Genetic diversity status and associations with sperm quality characteristics in farmed Arctic charr (Salvelinus alpinus L.) across Sweden

Abstract: The national breeding programme of Arctic charr (Salvelinus alpinus L.) has been of fundamental importance for the expansion of Arctic charr farming across Sweden. Selection has been ongoing since 1980s documenting approximately 10% improvement per generation regarding growth related traits. Currently, poor reproductive success (30-70%) as compared to other farmed salmonids is a major challenge for Arctic charr farming in Sweden. Both environmental and genetic factors could affect the reproductive performance in Arctic charr. The reduction of sequencing cost with the advent of next generation sequencing (NGS) provides opportunities for aquaculture genetics and breeding to investigate in-depth complex traits. Double digestion restriction associated DNA (ddRAD) sequencing is an efficient, robust, flexible, and cost-effective technology for identifying genome wide genetic markers. In the current study, ddRAD sequencing was applied on farmed Arctic charr males from four different farms across Sweden. A total of 5,159 single nucleotide polymorphisms (SNPs) were used for investigating the status of the genetic diversity and for associations with sperm quality characteristics (concentration, viable cells). The genetic diversity analysis indicated for low genetic differentiation among the sampled populations. Though, the level of genetic diversity within populations (heterozygosity estimates) was higher compared to prior ddRAD studies on farmed fish where no pedigree records were kept. The association analysis indicated for a significantly associated SNP (SNP_402577.127) with sperm cell viability located on chromosome number 31. This novel SNP could be a valuable tool for directing future selection practices and assisting to identify the male broodstocks with the highest sperm quality characteristics.