DNA sampling from mucus in the Nile tilapia,<i>Oreochromis niloticus</i>: minimally invasive sampling for aquaculture-related genetics research

Taslima, Khanam; Davie, Andrew; McAndrew, Brendan; Penman, David J.

doi:10.1111/are.12809

Cited by 25 publications

(24 citation statements)

References 22 publications

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“…While previous studies have used skin swabs to collect DNA samples from larger bodied fish species (e.g., bluegill sunfish Lepomis macrochirus , 13 Atlantic cod Gadus morhua , 14 African cichlids, 15 and the Nile tilapia Oreochromis niloticus 16 ) the technique is not routinely used in laboratory studies, which instead use fin clips from the caudal fins of live anesthetized fish. 9 However, there are a number of reasons why fin clipping may not be an ideal technique for use in laboratory studies.…”

Section: Discussionmentioning

confidence: 99%

A Low-Cost Method of Skin Swabbing for the Collection of DNA Samples from Small Laboratory Fish

et al. 2017

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Fin clipping of live fish under anesthesia is widely used to collect samples for DNA extraction. An alternative, potentially less invasive, approach involves obtaining samples by swabbing the skin of nonanesthetized fish. However, this method has yet to be widely adopted for use in laboratory studies in the biological and biomedical sciences. Here, we compare DNA samples from zebrafish Danio rerio and three-spined sticklebacks Gasterosteus aculeatus collected via fin clipping and skin swabbing techniques, and test a range of DNA extraction methods, including commercially available kits and a lower-cost, in-house method. We verify the method for polymerase chain reaction analysis, and examine the potential risk of cross contamination between individual fish that are netted together. We show that swabbing, which may not require the use of anesthesia or analgesics, offers a reliable alternative to fin clipping. Further work is now required to determine the relative effects of fin clipping and swabbing on the stress responses and subsequent health of fish, and hence the potential of swabbing as a refinement to existing DNA sampling procedures.

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Section: Discussionmentioning

confidence: 99%

A Low-Cost Method of Skin Swabbing for the Collection of DNA Samples from Small Laboratory Fish

et al. 2017

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“…Taking small fin clips is one of the non-invasive methods to collect DNA in fish, however, small laboratory fish especially suffer during this process or even end up dying, when the sample is taken by unexperienced staff. Swabbing skin mucus to collect DNA samples has been used in ecological studies of larger fish [9] and lately its use adopted for adult small laboratory fish species [10]. This technique potentially represents a less invasive alternative to fin clipping.…”

Section: Methods Detailsmentioning

confidence: 99%

Fast Multiplex real time PCR method for sex-identification of medaka (Oryzias latipes) by non-invasive sampling

et al. 2019

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“…SNPs were genotyped using fluorescence-based Kompetitive Allele Specific end-point PCR (KASP) genotyping system (KBioscience UK Ltd) following a previously published protocol [63,64]. The assay volume was 5 μL (c. 25 ng DNA) and the PCR was performed using the following cyclic conditions: the initial denaturation at 94°C for 15 min followed by 10 touchdown cycles (94°C for 20 s and touchdown 65°C for 1 min, reduced by 0.8°C per cycle) followed by 34 cycles of amplification (94°C for 20 s; 57°C for 1 min).…”

Section: Analysis Of Sex-linked Markers In Lg23mentioning

confidence: 99%

“…The assay volume was 5 μL (c. 25 ng DNA) and the PCR was performed using the following cyclic conditions: the initial denaturation at 94°C for 15 min followed by 10 touchdown cycles (94°C for 20 s and touchdown 65°C for 1 min, reduced by 0.8°C per cycle) followed by 34 cycles of amplification (94°C for 20 s; 57°C for 1 min). Microsatellite markers were analysed using a fluorescent labelled tailed primer method [64,65]. In brief, 5 μL (c. 25 ng DNA) PCR reaction volumes were prepared and the thermocycling conditions were the initial denaturation at 95°C for 1 min and 35 cycles of denaturation at 95°C for 15 s, annealing at 62°C for 15 s and extension at 72°C for 30 s.…”

Section: Analysis Of Sex-linked Markers In Lg23mentioning

confidence: 99%

Sex determination in the GIFT strain of tilapia is controlled by a locus in linkage group 23

et al. 2020

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Background: Tilapias (Family Cichlidae) are the second most important group of aquaculture species in the world. They have been the subject of much research on sex determination due to problems caused by early maturation in culture and their complex sex-determining systems. Different sex-determining loci (linkage group 1, 20 and 23) have been detected in various tilapia stocks. The 'genetically improved farmed tilapia' (GIFT) stock, founded from multiple Nile tilapia (Oreochromis niloticus) populations, with some likely to have been introgressed with O. mossambicus, is a key resource for tilapia aquaculture. The sex-determining mechanism in the GIFT stock was unknown, but potentially complicated due to its multiple origins. Results: A bulk segregant analysis (BSA) version of double-digest restriction-site associated DNA sequencing (BSA-ddRADseq) was developed and used to detect and position sex-linked single nucleotide polymorphism (SNP) markers in 19 families from the GIFT strain breeding nucleus and two Stirling families as controls (a single XY locus had been previously mapped to LG1 in the latter). About 1500 SNPs per family were detected across the genome. Phenotypic sex in Stirling families showed strong association with LG1, whereas only SNPs located in LG23 showed clear association with sex in the majority of the GIFT families. No other genomic regions linked to sex determination were apparent. This region was validated using a series of LG23-specific DNA markers (five SNPs with highest association to sex from this study, the LG23 sex-associated microsatellite UNH898 and ARO172, and the recently isolated amhy marker for individual fish (n = 284). Conclusions: Perhaps surprisingly given its multiple origins, sex determination in the GIFT strain breeding nucleus was associated only with a locus in LG23. BSA-ddRADseq allowed cost-effective analysis of multiple families, strengthening this conclusion. This technique has potential to be applied to other complex traits. The sex-linked SNP markers identified will be useful for potential marker-assisted selection (MAS) to control sex-ratio in GIFT tilapia to suppress unwanted reproduction during growout.

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

Cited by 25 publications

References 22 publications

A Low-Cost Method of Skin Swabbing for the Collection of DNA Samples from Small Laboratory Fish

A Low-Cost Method of Skin Swabbing for the Collection of DNA Samples from Small Laboratory Fish

Fast Multiplex real time PCR method for sex-identification of medaka (Oryzias latipes) by non-invasive sampling

Sex determination in the GIFT strain of tilapia is controlled by a locus in linkage group 23

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