De novo SNP calling from RAD sequences for a mink (Neovison vison) specific genotyping assay

Publikation: KonferencebidragPaperForskning

The genetic marker of choice in mink has until now been microsatellites, but recently has single nucleotide polymorphism (SNP) been used more and more in other species. In several species, SNP panels have been established through SNP chips. However, generations of such chips are expensive and require a large market to cover the cost. New technologies based on next generation sequencing (NGS) have made it possible to identify thousands of SNPs using a cost effective and fast method. The method can be used for non-model organisms in conservation biology and for production species with small population sizes.
The aim of this study was to create a mink specific SNP panel well suited for population genetic studies, parental testing and forensic investigations.
A SNP panel specific for American mink (Neovison vison) has been generated from Restriction site-Associated DNA (RAD) sequencing. Fourteen mink from Brown and Black color types were obtained. A mean of 49,789,860.2 (± 9,813,587.2) raw reads of high quality per sample were sequenced. SNPs were called using the software pipeline Stacks. The populations program was used to estimate population structure and genetic divergence between the two color types. 1,576,944 catalog tags were generated with a 10X minimum depth of coverage. 224,095 candidate SNPs polymorphic for the two color types were called. Using strict filtering criteria in order to increase the success of assay design a total of 1,256 SNPs were finally identified.
OriginalsprogEngelsk
Udgivelsesår13 aug. 2013
Antal sider9
StatusUdgivet - 13 aug. 2013
BegivenhedNJF Autumn meeting in Fur Animal Research - Reykjavik, Island
Varighed: 28 aug. 201330 aug. 2013
Konferencens nummer: 464

Konference

KonferenceNJF Autumn meeting in Fur Animal Research
Nummer464
LandIsland
ByReykjavik
Periode28/08/201330/08/2013

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