The First Haploid Linkage Map in a Coregonid (Coregonus artedi) Improves Knowledge of Chromosomal Evolution and Rediploidization across Salmonids

Abstract

Whole genome duplication (WGD) is an important evolutionary mechanism that can facilitate adaptation and speciation. The salmonid family represents an ideal model to study the effect of WGDs because of the extensive diversity that has evolved following WGD by autotetraploidization in the common ancestor. As salmonids evolved and diversified after the WGD, much of the genome returned to a diploid state. However, ~20% of the genome display residual tetrasomy, and the genomic processes that influence rediploization are still poorly understood. To refine the understanding of the effects of the WGD in salmonids, female (20,450 loci) and male (6,340 loci) linkage maps were constructed for cisco Coregonus artedi. These linkage maps identified homologous chromosomes for three coregonines and one representative species for each of Salmo, Salvelinus, and Oncorhynchus genera and the nonduplicated sister group of salmonids, Esox. Using this information, a cross species comparison of homeologous regions was conducted to identify regions that still exhibit residual tetrasomy, that diverged prior to speciation, and intermediate regions that are diverging independently. The further development of genomic resources in less described salmonids will aid in understanding genomic variation post-WGD. Additionally, the linkage map constructed here will facilitate future research with the aim of determining the degree of heritable genetic differences among cisco forms.