Analysis of Autozygosity Using Whole-Genome Sequence Data of Full-Sib Families in Pikeperch (Sander lucioperca)

Pikeperch (Sander lucioperca) has emerged as a high value species to the aquaculture industry. However, its farming techniques are at an early stage and its production is often performed without a selective breeding program, potentially leading to high levels of inbreeding. In this study, we identified and characterized autozygosity based on genome-wide runs of homozygosity (ROH) on a sample of parental and offspring individuals, determined effective population size (N-e), and assessed relatedness among parental individuals. A mean of 2,235 +/- 526 and 1,841 +/- 363 ROH segments per individual, resulting in a mean inbreeding coefficient of 0.33 +/- 0.06 and 0.25 +/- 0.06 were estimated for the progeny and parents, respectively. N-e was about 12 until four generations ago and at most 106 for 63 generations in the past, with varying genetic relatedness amongst the parents. This study shows the importance of genomic information when family relationships are unknown and the need of selective breeding programs for reproductive management decisions in the aquaculture industry.

Automated summary

This study identified and characterized autozygosity in European pikeperch, assessed relatedness among parental individuals, and determined the effective population size. The results highlight the potential risks of inbreeding in pikeperch aquaculture without selective breeding programs. This study emphasizes the importance of utilizing genomic information in the aquaculture industry.