3.2 | Genome-wide association analysis
Our genome-wide association study found 25,854 candidate SNPs with
strong associations with virus exposure (BF > 50), with the
PCA based on candidate loci revealing clear patterns of genetic
structuring between locations varying in historical AVG exposure (Figure
2). Estimates of LD were high at all locations (meanr 2 = 0.61 ± 0.01 SD ) indicating
non-random association of alleles, while comparisons ofr 2 between virus affected and unaffected stocks
did not significantly differ (P > 0.05). Analyses
suggest a genome wide patterns of selection, with regression analyses
indicating strong linear relationship between number of candidate loci
and scaffold length (R 2 = 0.83; Figure 3a).
However, scaffolds QXJH01000030.1 and QXJH01000212.1 exhibited a higher
number of candidate loci relative to scaffold length (deviating from the
linear distribution), with candidate SNPs comprising 0.0062% and
0.0108% of the total scaffold nucleotides, respectively. Pairwise
linkage among SNPs across the entirety of these scaffolds was high
(D ’ ≈ 1), with the detection of large haplotype blocks indicating
large sections of the genome linked to virus exposure (Figure 3b).