Abstract
Amidst global reef declines, large‐scale coral aquaculture is being developed to support reef intervention. Genetic diversity underpins population resilience and therefore it is critical that aquaculture methods maintain diversity. However, it remains unclear how genetic diversity of coral progeny is shaped by (1) parental genetic composition, (2) winnowing during aquaculture grow‐out, and (3) field deployment. We utilised single nucleotide polymorphisms to examine genetic diversity dynamics in two coral progeny cohorts produced from 5 and 14 parents, with standardised gamete input per parent. Cohorts were sampled over 1 month of aquarium rearing, and for the 14‐parent cohort, again after 2 years of field deployment. Parentage analysis confirmed that all parents contributed genetic material to surviving offspring at each cohort's end‐point. However, per‐parent contributions differed significantly, indicating skewed reproductive success despite equal gamete inputs. Temporal and parent‐pool differences in heterozygosity ( H o ) were observed during larval stages. At 12 h post‐fertilisation, H o was highest in the 5‐parent offspring cohort, and lowest in the 14‐parent cohort, reflecting high and low parental genetic dispersion among parents, respectively. By 84 h post‐fertilisation, H o decreased in 5‐parent and increased in 14‐parent cohorts, suggesting early development purges genetic defects from outbreeding or inbreeding depression, respectively. Importantly, H o was similar among cohorts and did not decline after 7 days in either cohort, nor after 2 years in the 14‐parent cohort, suggesting no evidence of a genetic bottleneck after settlement competency. These findings highlight that parental genetic diversity, rather than the number of parents contributing per se, is crucial to maintain genetic diversity in coral aquaculture, with implications for restoration.