Fate of genetic diversity within and between generations and implications for DNA parentage analysis in selective breeding of mass spawners: A case study of commercially farmed barramundi, Lates calcarifer

Mass spawning fish species pose significant challenges for the design and conduct of effective aquaculture breeding programs. This is because the hatchery manager has limited control over the individual contributions of broodstock within a spawn, and consequently, the number and size of families in the resulting progeny cohorts. While early broodstock contributions have been tracked in many mass-spawning species through early development, it is currently unknown if individuals from poorly represented families are lost by the time of harvest due to differential survival, or if they are still available until the critical moment of selection to contribute as parents to the next generation. In addition, there are no studies based on real harvest data that determine how differential contribution and growth of families seen in mass spawners impact on selection of candidate broodstock. This is particularly important to understand, as mixed families in every cohort require the application of costly DNA genotyping analyses to determine pedigrees. In order to assist in the design of selective breeding strategies for mass spawners, barramundi (Lates calcarifer) was used as a model species to evaluate how family survival and growth under skewed contributions may affect the selection of breeding candidates at harvest. In this study, 18 days-post-hatch (dph) larval offspring from three commercial cohorts were firstly genotyped and assigned to their family of origin. Later at harvest (273-469 dph), fish from these cohorts were weighed and genotyped. Results showed that relative family frequencies at harvest were in different proportions than those found in the hatchery phase (P < 0.05). However, the majority of families initially identified (124 families) and all 48 broodstock contributing to offspring detected in the hatchery were also detected at the end of the culture cycle (141 families), suggesting that differential family survival did not impact on genetic diversity. Further analyses confirmed no subsequent loss of genetic diversity from 18 dph through to harvest, as measured by effective population size, inbreeding rates, number of alleles, allelic richness, observed and expected heterozygosities and Rxy relatedness coefficient. Examination of family contributions and weights at harvest in the three commercial cohorts showed that sampling and genotyping the top 1.5% of the population (or 750 individuals > 2.17 S.D. heavier than the population mean) will capture > 75% of family-specific genetic diversity present. Continued sampling after this was ineffective, with each additional 170 fish sampled only returning 1% extra family-specific genetic diversity.