Scale drop emerged as a new and devastating disease of barramundi Lates calcarifer in 1992. The syndrome is characterized by fish losing their scales which in addition to the effect of the disease itself opens them up to other pathogens. Subsequent work has identified the causative agent as a Megalocytivirus (Iridoviridae). This disease is one of the biggest impactors on production in Asia and cause 40-75% mortalities in juveniles. Currently there are no effective commercial vaccines to protect fish from this virus making a genetic breeding approach targeting resistance the most practical and long-term solution to lower risk. For selective breeding to be effective, however, the trait under selection needs to have a heritable component (so called additive genetic variability).
To understand the heritability of Scale Drop Disease in barramundi, we genotyped 2,305 scale drop diseased juveniles (116.5 ± 65.3g) and 2,282 survivors (417.7 ± 249.8g) from four different commercial batches reared in seacages in Southern waters of Singapore. Scale drop virus was confirmed as the main causative agent of the disease by qPCR on spleen tissues of a subsample comprising 85 sick (95.3% infected with 38,196 ± 74,469 viral copies/200ng DNA) and 95 survivors (15.6% infected with 124 ± 331 viral copies/200ng DNA), although a low co-infection with Lates Calcarifer Herpes Virus (LCHV) was also observed in 12.9% of sick (15.3% infected with 26 ± 30 viral copies/200ng DNA) and 4.1% of survivors (10.4% infected with 21 ± 20 viral copies/200ng DNA). A double digest (Pstl & Mspl) restriction-site associated DNA sequencing (ddRAD-seq) at a mean depth of 4.07 was used as genotyping-by-sequencing (GBS) approach. Reads mapped against the V3 barramundi genome yielded 231,329 SNPs post-filtering. A genomic relationship matrix (GRM) adjusted for the depth of sequence reads at each individual SNP, combined with survival data adjusted to a liability scale allowed for estimation of the additive genetic variance through linear mixed models using Residual Maximum Likelihood approaches.
A resulting moderate heritability of 0.33 ± 0.01 for SDDV resistance (or survival at sea) indicates that selective breeding approaches have the potential to deliver similar rates of genetic improvement as those seen for growth traits in barramundi and other commercially important aquaculture fish.