Best use of scientific knowledge is required to maintain the fundamental role of seafood in human nutrition. While it is acknowledged that genomic-based methods allow the collection of powerful data, their value to inform fisheries management, aquaculture, and biosecurity applications remains underestimated. We review genomic applications of relevance to the sustainable management of seafood resources, illustrate the benefits of, and identify barriers to their integration. We conclude that the value of genomic information towards securing the future of seafood does not need to be further demonstrated. Instead, we need immediate efforts to remove structural roadblocks and focus on ways that support integration of genomic-informed methods into management and production practices. We propose solutions to pave the way forward.

Understanding the genetic basis of phenotypic variation is a major challenge in biology. Here, we systematically evaluate 146 quantitative trait loci (QTL) studies on teleost fish over the last 15 years to investigate (i) temporal trends and (ii) factors affecting QTL detection and fine-mapping. The number of fish QTL studies per year increased over the review period and identified a cumulative number of 3632 putative QTLs. Most studies used linkage-based mapping approaches and were conducted on nonmodel species with limited genomic resources. A gradual and moderate increase in the size of the mapping population and a sharp increase in marker density from 2011 onwards were observed; however, the number of QTLs and variance explained by QTLs changed only minimally over the review period. Based on these findings, we discuss the causative factors and outline how larger sample sizes, phenomics, comparative genomics, epigenetics and software development could improve both the quantity and quality of QTLs in future genotype-phenotype studies. Given that the technical limitations on DNA sequencing have mostly been overcome in recent years, a renewed focus on these and other study design factors will likely lead to significant improvements in QTL studies in the future.

Characterizing the genetic variation underlying phenotypic traits is a central objective in biological research. This research has been hampered in the past by the limited genomic resources available for most non-model species. However, recent advances in sequencing technologies and related genotyping methods are rapidly changing this. Here we report the use of genome-wide SNP data from the ecologically and commercially important marine fish species Chrysophrys auratus (snapper) to 1) construct the first linkage map for this species, 2) scan for growth QTL, and 3) search for putative candidate genes in the surrounding QTL regions. The newly constructed linkage map contained ∼11K SNP markers and is one of the densest maps to date in the fish family Sparidae. Comparisons with genome scaffolds of the recently assembled snapper genome indicated that marker placement was mostly consistent between the scaffolds and linkage map (R = 0.7), but that at fine scales (< 5 cM) some precision limitations occurred. Of the 24 linkage groups, which likely reflect the 24 chromosomes of this species, three were found to contain QTL with genome-wide significance for growth-related traits. A scan of 13 candidate growth genes located the growth hormone, myogenin, and parvalbumin genes within 5.3, 9.6, and 25.0 cM of these QTL, respectively. The linkage map and QTL found in this study will advance the investigation of genome structure and aquaculture breeding efforts in this and related species.

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Aquaculture is the fastest‐growing food production sector worldwide, yet industry has been slow to implement genomic techniques as routine tools. Applying genomics to new breeding programmes can provide important information about pedigree structure and genetic diversity; key parameters for a successful long‐term breeding programme. It can also provide insights on potential gains for commercially important, yet complex, quantitative traits such as growth rate. Here we investigated a population of 1100 captive‐bred F 1 silver trevally ( Pseudocaranx georgianus ), a promising new species for New Zealand aquaculture. We used whole‐genome information, coupled with image‐based phenotypic data collected over two years, to build the pedigree of the population, assess its genetic diversity, describe growth patterns of ten growth traits and estimate their genetic parameters. Successful parentage assignment of 664 F 1 individuals showed that the pedigree consisted of a complex mixture of full‐ and half‐sib individuals, with skewed reproductive success among parents, especially in females. Growth patterns showed seasonal fluctuations (average increase across all traits of 27.3% in summer and only 7% in winter) and strong inter‐family differences. Heritability values for growth traits ranged from 0.27 to 0.76. Genetic and phenotypic correlations between traits were high and positive, ranging from 0.57 to 0.94 and 0.50 to 1.00 respectively. The implications of these findings are threefold: first, the best on‐growing conditions are in warmer months, where highest growth peaks can be achieved; second, size‐ and family‐based selection can be used as early selection criterion if pedigree structure and inbreeding risks are closely monitored; third, selection for body length results in concomitant increases in height and weight, traits of paramount importance for aquaculture. It is concluded that there is substantial potential for genetic improvement of economically important traits, suggesting that silver trevally is a promising species for selective breeding for enhanced growth.