Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Salvelinus alpinus)

Simple Summary Animal breeding in recent years has benefited greatly from the availability of large-scale genetic information. The most widely applied genomic tools in selective breeding are specialized arrays that use DNA hybridization. However, the high financial investments accompanying this practice impair the profitability of emerging aquaculture species, including Arctic charr. The aim of the current study was to assess and compare the potential of two cost-efficient genotyping strategies applicable in a variety of breeding-related tasks, such as pedigree verification, genetic diversity screening and detection of genomic regions that are associated with phenotypes of economic importance. Both strategies are based on reduced representation sequencing but differ in sequencing coverage (low and high). The low coverage strategy offers a higher density of DNA markers, but also presents a greater proportion of missing data in the marker set and is characterized by more uncertainty in determining heterozygosity compared to high coverage. Our results show that while high coverage genotyping performs better in genetic diversity and kinship analyses, a low coverage strategy is more successful in identifying genomic regions associated with phenotypic traits, leading to the conclusion that both strategies could be of value into selection schemes. Incorporation of genomic technologies into fish breeding programs is a modern reality, promising substantial advances regarding the accuracy of selection, monitoring the genetic diversity and pedigree record verification. Single nucleotide polymorphism (SNP) arrays are the most commonly used genomic tool, but the investments required make them unsustainable for emerging species, such as Arctic charr (Salvelinus alpinus), where production volume is low. The requirement to genotype a large number of animals for breeding practices necessitates cost effective genotyping approaches. In the current study, we used double digest restriction site-associated DNA (ddRAD) sequencing of either high or low coverage to genotype Arctic charr from the Swedish national breeding program and performed analytical procedures to assess their utility in a range of tasks. SNPs were identified and used for deciphering the genetic structure of the studied population, estimating genomic relationships and implementing an association study for growth-related traits. Missing information and underestimation of heterozygosity in the low coverage set were limiting factors in genetic diversity and genomic relationship analyses, where high coverage performed notably better. On the other hand, the high coverage dataset proved to be valuable when it comes to identifying loci that are associated with phenotypic traits of interest. In general, both genotyping strategies offer sustainable alternatives to hybridization-based genotyping platforms and show potential for applications in aquaculture selective breeding.