Performance, heritability, and candidate genes for growth in dusky kob (Argyrosomus japonicus): Implications for genetic improvement during early phase domestication

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Dusky kob, is a Sciaenid finfish that has a global distribution and is indigenous to South Africa. Historically, the species was a prime target for fisheries, but is currently an emerging candidate for aquaculture due to declining wild populations. Aquaculture breeding pose challenges to conventional genetic selection methods, especially when species are new (essentially wild), and industries are small: Founder populations are limited, and sexual maturity is often late; mass spawning leads to large variances in broodstock contributions and pedigree records are difficult to keep; and production environments are often highly variable. To overcome such challenges, this study consolidated inferred pedigree and phenotypic data across three aquaculture facilities and was able to estimate robust heritability values for the correlated growth traits, wet weight (0.46 ± 0.29) and standard length (0.41 ± 0.27). We further suggest that conventional phenotypic selection be combined with marker assisted selection to improve potential genetic gains. To this aim a case-control association analysis was done using a candidate gene approach, prioritising, and validating genetic variants from a previously developed exome resource for dusky kob. Three genes with large effect sizes on phenotypes were identified: tankyrase [Haplotypic Odd Ratio (OR) = 22.98]; myoblast determination protein 1 (highest individual SNP OR = 5.28); and bone morphogenetic protein 2 (Haplotypic OR = 13.33). If a cooperative model for genetic improvement was to be implemented across farms, using a combinational approach, it could facilitate making genetic gains during the early phases of domestication.