Assessing SNP-markers to study population mixing and ecological adaptation in Baltic cod
2019
Atlantic cod(
Gadusmorhua) is a species of great ecological and economical importance in the
BalticSea. Here, two genetically differentiated stocks, the western and the eastern
Balticcod, display substantial mechanical mixing, hampering our understanding of cod ecology and impeding
stock assessmentsand management. Based on whole-genome re-sequencing data from reference samples obtained from the study area, we designed two different panels of Single Nucleotide Polymorphisms markers (SNPs), which take into account the exceptional genome architecture of cod. A minimum panel of 20 diagnostic SNPs and an extended panel (20 diagnostic and 18 biologically informative SNPs, 38 in total) were developed and validated to distinguish unambiguously between the western and the eastern
Balticcod stocks and to enable studies of
local adaptationto the specific environment in the
BalticSea, respectively. We tested both panels on cod sampled from the southern
BalticSea (n = 603) caught in 2015 and 2016. Genotyping results showed that catches from the mixing zone in the Arkona Sea, were composed of similar proportions of individuals of the western and the eastern stock. Catches from adjacent areas to the east, the Bornholm Basin and Gdansk Deep, were exclusively composed of eastern
Balticcod, whereas catches from adjacent western areas (Belt Sea andO¨ resund) were composed of western
Balticcod. Interestingly, the two
Balticcod stocks showed strong genetic differences at loci associated with life-history trait candidate genes, highlighting the species’ potential for ecological adaptation even at small geographical scales. The minimum and the extended panel of SNP markers presented in this study provide powerful tools for future applications in research and
fisheries managementto further illuminate the mixing dynamics of cod in the
BalticSea and to better understand
Balticcod ecology.
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