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...
Several crayfish species behave as biological invaders. Their establishment in an area has frequently been accompanied by the reduction or elimination of indigenous species. A laboratory study was designed to investigate whether the invasive crayfish Procambarus clarkii (Girard, 1852) is dominant over the indigenous (to Delaware) crayfish Procambarus acutus acutus (Girard, 1852) in either the absence or the presence of a shelter as a limited resource. As expected, we found that P. clarkii is more aggressive than the similarly sized P. a. acutus, thus confirming previous studies that demonstrated an inherent dominance of the invasive over the indigenous crayfish. We then hypothesized that species showing a lower preference for an offered shelter (P. clarkii) should be less motivated to defend it. To the contrary, in a competitive context P. clarkii excluded P. a. acutus from the shelter but did not use the resource. Caution must be used in extrapolating these laboratory studies to the field, and future studies should analyze multiple factors, including the autoecology of the two species and their reproductive potential and recruitment patterns. However, our results might help in highlighting the risks for freshwater biodiversity created by the uncontrolled translocations of P. clarkii and other similar invasive species.Résumé : Plusieurs espèces d'écrevisses se comportent comme des envahisseurs biologiques. Leur établissement dans une région s'accompagne souvent de la réduction ou de l'élimination des espèces indigènes. Nous avons mis au point une étude de laboratoire pour voir si l'écrevisse envahissante Procamburus clarkii (Girard, 1852) est dominante par rapport à l'écrevisse indigène (au Delaware) Procamburus acutus acutus (Girard, 1852) en présence ou en absence d'abris comme ressource limitée. Comme prévu, P. clarkii est plus agressif que P. a. acutus, un animal de même taille, ce qui confirme les études antérieures qui ont démontré l'existence d'une dominance inhérente de l'écrevisse envahissante par rapport à l'indigène. Nous avons alors posé l'hypothèse selon laquelle l'espèce qui montre le moins de préfé-rence pour l'abri offert (P. clarkii) devrait être moins motivée pour le défendre. Au contraire, dans une situation de compétition, P. clarkii élimine P. a. acutus de l'abri, sans pour autant s'en servir lui-même. Il faut être prudent en extrapolant ces résultats de laboratoire aux situations de terrain; les études futures devront analyser plusieurs facteurs, dont l'autécologie des deux espèces, leur potentiel reproductif et leurs patterns de recrutement. Néanmoins, nos résul-tats peuvent servir à souligner les risques pour la biodiversité créés par les transferts incontrôlés de P. clarkii et d'autres espèces envahissantes semblables.[Traduit par la Rédaction] Gherardi and Daniels 1932
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