Six diagnostic single nucleotide polymorphism markers for detecting introgression between cutthroat and rainbow trouts

Amanda J Finger; Molly R Stephens; Neil W Clipperton; Bernie May

doi:10.1111/j.1755-0998.2009.02532.x

Six diagnostic single nucleotide polymorphism markers for detecting introgression between cutthroat and rainbow trouts

Mol Ecol Resour. 2009 May;9(3):759-63. doi: 10.1111/j.1755-0998.2009.02532.x. Epub 2009 Feb 5.

Authors

Amanda J Finger¹, Molly R Stephens, Neil W Clipperton, Bernie May

Affiliation

¹ Genomic Variation Laboratory, Department of Animal Science, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA, California Department of Fish and Game, Water Branch, 830 S Street, Sacramento, CA 95811, USA.

PMID: 21564737
DOI: 10.1111/j.1755-0998.2009.02532.x

Abstract

Ten primer pairs were screened to develop single nucleotide polymorphism (SNP) TaqMan assays that will distinguish California golden trout and some rainbow trouts (Oncorhynchus mykiss sspp., O. m. aguabonita) from the Paiute and Lahontan cutthroat trouts (Oncorhynchus clarkii seleniris, O. c. henshawi). From these 10 primer pairs, one mitochondrial and five nuclear fixed SNP differences were discovered and developed into TaqMan assays. These six assays will be useful for characterizing and monitoring hybridization between these groups. Additional Oncorhynchus clarkii sspp. and Oncorhynchus mykiss sspp. were assayed to determine if these assays are useful in closely related species.