Genome-wide analysis of acute low salinity tolerance in the eastern oyster Crassostrea virginica and potential of genomic selection for trait improvement

As the global demand for seafood increases, research into the genetic basis of traits that can increase aquaculture production is critical. The eastern oyster (Crassostrea virginica) is an important aquaculture species along the Atlantic and Gulf Coasts of the United States, but increases in heavy rainfall events expose oysters to acute low salinity conditions, which negatively impact production. Low salinity survival is known to be a moderately heritable trait, but the genetic architecture underlying this trait is still poorly understood. In this study, we used ddRAD sequencing to generate genome-wide single-nucleotide polymorphism (SNP) data for four F2 families to investigate the genomic regions associated with survival in extreme low salinity (\u3c3). SNP data were also used to assess the feasibility of genomic selection (GS) for improving this trait. Quantitative trait locus (QTL) mapping and combined linkage disequilibrium analysis revealed significant QTL on eastern oyster chromosomes 1 and 7 underlying both survival and day to death in a 36-day experimental challenge. Significant QTL were located in genes related to DNA/RNA function and repair, ion binding and membrane transport, and general response to stress. GS was investigated using Bayesian linear regression models and prediction accuracies ranged from 0.48 to 0.57. Genomic prediction accuracies were largest using the BayesB prior and prediction accuracies did not substantially decrease when SNPs located within the QTL region on Chr1 were removed, suggesting that this trait is controlled by many genes of small effect. Our results suggest that GS will likely be a viable option for improvement of survival in extreme low salinity

Data from: Environmental DNA analysis of river herring in Chesapeake Bay: a powerful tool for monitoring threatened keystone species

Environmental DNA (eDNA) sampling has emerged as a powerful tool to detect and quantify species abundance in aquatic environments. However, relatively few studies have compared the performance of eDNA-based abundance estimates to traditional catch or survey approaches in the field. Here, we have developed and field-tested a qPCR assay to detect eDNA from alewife and blueback herring (collectively known as ‘river herring’), comparing eDNA-based presence and abundance data to traditional methods of quantification (ichthyoplankton sampling and adult observations). Overall, the qPCR assay showed very high target specificity in lab trials, and was successful in detecting river herring for 11/12 Chesapeake Bay tributaries in spring 2015 and 2016, with 106 out of 445 samples exhibiting positive eDNA hits. We found a strong correlation between eDNA abundance and ichthyoplankton count data (Spearman’s Rho = 0.52), and Phi-tests (correlation of presence/absence data) showed higher correlation between eDNA and ichthyoplankton data (Phi = 0.45) than adult data (Phi = 0.35). Detection probability was significantly lower on western vs. eastern shore tributaries of Chesapeake Bay, and blueback herring and alewife were more likely detected on the western and eastern shores, respectively. Temporal patterns of eDNA abundance over the spring spawning season revealed that alewife were present in high abundances weeks ahead of blueback herring, which aligns with known differences in spawning behavior of the species. In summary, the eDNA abundance data corresponded well to other field methods and has great potential to assist future monitoring efforts of river herring abundance and habitat use

Data from: Fine-scale temporal analysis of genotype-dependent mortality at settlement in the Pacific oyster Crassostrea gigas

Settlement and metamorphosis mark a critical transition in the life cycle of marine invertebrates, during which substantial mortality occurs in both field and laboratory settings. Previous pair-crossing experiments with the Pacific oyster Crassostrea gigas have revealed significant selective or genotype-dependent mortality around the metamorphic transition, but the fine-scale nature and timing of this mortality is not known, particularly whether it occurs before, during or after metamorphosis. In this laboratory study, microsatellite marker segregation ratios were followed daily throughout the settlement and metamorphosis of an F2 cross of the Pacific oyster to examine the fine-scale patterns of genotype dependent mortality at this transition and whether settlement timing (early vs. late) might be under genetic control and affect inference of genotype dependent mortality. Settlement occurred over nine days (day 18 to day 27 post-fertilization) with 68% of individuals settling either early (day 19) or late (day 24). Tracking the survival of spat for 40 days after initial settlement revealed almost no mortality and thus no appreciable genetic mortality. Temporal genetic analysis revealed that 3/11 loci exhibited genotype dependent mortality around the metamorphic transition, one of which (Cg205) was followed throughout settlement and metamorphosis. Alternative temporal patterns of strong selection against each homozygous genotype at Cg205 revealed possible defects in both the competency pathway (inability to initiate metamorphosis) and the morphogenesis pathway (mortality during the metamorphic transition). Quantitative trait locus (QTL) mapping of settlement timing identified three individual and one epistatic QTL with significant genetic effects on this trait (29% of the variance explained in total); however, two of these loci were linked to markers exhibiting selective mortality at metamorphosis, potentially confounding their apparent association with settlement timing. Overall, the results of this study highlight the complex nature of mortality and behavior during settlement and metamorphosis in oysters and suggest that endogenous sources of mortality at settlement may play an important role in the recruitment dynamics of oysters and possibly other broadcast spawning marine invertebrates

Data from: Environmental stress increases selection against and dominance of deleterious mutations in inbred families of the Pacific oyster Crassostrea gigas

The deleterious effects of inbreeding are well documented and of major concern in conservation biology. Stressful environments have generally been shown to increase inbreeding depression; however, little is known about the underlying genetic mechanisms of the inbreeding-by-stress interaction and to what extent the fitness of individual deleterious mutations is altered under stress. Using microsatellite marker segregation data and quantitative trait locus (QTL) mapping methods, I performed a genome scan for deleterious mutations affecting viability (viability or vQTL) in two, inbred families of the Pacific oyster Crassostrea gigas, reared in a stressful, nutrient-poor diet and a favorable, nutrient-rich diet, which had significant effects on growth and survival. Twice as many vQTL were detected in the stressful diet compared with the favorable diet, resulting primarily from substantially greater mortality of homozygous genotypes. At vQTL, estimates of selection (s) and dominance (h) were significantly greater in the stressful environment (s ̅ = 0.86 vs. 0.54 and h ̅ = 0.35 vs. 0.18, in stressful and non-stressful diets, respectively). There was no evidence of interaction between vQTL. Individual vQTL differed across diets in selection only, or in both selection and dominance, and some vQTL were not affected by diet. These results suggest that stress-associated increases in selection against individual deleterious alleles underlie greater inbreeding depression with stress. Furthermore, the finding that inbreeding-by-environment interaction appears, to some extent, to be locus-specific, helps to explain previous observations of lineage-specific expression of inbreeding depression and environment-specific purging, which have important implications for conservation and evolutionary biology

Full SNP dataset for 2 North American populations

This file contains SNP genotype data in genepop format (.gen) for 9864 loci from two blue crab populations : Agawam river MA (AR populatioN) and Panama City Beach, FL (PCB population). Genotype data were filtered for coverage and >85% genotypes called for individuals, and HWE, but not for linkage disequilibrium (LD). Data were exported from Stacks v.1.34 or above

Genotype Data for oyster spat (C. gigas) from early and late settlement

This excel sheet contains microsatellite marker genotypes for oyster spat settling on day 19 or day 24. Genotypes were called by eye (and compared to parent genotypes) on a ABI 377 prism instrument using the Genescan software. These data form the basis of the QTL mapping analyses and chi-square comparisons of early vs. late settlement in Plough 2018. Column A contains the individual Spat ID, and columns C through BK contain the genotype data. Microsatellite marker names are prefixed by "Cg" and are presented in pairs of columns for each marker: one for spat settling on day 19, the other for day 24 (Row 1). Row 2 contains the cross-type of the parents (e.g. abxab) and Row 3 contains the C. gigas linkage group (LG) information for a given marker (LGs 1-10)

Data from: Population genomic analysis of the blue crab Callinectes sapidus using genotyping-by-sequencing

Previous genetic studies of the blue crab Callinectes sapidus along the U.S. Atlantic and Gulf coasts have reported weak or temporally variable spatial structure, suggesting high gene flow among distant populations possibly facilitated by long-distance larval dispersal or other features of blue crab life history. The use of relatively few genetic markers, however, may have limited power to detect subtle but significant structure that could inform fisheries management. In this study, the potential for genome-scale datasets to uncover subtle patterns of population structure in the blue crab was examined using a high-throughput genotyping approach (genotyping-by-sequencing) that generated data for more than 9,600 single nucleotide polymorphisms (SNPs) in crabs from three populations: Panama City Beach, FL, Agawam River, MA, and Porto Alegre, Brazil. Principle components analyses among the three populations revealed very distinct clustering of the Brazilian samples from U.S. populations, likely reflecting restricted gene flow across the equator. Detailed analysis of population structure between the two U.S. populations revealed low but significant genetic differentiation (FST = 0.0103), with FST values ranging from -0.05 to 0.48. Previous studies have failed to detect significant genetic structure on a similar geographic scale. FST outlier analysis identified 242 loci (2.45% of total) with statistically extreme values at the false discovery rate α = 0.05 level, only 16 of which showed significant sequence homology to annotated proteins via BLASTx alignment. Top BLASTx hits were to crustacean or arthropod sequences and 8 of the 16 had high sequence similarity to transposable elements or related machinery. Finally, results of population assignment tests for the two U.S. populations showed that the full marker dataset provided good power to assign individuals back to their population of origin (∼83% and 92% success for Panama City Beach and Agawam River, respectively), which dropped significantly when using only 500 randomly selected SNPs (∼61% and 72% success). Overall, this study demonstrates the great utility of high-throughput sequencing technologies for characterizing fine-scale patterns of genetic structure in blue crabs, and this approach should substantially improve the delineation of stock structure and further advance our understanding of blue crab population connectivity and ecology

Filtered SNP genotype data set for Brazil, Massachussets and Florida

This is a genepop formatted file (.gen) with SNP data for the three populations examined in this study (Porto Allegre, Brazil, Panama city beach FL, and Agawam river MA, USA). File contains data for 2,783 SNPs which were filtered for HWE, LD, and coverage. Genotype data was exported from the Stacks pipeline v. 1.34 or higher

Microsatellite genotypes for Mol. Ecology environmental stress study in C. gigas 5_23_12

Microsatellite genotypes for Mol. Ecology environmental stress study in C. gigas 5_23_1