Understanding the connectivity of marine populations is vital for conservation and fisheries management, particularly for the strategic design of reserve systems.A recent proliferation of molecular and statistical tools allows increasingly sophisticated integration of genetic and geographic data (e.g., Manel et al., 2003). Such advances have fueled considerable hope that the challenging problem of tracking movement of individuals within the vast ocean will soon be solved. Here, we focus on some of the inherent limitations of genetic approaches to inferring connectivity, particularly in marine environments. More optimistically, we also point to a number of situations where genetic approaches have been particularly successful in the past, as well as newer integrative approaches that deserve further attention. structure of Marine PopulationsEstimating connectivity depends on the extent of spatial genetic variation.

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Differences in genetic composition among samples of larvae produced during a single spawning season by a semi-isolated population of Pacific oysters (Crassostrea gigas) in Dabob Bay, Washington, confirm a specific prediction of the hypothesis that this and other marine animals have large variances in reproductive success. To study the genetics of single larvae, we cloned and sequenced part of the mitochondrial genome and developed polymerase chain reaction (PCR) primers to amplify four segments totaling nearly 2300 base pairs, or 13% of the genome. PCR products were digested with restriction enzymes into smaller fragments, which were then screened for single-strand conformational polymorphisms (SSCP). Seven plankton samples (total N = 877), taken between 10 and 21 August 1993, showed a common composite PCR-SSCP haplotype that comprised from 53 to 85% of samples. Nevertheless, exact probability and permutation tests reveal that early and late samples from north Dabob Bay differed significantly from the rest. These differences cannot be ascribed to spatial variation and are consistent with the hypothesis that larvae are produced by relatively few adults, in accord with previous observations of substantial genetic drift in this large population.

Advancing the production efficiency and profitability of aquaculture is dependent upon the ability to utilize a diverse array of genetic resources. The ultimate goals of aquaculture genomics, genetics and breeding research are to enhance aquaculture production efficiency, sustainability, product quality, and profitability in support of the commercial sector and for the benefit of consumers. In order to achieve these goals, it is important to understand the genomic structure and organization of aquaculture species, and their genomic and phenomic variations, as well as the genetic basis of traits and their interrelationships. In addition, it is also important to understand the mechanisms of regulation and evolutionary conservation at the levels of genome, transcriptome, proteome, epigenome, and systems biology. With genomic information and information between the genomes and phenomes, technologies for marker/causal mutation-assisted selection, genome selection, and genome editing can be developed for applications in aquaculture. A set of genomic tools and resources must be made available including reference genome sequences and their annotations (including coding and non-coding regulatory elements), genome-wide polymorphic markers, efficient genotyping platforms, high-density and high-resolution linkage maps, and transcriptome resources including non-coding transcripts. Genomic and genetic control of important performance and production traits, such as disease resistance, feed conversion efficiency, growth rate, processing yield, behaviour, reproductive characteristics, and tolerance to environmental stressors like low dissolved oxygen, high or low water temperature and salinity, must be understood. QTL need to be identified, validated across strains, lines and populations, and their mechanisms of control understood. Causal gene(s) need to be identified. Genetic and epigenetic regulation of important aquaculture traits need to be determined, and technologies for marker-assisted selection, causal gene/mutation-assisted selection, genome selection, and genome editing using CRISPR and other technologies must be developed, demonstrated with applicability, and application to aquaculture industries.Major progress has been made in aquaculture genomics for dozens of fish and shellfish species including the development of genetic linkage maps, physical maps, microarrays, single nucleotide polymorphism (SNP) arrays, transcriptome databases and various stages of genome reference sequences. This paper provides a general review of the current status, challenges and future research needs of aquaculture genomics, genetics, and breeding, with a focus on major aquaculture species in the United States: catfish, rainbow trout, Atlantic salmon, tilapia, striped bass, oysters, and shrimp. While the overall research priorities and the practical goals are similar across various aquaculture species, the current status in each species should dictate the next priority areas within the species. This paper is an output of the USDA Workshop fo...

A unique feature of sex in Crassostrea oysters is the coexistence of protandric sex change, dioecy, and hermaphroditism. To determine whether such a system is genetically controlled, we analyzed sex ratios in 86 pair-mated families of the Pacific oyster, Crassostrea gigas Thunberg. The overall female ratios of one-, two-, and three-year-old oysters were 37%, 55%, and 75%, respectively, suggesting that a significant proportion of oysters matured first as males and changed to females in later years. Detailed analysis of sex ratios in factorial and nested crosses revealed significant paternal effects, which corresponded to two types of sires. No major maternal effects on sex were observed. Major genetic control of sex was further indicated by the distribution of family sex ratios in two to four apparently discreet groups. These and other data from the literature are compatible with a single-locus model of primary sex determination with a dominant male allele (M) and a protandric female allele (F), so that MF are true males and FF are protandric females that are capable of sex change. The rate of sex change of FF individuals may be influenced by secondary genes and/or environmental factors. Strong maternal and weak paternal effects on sexual maturation or time of spawning were also suggested.