Sandfish generations: Loss of genetic diversity due to hatchery practices in the sea cucumber Holothuria (Metriatyla) scabra

Hatcheries are indispensable for seed production of many commercial aquaculture species. However, for massspawning species in particular, they can be capricious environments where genetic diversity among progeny may be lost due to small effective broodstock population sizes, variable parental contributions and differential family survival. Understanding the genetic impacts of hatchery production is therefore important for addressing these problems and optimising propagation methods. We used 6051 genome-wide Single Nucleotide Polymorphisms (SNPs) to analyse genetic diversity, parental contributions and offspring kinship during a commercial-scale hatchery production run of sandfish (Holothuria scabra), a high-value sea cucumber grown in mariculture operations across the Indo-Pacific region. Broodstock contributions were highly skewed, with up to 26% of the parent pool contributing and kinship analyses determined that just two parents sired between 44.4 and 67.5% of all offspring genotyped. Effective population sizes were reduced as expected between broodstock and offspring groups (NeLD = 1121.2 vs. 19.4, respectively), while losses of allelic diversity but not overall heterozygosity were apparent. Numbers of families surviving (13-16) to the juvenile stage were low, suggesting low effective population sizes among offspring cohorts is an issue for sandfish hatchery operations. To address variability in family compositions and broodstock contributions, pedigree tracking and batch spawning may be used to optimize broodstock management and hatchery protocols, to ensure production of genetically diverse offspring for routine culture and restocking operations. As many sandfish broodstock remain wild-sourced, maintenance of healthy wild populations as reservoirs of genetic diversity is important, along with selection for spawning of genetically diverse individuals which are as distantly-related as possible.