Genetics of mercury accumulation in Stickleback, genotypes and metal accumulation phenotypes

Anthropogenic stressors, such as pollutants, act as selective factors that
can leave measurable changes in allele frequencies in the
genome.  Metals are of particular concern among pollutants,
because of interference with vital biological pathways. We use the
three-spined stickleback as a model for adaptation to mercury pollution in
natural populations. We collected sticklebacks from 21 locations in
Flanders (Belgium), measured the accumulated levels of mercury in the
skeletal muscle tissue, and genotyped the fish by sequencing (GBS). The
spread of muscle mercury content across locations was considerable,
ranging from 21.5 to 327 ng/g dry weight (DW). We then conducted a genome
wide association study (GWAS) between 28,450 SNPs and the accumulated
levels of mercury, using different approaches. Based on a linear mixed
model analysis, the GWAS yielded multiple hits with a single top hit on
Chromosome 4, with eight more SNPs (Single Nucleotide
Polymorphism)  suggestive of association. A second approach, a
latent factor mixed model analysis, highlighted one single SNP on
Chromosome 11. Finally, an outlier test identified one additional SNP on
chromosome 4 that appeared under selection. Out of all ten SNPs we
identified as associated with mercury in muscle, three SNPs all located on
Chromosome 4 and positioned within a 2.5 kbp distance of an annotated
gene. Based on these results and the genome coverage of our SNPs, we
conclude that the selective effect of mercury pollution in Flanders causes
a significant association with at least one locus on Chromosome 4 in
three-spined stickleback.