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).