ECTS credits ECTS credits: 3
ECTS Hours Rules/Memories Student's work ECTS: 51 Hours of tutorials: 3 Expository Class: 9 Interactive Classroom: 12 Total: 75
Use languages Spanish, Galician
Type: Ordinary subject Master’s Degree RD 1393/2007 - 822/2021
Departments: External department linked to the degrees, Zoology, Genetics and Physical Anthropology
Areas: Área externa M.U en Acuicultura (3ª ed), Genetics
Center Faculty of Biology
Call: Second Semester
Teaching: With teaching
Enrolment: Enrollable | 1st year (Yes)
Acquire knowledge about basic principles of genomics, and their application for the sustainable genetic improvement of aquaculture species.
Acquire knowledge on techniques:
Structural and Functional genomic analysis
Bioinformatic analysis of genomic data
Unit 1. Structure and organization of genomes. Genomic analysis.
Size and organization of genomes. Fragmentation and separation of genomic sequences. Isolation of chromosomes. In situ hybridization. Genomic libraries. Vectors. Strategies of genomic sequencing. Modifications of Sanger method. NGS (next generation sequencing). Revision in aquaculture.
Unit 2. Genetic maps and comparative mapping.
Linkage and recombination. Segregating populations and genetic markers. Genetic cartography, High-resolution linkage mapping. Comparative mapping and evolutionary genomics. Identification of QTL (quantitative trait loci). Integration of genetic and physical maps. Fine mapping. Positional cloning. Genome mining. Targeted sequencing. Genome Mining. Detection of candidate genes. Genome wide association analysis (GWAS). Revision and applications in aquaculture.
Unit 3. Functional Genomics.
Functional genomics. Microarray. RNAseq. Regulatory regions. Epigenomics: 3D structure of DNA, DNA methylation, histone modification, access to DNA. Metagenomics. Genomic edition. Single-cell genomic technologies. Identification of candidate genes and pathways related to biological processes of productive and evolutionary interest. Applications in aquaculture.
Practical classes:
-FUNCTIONAL GENOMIC ANALYSIS OF GENE EXPRESSION: Extraction of RNA: amount and quality for genomic analyses. Analysis of gene expression data from RNAseq. Practical cases in aquaculture: Gene expression analysis to study the genetic basis of productive traits.
-BIOINFORMÁTICS. Management, annotation of genomic sequences. In silico characterization and genotyping of microsatellite and SNP markers. Genetic and comparative mapping. Genome mining. Analysis of differential expression starting from RNAseq data. Practical cases in aquaculture species
Basic
-Figueras A. y Martínez P. 2009. Genética y Genómica en Acuicultura (Coord.: P. Martínez y A. Figueras).Publicaciones Científicas y Tecnológicas de la Fundación OESA, CSIC. Madrid. http://www.fundacionoesa.es/images/stories/publicaciones/libros/genetic…
-Lesk, AM. 2012. Introduction to genomics. Oxford University Press, Oxford.
-Liu Z. 2017. Bioinformatics in Aquaculture: Principles and Methods. John Wiley & Sons Ltd. Online Books. https://onlinelibrary.wiley.com/doi/book/10.1002/9781118782392
-Pierce, B.A. 2015. Genética: Un enfoque conceptual. 5ª edición Editorial Médica Panamericana, Madrid.
Complementary
-Chandhini S, et al. 2019.Transcriptomics in aquaculture: current status and applications. Rev Aquacult 11, 1379-97.
-De Lorgeril J, et al. 2020 Differential basal expression of immune genes confers Crassostrea gigas resistance to Pacific oyster mortality syndrome. BMC Genomics 21: 63
-Figueras A et al. 2016. Whole genome sequencing of turbot (S. maximus; Pleuronectiformes): a fish adapted to demersal life. DNA Res 23: 181-192.
-Gavery and Roberts. 2017. Epigenetic considerations in aquaculture. PeerJ 5:e4147
-Maroso F et al. (2018) Highly dense linkage maps from 31 full-sibling families of turbot (S. maximus) provide insights into recombination patterns and chromosome rearrangements throughout a newly refined genome assembly. DNA Res 25: 439–450.
-MacKenzie SA, Jentoft S (eds) 2016. Genomics in aquaculture. Academic Press, Elsevier. Londres.
-Macqueen et al. 2017. Functional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture. BMC Genomics 18: 484.
-Nguyen TV, Alfaro AC. 2020. Applications of omics to investigate responses of bivalve haemocytes to pathogen infections and environmental stress. Aquaculture 518: 734488
-Robledo D et al. 2018. Applications of genotyping by sequencing in aquaculture breeding and genetics. Rev Aquacult 10: 670–682.
-Rodríguez-Ramilo ST et al. 2014. Identification of QTL associated with resistance to viral haemorrhagic septicaemia (VHS) in turbot (S. maximus): a comparison between bacterium,parasite and virus diseases. Mar Biotech,16:265-76.
-Yue GH, Wang L. 2017. Current status of genome sequencing and its applications in aquaculture. Aquaculture 468: 337-347.
- Hwang B, Lee JH, Band D. 2019. Single-cell RNA sequencing technologies and bioinformatics pipelines. Exp Mol Med 50:96.
- Peters L et al. 2018. Environmental DNA: a new low-cost monitoring tool for pathogens in salmonid aquaculture. Front Microbiol 9:3009.
WEB Resources:
Bases de datos de secuencias genómicas y transcriptómicas. Genomas animales y de especies en acuicultura. Recursos de mapeo genético y comparativo. Herramientas bioinformáticas.
http://www.ensembl.org/
http://www.ncbi.nlm.nih.gov/
https://gold.jgi.doe.gov/
General competences
• CG03- Importance of multidisciplinary analysis and relation between knowledge to solve problems and analyse critical points.
• CG04- Use of proper scientific terminology.
• CX08- Promote the use of foreign languages.
Specific competences
• CE10- Identifying significant research aims and planning strategies to reach goals.
• CE11- Acquire basic and applied knowledge in genetics, genomics and proteomics in aquaculture.
Basic competences:
• CB02- Warranting students to be able to apply acquired knowledge and problem-solving within pioneering, multidisciplinary contexts, related to the field of study.
Transversal competences:
• CT2 - Capacity for autonomous work and decision making.
• CT4 - Ability for searching, analysing and interpreting different information sources in distinct languages (preferably English).
-Classes and seminars. Multimedia presentations and proposal of exercises/case studies to support the conceptual development of the program.
-Practical activities. Laboratory (experimental development for functional and structural genomic analysis), bioinformatics (analysis and management of genomic and transcriptomic sequences, genetic and comparative mapping, genome mining, differential gene expression analysis from RNAseq data). Practical classes will be held in USC-Campus Terra, Lugo.
-Tutorial support for solving doubts and support to achieve the proposed aims of the course.
ASSESMENT SYSTEM
Exam (60%); participation of practical activities (15%); realization of seminars (15%); attendance and participation (10%).
Presencial time: Classes (7 hours), seminars (3 h), practical activities (9 h).
Tutorial support (3 h). Exam realization and revision (2h)
Individual work: 51 h (study time, resolution of problems, preparation of seminars/works and exam).
Total time: 75 h.
Attendance to expositive and interactive classes, practical sessions and seminars. Participate in classes. Study regularly. Consult questions about the class presentations and guides to support practical activities. Consult the recommended literature. Use the tutorial support and.
Adaptation of the MA to the measures taken by the Univs. for containment of COVID19:
IN THE SITUATION FOR THE BEGINNING OF THE COURSE
Expositive and interactive teaching: For not exceeding the classroom capacity allowed by the UVigo and UDC standards, and adjusting to scenario 2 of the USC standards, the theory and blackboard expository classes may be in-person, as long as fitting the situation and general measures imposed by the authorities.
Interactive laboratory teaching: Maintaining the safety distance of 1.5 m is essential; mainly in wet laboratories. For this reason, if necessary, the practice groups must be split to follow this basic rule. In the event that the split already effective in the first semester subjects (and some of the second semester) was not enough to adjust to the reduced capacity of the laboratory, a reduction of the prsential practices should be applied (transforming some on blackboard), in order to apply a expansion of the number of groups (with the consequent reduction in the number of students per group).
Exam: Like expository teaching, due to not exceeding the capacity of the classrooms, the exams may be presential.
General rule: The use of a mask and the maintenance of the safety distance will be mandatory in any case.
CHANGE OF SITUATION
In the case of a change in the situation and the rules imposed by the authorities, all theory classes (expository) and blackboard will be taught by electronic means, Skype, Teams, or similar, to allow the student assistance from home, having previously verified that all of them have sufficient band width.
Regarding the teaching of laboratory practices, as far as possible they will also become blackboard classes, through exercises, videos or similar material, which will be shared through the Master's cloud folder or, in the case of exceeding capacity, by means such as WeTransfer.com or similar options.
Only in those cases in which the laboratory practices are essential and transcendental [as is the case of the cultive subjects], the MA will wait to see the evolution of events and, only if the Competent Authority lifted the quarantine in time, would they be taught and would be qualified. Otherwise, not being able to teach them, the evaluation of the subject must be done only with the teaching given until the official closing of the course, using telematic means also for the exam, which obviously cannot be presential.
However, on a voluntary basis for both teachers and students, the laboratory practices could be recovered, after the end of the course, although without the possibility of evaluation, on mutually agreed date and conditions. The latter, provided that the universities ensure the extension of the course and civil responsability insurance of their students.
M Carmen Bouza Fernandez
Coordinador/a- Department
- Zoology, Genetics and Physical Anthropology
- Area
- Genetics
- mcarmen.bouza [at] usc.es
- Category
- Professor: University Lecturer
María Belén Gómez Pardo
- Department
- Zoology, Genetics and Physical Anthropology
- Area
- Genetics
- Phone
- 982822428
- belen.gomez [at] usc.es
- Category
- Professor: University Lecturer
Diego Robledo Sanchez
- Department
- External department linked to the degrees
- Area
- Área externa M.U en Xenómica e Xenética
- diego.robledo.sanchez [at] usc.es
- Category
- External area professor
| Thursday | |||
|---|---|---|---|
| 10:00-12:00 | Grupo /CLE_01 | Spanish | Videoconference Classroom. Sir David Attenborough |