DNA sampling from mucus in the Nile tilapia, Oreochromis niloticus: Minimally invasive sampling for aquaculture-related genetics research

Abstract

First paragraph: Genotypic information is widely used in the conservation and management of wild fish (Schwartz, Luikart & Waples 2007) and is increasingly valuable in the management of captive populations (e.g. for verification of pedigree or for marker-assisted selection; Perez-Enriquez, Takagi & Taniguchi 1999; Sonesson 2007). Obtaining DNA most commonly involves taking tissue samples from live fish, such as blood or a fin biopsy (Campanella & Smalley 2006), or killing fish (particularly if too small to take biopsy samples: Mirimin, O'Keeffe, Ruggiero, Bolton-Warberg, Vartia & Fitzgerald 2011). Tissue biopsy may have negative impacts on fish, potentially including infection and effects on survival, growth or behaviour (Le Vin, Adam, Tedder, Arnold & Mable 2011); e.g. the adipose fin, commonly removed from salmonids for marking and DNA extraction, is now known to show sexual dimorphism (Hisar, Sönmez, Hisar, Budak & Gültepe 2013) and is thought to function as a flow sensor (Buckland-Nicks, Gillis & Reimchan 2011). In studies on wild fish populations, particularly rare or uncommon species with small body size, it is undesirable to kill large numbers, and this has led to recent publications investigating extraction of DNA from mucus taken from the skin or mouth cavity (Campanella & Smalley 2006; Livia, Antonella, Hovirag, Mauro & Panara 2006; Le Vin etal. 2011; Mirimin etal. 2011; Reid, Kidd & Wilson 2012; de Verdal, Vandeputte, Pepey, Vidal & Chatain 2014). Brush swabbing is one of the less invasive sampling strategies, which is used in a range of other groups of organisms, e.g. humans (Clarke, Prost, Stanton, White, Kaplan & Matisoo-Smith 2014), amphibia (Pidancier, Miquel & Miaud 2003) and molluscs (Henley, Grobler & Neves 2006). The reduced invasiveness of such sampling techniques, and reduced likelihood of impact on the welfare of the fish concerned, also makes them less likely to come under regulations on animal experimentation; swab samples can also be collected without the use of anaesthesia, required under UK regulations for tissue biopsy (Le Vin etal. 2011). Potential drawbacks of such methods may include sample contamination, low DNA quantity or poor quality DNA (Taberlet, Waits & Luikart 1999; Lieber, Berrow, Johnston, Hall, Hall, Gubili, Sims, Jones & Noble 2013).