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Mitigating the effects of escaped farmed Atlantic salmon: Combining single nucleotide polymorphisms, lipid acid profiling, and statistical methods to trace escaped salmon back to origin

Skaala, Øystein; Besnier, Francois; Glover, Kevin A.
Working paper
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http://hdl.handle.net/11250/116786
Issue date
2013-06
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  • Rapport fra havforskningen (2007- ) [244]
Abstract
Comparisons between 300 polymorphic SNPs and 14 short tandem repeats (STRs) were

conducted on a data set consisting of approximately 500 Atlantic salmon arranged in 10

samples/populations. Global FST ranged from 0.033-0.115 and -0.002-0.316 for the 14 STR

and 300 SNP loci respectively. The best 15 SNPs (30 alleles) gave a similar level of selfassignment

to the best 4 STR loci (83 alleles), however, addition of further STR loci did not

lead to a notable increase assignment whereas addition of up to 100 SNP loci increased

assignment.

In 2003, a common garden experiment was initiated in the Guddal river to evaluate and

compare the performance of Farm, Wild and Hybrid Salmon in the river habitat. Significant

differences in growth, body shape (condition factor) and mortality were reported between

these three types (Skaala et al. 2012). The aims of this two years post-doctoral project was to

provide better understanding on the genetic bases for the observed differences in growth,

body shape and mortality between wild, farm, and hybrid salmon. Genome scan for QTL

affecting length (L), weight (W), and condition factor (CF) revealed several genomic regions

significantly affecting these three phenotypes. The genomic positions of these QTL as well as

proportion of the trait variance explained are identified.

Weight is significantly affected by two QTL: one on chromosome 2 that explains 8.4% of the

observed weight variance in our population, and one on chromosome 11 responsible for 7.7%

of observed weight variance. Collectively, these two QTL are responsible for 14.8% of the

weight variance.

QTL position on chromosome 2 appears to be a particularly interesting region that both

affects growth and survival in the river habitat. Moreover, this genomic region displays a

strong reduction in genetic variability in the farm population whereas genetic variability is

still very high in the wild population. QTL on chromosome 2 appears thus to be a genomic

region potentially bearing the footprint of ongoing domestication in salmon. This study

represents the first investigation into the genetic architecture underlying the relative

performance of farmed and wild Atlantic salmon in the natural habitat.
Description
MENTOR (NRC project no: 190467)
Publisher
Havforskningsinstituttet
Series
Rapport fra Havforskningen;Nr. 18-2013

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