Advancing genetic improvement in the omics era: status and priorities for United States aquaculture.

Background: The innovations of the "Omics Era" have ushered in significant advancements in genetic improvement of agriculturally important animal species through transforming genetics, genomics and breeding strategies. These advancements were often coordinated, in part, by support provided over 30 years through the 1993-2023 National Research Support Project 8 (NRSP8, National Animal Genome Research Program, NAGRP) and affiliate projects focused on enabling genomic discoveries in livestock, poultry, and aquaculture species. These significant and parallel advances demand strategic planning of future research priorities.

Assessment of genomic diversity within and between two cryptic shiners, the West Texas shiner (Notropis megalops) and the Texas shiner (Notropis amabilis).

The presence of cryptic species can hinder effective conservation planning and implementation, as has been the case for speciose groups of freshwater fishes that are difficult to differentiate due to conserved morphologies. The West Texas shiner Notropis megalops and the Texas shiner Notropis amabilis are a cryptic pair of leuciscids (minnows) that co-occur in spring-fed tributaries of the Rio Grande in Texas and Mexico. Both N.

Complete mitochondrial genomes of and (Cypriniformes: Leuciscidae).

The Leuciscidae (minnows, shiners and relatives) is a diverse family of freshwater fishes with many species endangered due to anthropogenic stressors. and are two shiners found only in the upper Brazos River basin in Texas, USA and listed as endangered due to contracted habitat. The complete mitochondrial genome was sequenced for two vouchered specimens for each species; having a total mitogenome length of 16,711 bp and having a total mitogenome length 16685-16686 bp, with both including 13 protein-coding genes, 22 transfer RNAs genes, and 2 ribosomal RNA genes.

Biological efficacy of simulated radiolabeled Lipiodol® ultra-fluid and microspheres for various beta emitters: study based on VX2 tumors.

Background: Radioembolization is one therapeutic option for the treatment of locally early-stage hepatocellular carcinoma. The aim of this study was to evaluate the distribution of Lipiodol® ultra-fluid and microspheres and to simulate their effectiveness with different beta emitters (Y, Re, P, Ho, I, and Lu) on VX2 tumors implanted in the liver of 30 New Zealand rabbits.

Results: Twenty-three out of 30 rabbits had exploitable data: 14 in the group that received Lipiodol® ultra-fluid (group L), 6 in the group that received microspheres (group M), and 3 in the control group (group C).

Development and Evaluation of High-Density SNP Arrays for the Eastern Oyster Crassostrea virginica.

The eastern oyster Crassostrea virginica is a major aquaculture species for the USA. The sustainable development of eastern oyster aquaculture depends upon the continued improvement of cultured stocks through advanced breeding technologies. The Eastern Oyster Breeding Consortium (EOBC) was formed to advance the genetics and breeding of the eastern oyster.

Temperature-associated selection linked to putative chromosomal inversions in king scallop ().

The genomic landscape of divergence-the distribution of differences among populations or species across the genome-is increasingly characterized to understand the role that microevolutionary forces such as natural selection and recombination play in causing and maintaining genetic divergence. This line of inquiry has also revealed chromosome structure variation to be an important factor shaping the landscape of adaptive genetic variation. Owing to a high prevalence of chromosome structure variation and the strong pressure for local adaptation necessitated by their sessile nature, bivalve molluscs are an ideal taxon for exploring the relationship between chromosome structure variation and local adaptation.

Disentangling complex genomic signals to understand population structure of an exploited, estuarine-dependent flatfish.

Interpreting contemporary patterns of population structure requires an understanding of the interactions among microevolutionary forces and past demographic events. Here, 4,122 SNP-containing loci were used to assess structure in southern flounder () sampled across its range in the US Atlantic Ocean (Atlantic) and Gulf of Mexico (Gulf) and relationships among components of genomic variation and spatial and environmental variables were assessed across estuarine population samples in the Gulf. While hierarchical amova revealed significant heterogeneity within and between the Atlantic and Gulf, pairwise comparisons between samples within ocean basins demonstrated that all significant heterogeneity occurred within the Gulf.

Regulation of growth-related genes by nutrition in paralarvae of the common octopus (Octopus vulgaris).

The common octopus (Octopus vulgaris) is a species of great interest to the aquaculture industry. However, the high mortalities registered during different phases of the octopus lifecycle, particularly the paralarvae stage, present a challenge for commercial aquaculture. Improvement of diet formulation is seen as one way to reduce mortality and improve growth.

Demonstration of the Use of Environmental DNA for the Non-Invasive Genotyping of a Bivalve Mollusk, the European Flat Oyster ().

Accurate SNP (single nucleotide polymorphism) genotype information is critical for a wide range of selective breeding applications in aquaculture, including parentage assignment, marker-assisted, and genomic selection. However, the sampling of tissue for genetic analysis can be invasive for juvenile animals or taxa where sampling tissue is difficult or may cause mortality (e.g.

Evolution of population structure in an estuarine-dependent marine fish.

Restriction site-associated DNA (RAD) sequencing was used to characterize neutral and adaptive genetic variation among geographic samples of red drum, , an estuarine-dependent fish found in coastal waters along the southeastern coast of the United States (Atlantic) and the northern Gulf of Mexico (Gulf). Analyses of neutral and outlier loci revealed three genetically distinct regional clusters: one in the Atlantic and two in the northern Gulf. Divergence in neutral loci indicated gradual genetic change and followed a linear pattern of isolation by distance.

When Family Matters Most: A Test of the Association Between Sexual Minority Identity Disclosure Context and Diurnal Cortisol in Sexual Minority Young Adults.

Objective: Revealing one's sexual identity to others is a complex process marked by a shift in the types of stressors faced by sexual minority young adults. Such stressors influence the secretion of health-relevant hormones, including cortisol, yet how dimensions of disclosure (i.e.

Genomic Tools and Selective Breeding in Molluscs.

The production of most farmed molluscs, including mussels, oysters, scallops, abalone, and clams, is heavily dependent on natural seed from the plankton. Closing the lifecycle of species in hatcheries can secure independence from wild stocks and enables long-term genetic improvement of broodstock through selective breeding. Genomic techniques have the potential to revolutionize hatchery-based selective breeding by improving our understanding of the characteristics of mollusc genetics that can pose a challenge for intensive aquaculture and by providing a new suite of tools for genetic improvement.

These aren't the loci you'e looking for: Principles of effective SNP filtering for molecular ecologists.

Sequencing reduced-representation libraries of restriction site-associated DNA (RADseq) to identify single nucleotide polymorphisms (SNPs) is quickly becoming a standard methodology for molecular ecologists. Because of the scale of RADseq data sets, putative loci cannot be assessed individually, making the process of filtering noise and correctly identifying biologically meaningful signal more difficult. Artefacts introduced during library preparation and/or bioinformatic processing of SNP data can create patterns that are incorrectly interpreted as indicative of population structure or natural selection.

Genetic mapping and comparative genomics to inform restoration enhancement and culture of southern flounder, Paralichthys lethostigma.

Background: Southern flounder, Paralichthys lethostigma, historically support a substantial fishery along the Atlantic and Gulf coasts of the southern United States. Low year-class strengths over the past few years in the western Gulf of Mexico have raised concern that spawning stocks may be overfished. Current management of the resource includes releasing hatchery-raised juveniles to restock bays and estuaries; additionally, there is a growing interest in the potential for commercial aquaculture of the species.

Trait Rumination Predicts Elevated Evening Cortisol in Sexual and Gender Minority Young Adults.

Stress may contribute to illness through the impaired recovery or sustained activity of stress-responsive biological systems. Rumination, or mental rehearsal of past stressors, may alter the body's stress-responsive systems by amplifying and prolonging exposure to physiological mediators, such as cortisol. The primary aim of the current investigation was to test the extent to which the tendency to ruminate on stress predicts diminished diurnal cortisol recovery (i.

Rapid genetic and morphologic divergence between captive and wild populations of the endangered Leon Springs pupfish, Cyprinodon bovinus.

The Leon Springs pupfish (Cyprinodon bovinus) is an endangered species currently restricted to a single desert spring and a separate captive habitat in southwestern North America. Following establishment of the captive population from wild stock in 1976, the wild population has undergone natural population size fluctuations, intentional culling to purge genetic contamination from an invasive congener (Cyprinodon variegatus) and augmentation/replacement of wild fish from the captive stock. A severe population decline following the most recent introduction of captive fish prompted us to examine whether the captive and wild populations have differentiated during the short time they have been isolated from one another.

Linkage Mapping and Comparative Genomics of Red Drum () Using Next-Generation Sequencing.

Developments in next-generation sequencing allow genotyping of thousands of genetic markers across hundreds of individuals in a cost-effective manner. Because of this, it is now possible to rapidly produce dense genetic linkage maps for nonmodel species. Here, we report a dense genetic linkage map for red drum, a marine fish species of considerable economic importance in the southeastern United States and elsewhere.

Haplotyping RAD loci: an efficient method to filter paralogs and account for physical linkage.

Next-generation sequencing of reduced-representation genomic libraries provides a powerful methodology for genotyping thousands of single-nucleotide polymorphisms (SNPs) among individuals of nonmodel species. Utilizing genotype data in the absence of a reference genome, however, presents a number of challenges. One major challenge is the trade-off between splitting alleles at a single locus into separate clusters (loci), creating inflated homozygosity, and lumping multiple loci into a single contig (locus), creating artefacts and inflated heterozygosity.

Isotope geochemistry reveals ontogeny of dispersal and exchange between main-river and tributary habitats in smallmouth bass Micropterus dolomieu.

Radiogenic strontium isotope ratios ( Sr: Sr) in otoliths were compared with isotope ratios predicted from models and observed in water sampling to reconstruct the movement histories of smallmouth bass Micropterus dolomieu between main-river and adjacent tributary habitats. A mechanistic model incorporating isotope geochemistry, weathering processes and basin accumulation reasonably predicted observed river Sr: Sr across the study area and provided the foundations for experimental design and inferring fish provenance. Exchange between rivers occurred frequently, with nearly half (48%) of the 209 individuals displaying changes in otolith Sr: Sr reflecting movement between isotopically distinct rivers.

A method for detecting recent changes in contemporary effective population size from linkage disequilibrium at linked and unlinked loci.

Estimation of contemporary effective population size (Ne) from linkage disequilibrium (LD) between unlinked pairs of genetic markers has become an important tool in the field of population and conservation genetics. If data pertaining to physical linkage or genomic position are available for genetic markers, estimates of recombination rate between loci can be combined with LD data to estimate contemporary Ne at various times in the past. We extend the well-known, LD-based method of estimating contemporary Ne to include linkage information and show via simulation that even relatively small, recent changes in Ne can be detected reliably with a modest number of single-nucleotide polymorphism (SNP) loci.

Selection and sex-biased dispersal in a coastal shark: the influence of philopatry on adaptive variation.

Sex-biased dispersal is expected to homogenize nuclear genetic variation relative to variation in genetic material inherited through the philopatric sex. When site fidelity occurs across a heterogeneous environment, local selective regimes may alter this pattern. We assessed spatial patterns of variation in nuclear-encoded, single nucleotide polymorphisms (SNPs) and sequences of the mitochondrial control region in bonnethead sharks (Sphyrna tiburo), a species thought to exhibit female philopatry, collected from summer habitats used for gestation.

Contemporary population structure and post-glacial genetic demography in a migratory marine species, the blacknose shark, Carcharhinus acronotus.

Patterns of population structure and historical genetic demography of blacknose sharks in the western North Atlantic Ocean were assessed using variation in nuclear-encoded microsatellites and sequences of mitochondrial (mt)DNA. Significant heterogeneity and/or inferred barriers to gene flow, based on microsatellites and/or mtDNA, revealed the occurrence of five genetic populations localized to five geographic regions: the southeastern U.S Atlantic coast, the eastern Gulf of Mexico, the western Gulf of Mexico, Bay of Campeche in the southern Gulf of Mexico and the Bahamas.

dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms.

Restriction-site associated DNA sequencing (RADseq) has become a powerful and useful approach for population genomics. Currently, no software exists that utilizes both paired-end reads from RADseq data to efficiently produce population-informative variant calls, especially for non-model organisms with large effective population sizes and high levels of genetic polymorphism. dDocent is an analysis pipeline with a user-friendly, command-line interface designed to process individually barcoded RADseq data (with double cut sites) into informative SNPs/Indels for population-level analyses.

A comparison of neutral and immune genetic variation in Atlantic salmon, Salmo salar L. in Chilean aquaculture facilities.

Genetic diversity was assessed in samples of cultured Atlantic salmon, Salmo salar L., obtained from facilities in Chile between 2005 and 2010, a period of time during which the infectious pathogens Infectious Salmon Anemia (ISA) virus, Caligus rogercresseyi (sea lice), and Piscirickettsia salmonis (salmon rickettsial syndrome) were common. Two panels of microsatellite markers were utilized: one with microsatellites with no known gene associations (neutral) and one featuring microsatellites linked to putative immune-related genes (immune-related).