Diversification of marine aquaculture through genomics: applications to breeding programs in novel species
Professor Victor Martinez Moncada, PhD
FAVET-INBIOGEN, Universidad de Chile
Many countries are actively investing in the development of new species in marine aquaculture because this sector offers considerable potential to address food security and growing demands in consumer choice. In Chile, there is significant interest in the use of endemic species to diversify the existing industry, which in turn supports a significant component of the economy. However, new breeding programs based on wild broodstock are challenged by lack of knowledge on trait variation and breeding values, extent of population structure and local adaptation in source populations, and on breeding systems. The latter in particular is problematic, because controlled crosses are not feasible in species that rely on communal spawning behaviors. Therefore, the relationship between effective and census population sizes is often unknown. This lack of knowledge hinders accurate assessment of relatedness and in-breeding, and limits genetic gains.
Here, we describe the development and use of genomics tools for the rapid development of sound breeding programs in the kingfish Seriola lalandii, a species of high interest to the seafood industry. We first developed sex-specific genome assemblies from 50 fully sequenced individuals, and used genome-wide association studies and haplotype diversity measures to identify the locus underlying sex determination. Allele-specific gene expression derived from transcriptomic data of developing larvae was used to pinpoint causal loci involved in deformities. The transcriptome data was also used to annotate the genome.
Estimates of genetic diversity and population structure in putative founder broodstock collected in fisheries were obtained using an Applied Biosystems Axiom 90K SNP array that was developed as part of our efforts. We found high levels of individual in-breeding in some founders, but the overall haplotype diversity indicated a high effective population size in the founders. The extent of linkage disequilibrium was efficiently captured by the array, given the genome size. We identified the likely sex ratio in communal breeding in captivity, revealing the contribution of one or two individuals in any spawning event. This information informed breeding protocols going forward, and will also aid breeding programs for other species of the genera.
Finally, deterministic simulations have been used to demonstrate the feasibility of genome selection to improve genetic gains. The information, tools and techniques are being incorporated into breeding programs aimed at increasing the profitability of Seriola production and adding to the diversification of Chilean aquaculture.