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Table 1
States, and state skipping, describing the development and application of genetic and genomic tools in aquaculture and conservation breeding programs, with selected examples under each category as available.
| State | Description of state | Applications / categories of research questions | Tools | Examples commercial aquaculture | Examples conservation aquaculture |
|---|---|---|---|---|---|
| State 0 | No previously developed DNA markers or genomic information | No genetic resources exist for this species for wild or cultured programs; markers may be available in related species, or through the use of universal primers. | No species-specific tools are available to utilise for genetic / genomic projects. Newer technologies make it easier to develop these tools de novo. | Tripletail (Lobotes surinamensis) (Saillant et al., 2021); golden Shiner (Notemigonus crysoleucas) (Stone et al., 2016) | Dwarf oysters (Ostrea stentina species complex) (Prado et al., 2022) |
| State 1 | Stock choice, use of population genetic or genomic information | Characterise the population(s) or the species of interest (e.g., determination of effective population sizes, population genetic structure, degree of differentiation, genetic diversity). | Allozymes, Sanger sequencing of small sections of nuclear or mitochondrial regions, microsatellites, SNPs | Lumpfish (Cyclopterus lumpus) (Jansson et al., 2023); Atlantic salmon (Salmo salar) (Gjedrem et al., 1991) | Atlantic salmon (Bradbury et al., 2018; Lehnert et al., 2023); Atlantic whitefish (Coregonus huntsmani) (Murray, 2005); eastern sand darter (Ammocrypta pellucida) (Ginson et al., 2015); redside dace (Clinostomus elongatus) (Serrao et al., 2018) |
| State 2 | Individual genetic tagging | Individual identification, parentage and pedigree analyses, trace the individual back to their breeding program, or origin, diversity estimates compared to wild populations. | Microsatellites, SNPs, Sanger sequencing of small sections of nuclear or mitochondrial regions, RAD-Seq, low-coverage genome sequencing | California yellowtail (Seriola dorsalis) (Schmidt et al., 2021); Atlantic halibut (Hippoglossus hippoglossus) (Jackson et al., 2003) | white abalone (Haliotis sorenseni; C. Purcell, pers. inform.); Atlantic salmon (S. salar) (Karlsson et al., 2016; DFO, 2018); rainbow trout (Oncorhynchus mykiss) (Steele et al., 2013); Delta smelt (Hypomesus transpacificus) (Lew et al., 2015) |
| State 3 | Linking phenotypes/traits and genotypes | Link genotypes to phenotypes for simple traits (Mendelian inheritance) or for genes (and markers) of major effect; implement marker-assisted selection to guide broodstock development or to improve traits. | Genotyping-by-sequencing approaches (e.g., RADSeq, ddRADSeq, WGS); screening using SNPs, PCR, microsatellites. | Atlantic salmon (S. salar)(Houston et al., 2012); rainbow trout (O. mykiss) (Wringe et al., 2010); Atlantic halibut (H. hippoglossus) (Palaiokostas et al., 2013) | Chinook salmon (O. tshawytsha) (Waters et al., 2018); Coho salmon* (O. kisutch) (Horn et al., 2020) |
| State 4 | Genomic selection and/or genomic imputation and prediction using family- or pedigree-based selection. | Implement genomic selection, utilising family- or pedigree-based selection for complex polygenic traits, typically requiring breeding programs and/or genomic selection/imputation to improve trait outcomes. | SNP arrays, genomic resequencing (e.g., GenCove − use resequencing for genome imputation and prediction instead of developing SNP panel) | Atlantic salmon (S. salar) (Kijas et al., 2017); rainbow trout (O. mykiss) (Vallejo et al., 2017); Pacific oyster (Crassostrea gigas) (Jourdan et al., 2023) | |
| State 5 | Gene editing | Utilise gene editing to precisely modify genes already present in the organism (or from another organism − transgenic), to inactivate genes/genetic sequences or to add genetic material at specific locations of the genome. | Zinc fingers, TALENs, CRISPR-Cas | Siamese fighting fish (Betta splendens) (DFO, 2021); tiger barb (Puntigrus tetrazona) (Dietrich et al., 2022); Atlantic salmon (S. salar) (Du et al., 1992) | |
| State skipping | Beginning research at any State relevant to the needs of the breeding program. | Develop genomic resources with broad applicability (e.g., such as reference genomes) that will allow for the development of tools tailored to pressing research questions or breeding program applications. | Varied tools, but frequently de novo development of a high-quality reference genome. | New Zealand trevally (Pseudocaranx georgianus) (Catanach et al., 2021; Valenza-Troubat et al., 2022; Valenza-Troubat et al., 2022); Australasian snapper (Chrysophrys auratus) (Ashton et al., 2019; Sandoval-Castillo et al., 2022) | Barrens topminnow (Fundulus julisia) (Hurt and Harman, 2017) |
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