Environmental DNA and novel molecular approaches in production

Semester 1

Semester 2

Semester 3

Semester 4

ECTS
5

PRODUCTION

Applied genetics and animal welfare in production
Galway Mayo Institute of Technology

Synopsis

Recent technological advances are allowing the development of fast, effective and reliable molecular tools for the study of organisms both in the wild and in captivity. Modern production systems rely on such approaches in order to be sustainable and profitable at the same time. This course provides an overview of modern genetic approaches, with particular attention to environmental DNA approaches.

Content

History of eDNA. Methodological pipelines in eDNA studies (reference library preparation, assay design, in silico testing, in vitro testing, limit of detection, limit of quantification, power of detection, internal positive controls, negative controls, field work and water sampling, replication, data validation and interpretation). History of eDNA and NGS technology. Overview of NGS platforms. Data production, handling, storage and bioinformatics. eDNA and RT-qPCR as a tool to monitoring target organisms, including pathogens and parasites. Metabarcoding in eDNA studies. Experimenting with eDNA. Case studies, from concepts to practical application.
The above concepts will be covered in the theoretical component of the course by means of lectures and interactive classes. The practical part of this course will include a one day field trip, laboratory work, series of in-class practical and computer work (bioinformatics) and interactions with researchers from the Marine and Freshwater Research Centre (MFRC) in order to get acquainted with up-to-date infrastructure and research facilities.

Pre-requisites

Bachelor level in science. Basic knowledge of genetics is recommended.

Aims

To understand state-of-the-art genetic approaches such as environmental DNA (eDNA) and Next Generation Sequencing (NGS) technology and their application to wild and farmed organisms.

Objectives

On completion of this module the learner will/should be able to demonstrate a basic understanding of environmental DNA (eDNA) approaches and Next Generation Sequencing (NGS) technology, to understand their current and future application in production systems as well as other areas of research and critically interpret results from an eDNA experiment.

Key skills acquired

To be familiar with the concepts of eDNA and NGS technology, their advantages and limitations and to critically interpret results from an eDNA experiment.

Bibliography

Liu Z. (2007) Aquaculture genome technologies — 1st ed. ISBN-13: 978-0-8138-0203-9
Goldberg C., Strickler K. and Pilliod D. (2015) Special Issue: Environmental DNA: A powerful new tool for biological conservation. Biological Conservation 183, Pages 1-102.
Goodwin S., McPherson J.D. and McCombie W.R. (2016) Coming of age: ten years of next-generation sequencing technologies. Nature Reviews Genetics 17, 333–351 doi:10.1038/nrg.2016.49

Assessment

All assessments are formative and summative, hence contributing to the course grade. This course is 100% continuous assessment.

Involved teachers

Luca Mirimin (luca.mirimin@gmit.ie)

Contact hours

lectures
12

practicals
8

seminars

computerclass
8

fieldwork

other
11