Tuesday, 1 August 2017

New paper: rare but significant colocalisation and synteny of ecologically relevant QTL in salmonids

The organization of functional regions within genomes has important implications for the evolutionary potential of species. We compared the distribution of nearly a thousand ecologically relevant QTL within and across six salmonids (Arctic charr, Atlantic salmon, lake whitefish, rainbow trout, chinook salmon, coho salmon ) to understand their distribution across the genome. Using a novel analytical framework for comparative mapping and significance testing, we identified synteny blocks and co-localized clusters for phenotypic traits across and within species. Specifically, only two or three pairs of traits were significantly co-localized in three species (lake whitefish, coho salmon, and rainbow trout). These findings suggest genetic linkage between traits within species is relatively rare, advancing our understanding of the renowned ecological and phenotypic variability in salmonid fishes.

This project was a collaboration based on an idea hatched by Kathryn, consultation and insights from Karim in Edinburgh Genomics as an expert on genetic mapping in salmonids, detailed literature review and database building by Robyn during her MVLS-DTP mini-project, clever analytical approaches by Mel co-housed in Maths & Stats, and most importantly outstanding analysis, synthesis and drafting by Arne. Well done team!

We hope the database is of use to other salmonid researchers, as it can be supplemented as new information arises. All information is shared in the supplementary material of the paper.

Jacobs A, Womack R, Chen M, Gharbi K, Elmer KR (2017) Significant synteny and co-localization of ecologically relevant quantitative trait loci across salmonid species. Genetics, early online

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