagenesis, detection and characterization of knockout mutants. Genetic dissection of biosynthetic pathways and developmental processes. TE mutagenesis: co-segregation analysis and gene sequence isolation. Reverse genetics: organization of mutant collections, survey for single mutant detection, insertion libraries assembly. Single gene variants in crop improvement: genes of the green revolution.

UD2. 'K06-48-B' - 'Advanced plant breeding'
Genome architecture. Different components of the eukaryotic genome: single DNA sequences, single genes and gene families, repetitive DNA sequences, tandem and intersperse repeats. Genetic maps: visible phenotypic markers, DNA molecular markers and linkage analysis. Transposable elements (TE): class I and II elements, molecular and functional features; main TE families in maize, from their discovery to the study of their role in genome and gene evolution. Comparative analysis of plant genome structure and size, colinearity of genomes in cereal species. Orthologous and paralogous genes, evolution of gene families.
Gene expression. Different levels of regulation of gene expression. Regulation of transcription: cis-regulatory sequences and transcription factors; epigenetic changes, DNA methylation and histone modifications. Role of environmental (light, temperature) and internal (developmental stage, hormones) signals on gene expression. Variants of transcription factors and their role in the domestication process, examples in rice, maize and tomato. Regulation of gene expression and plant development: seed origin and domain differentiation.
Functional genomics. Forward genetics: mutagenesis, detection and characterization of knockout mutants. Genetic dissection of biosynthetic pathways and developmental processes. TE mutagenesis: co-segregation analysis and gene sequence isolation. Reverse genetics: organization of mutant collections, survey for single mutant detection, insertion libraries assembly. Single gene variants in crop improvement: genes of the green revolution.
Prerequisites for admission
General genetic course
Teaching methods
Lectures and laboratories.
Bibliography
Russel, Genetica - Un approccio molecolare, Pearson
Grotewold, Chappell, Kellogg, Plant Genes, Genomes and Genetics, Wiley-Blackwell
Lorenzetti et al. Miglioramento genetico delle piante agrarie - edagricole
Lewin's Gene XIII - Jones and Bartlet
Genetica e Genomica (vol. II e III). (Barcaccia e Falcinelli)
Principles of genetics and breeding (G. Acquaah)
Plant biotechnology and genetics (C.N. Stewart, JR)

Articles on specific topics and main slides of the lectures will be available on the Ariel platform
Assessement methods and criteria
The exam includes a written test and an oral test.
The written test on the first part of the program can be carried out during the course, halfway through the semester, while the oral interview takes place at the end of the course.
During the tests will be evaluated: 1) The knowledge and ability to connect the topics covered in the UD 2) The skills in the use of genetic analysis, in silico analysis and molecular biology tools for the study of the gene function 3) The ability to link genetic variants and phenotypes related to characters of importance for the genetic improvement of cultivated plants.
The final interview also includes the discussion of the activities carried out and the results obtained during the laboratory exercises. The student may present a report, consisting of a text or a "power point" presentation, which reports these activities.
Genetica e genomica vegetale
AGR/07 - AGRICULTURAL GENETICS - University credits: 7
Single bench laboratory practical: 16 hours
Lessons: 48 hours
Professor: Consonni Gabriella
Miglioramento genetico avanzato
AGR/07 - AGRICULTURAL GENETICS - University credits: 5
Laboratories: 16 hours
Lessons: 32 hours