Important notice
The course guide is provisional.
The PDF version of the course guide may take a few days to become available in the DDD.
Plant Genomics
Code: 44782Credits: 6
| Degree programme | Type | Course |
|---|---|---|
| Plant Biology, Genomics and Biotechnology | OB | 1 |
Contact lecturer
- Name :
- Narciso Campos Martinez
- Email :
- narciso.campos@uab.cat
Teaching staff
- Maria Jose Aranzana Civit
- Pau Carnicero Campmany
- L. Maria Lois Rojas
- Werner Howad
- Raul Castanera Andres
- Pere Arús Canals
- Ana Martin Hernandez
Teaching staff (external to UAB)
- Alfonso Saera Vila
- Igor Flórez Sarasa
Group languages
You can consult this information at the end of the document.
Prerequisites
Good command of English
Good background in genetics, molecular biology and genetic engineering
Objectives
Describe the theoretical and technological bases of the organization, function and evolution of plant genomes and their applications for the improvement of crop plants.
Learning outcomes
- CA05 (Recognise the ethical, social responsibility and legal considerations related to the use of genomic data, valuing respect for human and fundamental rights and the economic and environmental impact to apply them to the scientific and professional environment, in accordance with the Sustainable Development Goals.) Recognise the ethical, social responsibility and legal considerations related to the use of genomic data, valuing respect for human and fundamental rights and the economic and environmental impact to apply them to the scientific and professional environment, in accordance with the Sustainable Development Goals.
- CA06 (Apply the knowledge acquired in new or unfamiliar environments within broader (or multidisciplinary) contexts related to Plant Biology, Genomics and Biotechnology.) Apply the knowledge acquired in new or unfamiliar environments within broader (or multidisciplinary) contexts related to Plant Biology, Genomics and Biotechnology.
- KA05 (Recognise the role of female scientists in the field of genetics and genomics.) Recognise the role of female scientists in the field of genetics and genomics.
- KA06 (Define concepts related to plant genomics and select the most appropriate methodologies for sequencing and annotating plant genomes.) Define concepts related to plant genomics and select the most appropriate methodologies for sequencing and annotating plant genomes.
- SA09 (Communicate the results of research into the organisation and function of plant genomes in English orally and in writing using appropriate scientific terminology.) Communicate the results of research into the organisation and function of plant genomes in English orally and in writing using appropriate scientific terminology.
- SA10 (Apply knowledge of plant genomics to the study of evolutionary mechanisms and plant and fungi systematics.) Apply knowledge of plant genomics to the study of evolutionary mechanisms and plant and fungi systematics.
- SA11 (Apply an omics approach to the identification of new genes and processes of interest in basic and applied research.) Apply an omics approach to the identification of new genes and processes of interest in basic and applied research.
- SA12 (Apply bioinformatic tools to genomic studies of plant systematics and phylogeny.) Apply bioinformatic tools to genomic studies of plant systematics and phylogeny.
Contents
- Plant genome organization, function and regulation.
- Analysis and functions of RNA
- Molecular evolution of plants.
- Genetic markers and molecular breeding.
- Genome sequencing strategies and annotation.
- Omic approaches
- Bioinformatics tools applied to omics and evolutionary studies.
Learning activities and methodology
| Title | Hours | ECTS | Learning outcomes |
|---|---|---|---|
| Bioinformatic sessions | 10 | 0.4 | |
| Personal work and learning | 52 | 2.08 | |
| Classroom practices | 4 | 0.16 | |
| Seminars | 5 | 0.2 | |
| Preparation of oral presentations and written report for the seminars | 51 | 2.04 | |
| Lectures | 22 | 0.88 | |
| External visit | 4 | 0.16 |
- Lectures covering the different topics of the program. Powerpoint presentations will be available at the Campus Virtual UAB.
- Reading and analysis of research papers selected by the students, for their presentation and discussion in the seminar sessions.
- Practical sessions on bioinformatics tools applied to omics and evolutionary studies
- Visit to the Centre for Research in Agricultural Genomics (CRAG) at the Campus of UAB.
In this course, the use of Artificial Intelligence (AI) technologies is permitted exclusively for bibliographic or information searches. Students must clearly identify which parts of the information were generated using this technology and specify the tools used. Lack of transparency regarding the use of AI in assessable activities will be considered academic dishonesty and may result in a partial or full penalty on the activity grade, or more severe sanctions in serious cases.
Assessment
Continuous assessment activities
| Title | Weight | Hours | ECTS | Learning outcomes |
|---|---|---|---|---|
| Written report (phylogenomics) | 15 | 0 | 0 | CA05, CA06, KA05, KA06, SA09, SA10, SA11 |
| Oral presentation (seminar) | 25 | 0 | 0 | CA05, CA06, KA05, KA06, SA09, SA10, SA11, SA12 |
| Written report (seminar) | 25 | 0 | 0 | CA05, CA06, KA05, KA06, SA09, SA10, SA11, SA12 |
| Written exam | 35 | 2 | 0.08 | CA05, CA06, KA05, KA06, SA09, SA10, SA11, SA12 |
- Multiple choice test
- Written report on the phylogenomics practice
- Written report on a scientific article (research paper or review)
- Oral presentation of the scientific article in a seminar session
- Attendance and participation in the classroom and seminar sessions
- The student will pass the subject when the sum of his/her marks reaches a minimum score of 5 out of 10
This subject does not include the single assessment system.
In this course, the use of Artificial Intelligence (AI) technologies is permitted exclusively for bibliographic or information searches. Students must clearly identify which parts of the information were generated using this technology and specify the tools used. Lack of transparency regarding the use of AI in assessable activities will be considered academic dishonesty and may result in a partial or full penalty on the activity grade, or more severe sanctions in serious cases.
Bibliography
|
|
- Plant genes, genomes and genetics (Wiley, 2015) -- Erich Grotewold, Joseph Chappell, Elizabeth A. Kellogg. [ https://bibcercador.uab.cat/permalink/34CSUC_UAB/1qnjagj/alma991010871780206709 ]
- Molecular Plant Breeding (Iowa State University Digital Press, 2023) — eds. Suza & Lamkey. Accés obert, llicència Creative Commons [ https://www.iastatedigitalpress.com/plugins/books/133/ ]
- Molecular Plant Breeding (CABI Digital Library 2010) eds. Yunbi Xu [ https://www.cabidigitallibrary.org/doi/book/10.1079/9781845933920.0000 ] Paperback: ISBN : 978-1-84593-982
- Plant Molecular Breeding in Genomics Era (Springer, 2024) — eds. Al-Khayri, Ingle, Jain & Penna (Advances in Plant Breeding Strategies, vol. 3) [ https://www.amazon.com/Plant-Molecular-Breeding-Genomics-Era/dp/3031685857 ]
In addition, specific readings (books, book chapters, and journal articles) for each course session will be provided.
Useful web links will also be provided.
Software
Plant Genomics, subject presentation. Sessions program. Seminars. Evaluation. Visit to the CRAG.
Organization of plant genomes. Nuclear genome. Ploidy. Coding and non-coding regions in the genome. Repetitive DNA. Gene evolution. Pseudogenes. Genomic annotation. Plastid and mitochondrial genomes. RNA editing. Interaction between cell genomes.
Plant genome plasticity and transposable elements. Impact of transposable elements in the structure and evolution of plant genomes.
Coding and non-coding RNAs: types and biological functions. RNA polymerases. Roles of RNAs in protein synthesis and processing. RNAi silencing mechanisms: transcriptional and posttranscriptional. Small RNAs: siRNAs and hpRNAs. miRNAs: action, roles, and applications. lncRNAs.
Epigenomics. Chromatin structure and activity state. Epigenetic marks in plants. DNA methylation. Histone code.
Proteomics.
Metabolomics.
Molecular markers. Definition. Types of molecular markers. Methods to obtain molecular markers. Genotyping methods.
Genetic linkage: mapping genes and quantitative traits (QTLs).
Linkage disequilibrium and Genome-Wide Association (GWAS).
Hands-on seminar/computer practical: Playing with genotyping data and map construction.
Plant phylogenetics and evolution. Plant molecular evolution. Introductory concepts on phylogenetics. Gene trees versus species trees: Homology, orthology, paralogy. Concerted evolution. Hybridization and introgression. Polyploidy. Lineage sorting or deep coalescence. Molecular markers used in plant phylogenetics and phylogenomics.
Bioinformatics tools in phylogenomic studies. Orthology assessment and multiple sequence alignment. Genetic distances and nucleotide substitution models. Phylogenetic inference. Parsimony analysis. Probabilistic Methods (Maximum Likelihood). Measurements of statistical support. Coalescent-based species trees.
High throughput sequencing. Introduction to Next-Generation Sequencing Platforms. Examples of applications: de novo genome sequencing, genome re-sequencing, exome sequencing, methylome sequencing.
Next-Generation Sequencing Technologies for transcriptomics. Design of RNA-seq experiments. RNA-seq (Illumina) data analysis: identification of differentially expressed genes. Practical use of the AIR platform.
Visit to the Centre for Research in Agricultural Genomics (CRAG).
Seminars. Oral presentation of published research by students.
Course groups and languages
The information provided is provisional until November 30. After this date, you will be able to consult the language of each group through this link. To access the information, you will need to enter the course CODE
| Type of teaching | Group | Language | Semester | Shift |
|---|---|---|---|---|
| (TEm) Theory (master) | 1 | English | first semester | morning-mixed |
| (PLABm) Practical laboratories (master) | 1 | English | first semester | morning-mixed |
| (SEMm) Seminars (master) | 1 | English | first semester | morning-mixed |