4.1 | Evidence of rapid evolution in H. rubra
Our analyses identified approximately 25,000 SNP loci associated with AVG exposure in H. rubra , suggesting that selection has driven advantageous genetic variants to higher frequencies in virus affected populations. The number of positively associated candidates is a substantial proportion of the total number of SNPs included in our analyses (0.4%). The strong linear relationship between genome scaffold length and density of candidate SNPs suggests a genome wide response to selection pressure. However, only some SNPs identified here may contribute to pathogen resistant phenotypes, given linkage disequilibrium among loci and the fact that alleles contributing to resistance will be embedded in large haploblocks. Nevertheless, we did find a higher incidence of significant SNPs on two scaffolds, which could be indicative of important regions of adaptation. The genes annotated within these regions are not known for providing virus resistance, but further work is needed to test for possible functional significance of these regions.
Despite the potential for linkage between loci, our analyses indicate that some candidate loci may be directly involved in disease adaptation in H. rubra . In particular, functional annotations of candidate loci point to associations with genes and protein domains that contribute to HaHV-1 immunity in the New Zealand pāua (H. iris ). Neave et al. (2019) first characterised genes associated with HaHV-1 immunity in H. iris through transcriptome analyses of animals subject to HaHV-1 immersion challenge tests. This study was the first to characterise the molecular basis of HaHV-1 immunity in a haliotid species, and our study complements these findings by identifying a common set of genes involved in haliotid host response to HaHV-1 exposure. Functional annotations of candidate loci also point to associations with genes and protein domains contributing to herpes simplex virus responses and immune responses in various haliotids and other animal systems. These findings strongly support the notion that emergent genomic architectures have resulted in divergent adaptation and possible selection for disease resistance phenotypes in H. rubrafishing stocks impacted by AVG.
The results of this study point to heritable genetic changes in H. rubra fishing stocks impacted by disease. However, experimental validation will be needed to link any genetic changes to disease resistance. Challenge tests involving the exposure of animals with putatively resistant genotypes to HaHV-1 will help to determine if, and how much, HaHV-1 resistance is determined by the candidate genotypes (Crane et al. 2013; Corbeil et al. 2016). Given that a large number of loci appear to be responding to the virus, we suspect that changes in resistance will represent a polygenic response that can be followed by controlled breeding studies (Guarna et al. 2017; Gutierrez et al. 2018). The response to selection in these studies will depend on levels of heritable variation as well as the intensity of selection which will determine the impact of the phenotypic change. Breeding studies and experimental trials will also be essential to assess trait heritability and genotype-environment interactions, particularly if industry intend to control for resistance traits in a culture environment for breeding purposes (discussed below).