Genetic improvement of cultured Pacific oysters by selection : 1996 Coastal Marine Experiment Station Annual Report

Published January 1997. Facts and recommendations in this publication may no longer be valid. Please look for up-to-date information in the OSU Extension Catalog: http://extension.oregonstate.edu/catalo

High-Density Linkage Maps Based on Genotyping-by-Sequencing (GBS) Confirm a Chromosome-Level Genome Assembly and Reveal Variation in Recombination Rate for the Pacific Oyster Crassostrea gigas

Studies of linkage and linkage mapping have advanced genetic and biological knowledge for over 100 years. In addition to their growing role, today, in mapping phenotypes to genotypes, dense linkage maps can help to validate genome assemblies. Previously, we showed that 40% of scaffolds in the first genome assembly for the Pacific oyster Crassostrea gigas were chimeric, containing single nucleotide polymorphisms (SNPs) mapping to different linkage groups. Here, we merge 14 linkage maps constructed of SNPs generated from genotyping-by-sequencing (GBS) methods with five, previously constructed linkage maps, to create a compendium of nearly 69 thousand SNPs mapped with high confidence. We use this compendium to assess a recently available, chromosome-level assembly of the C. gigas genome, mapping SNPs in 275 of 301 contigs and comparing the ordering of these contigs, by linkage, to their assembly by Hi-C sequencing methods. We find that, while 26% of contigs contain chimeric blocks of SNPs, i.e., adjacent SNPs mapping to different linkage groups than the majority of SNPs in their contig, these apparent misassemblies amount to only 0.08% of the genome sequence. Furthermore, nearly 90% of 275 contigs mapped by linkage and sequencing are assembled identically; inconsistencies between the two assemblies for the remaining 10% of contigs appear to result from insufficient linkage information. Thus, our compilation of linkage maps strongly supports this chromosome-level assembly of the oyster genome. Finally, we use this assembly to estimate, for the first time in a Lophotrochozoan, genome-wide recombination rates and causes of variation in this fundamental process

Understanding How Disease and Environment Combine to Structure Resistance in Estuarine Bivalve Populations

Delaware Bay oyster (Crassostrea virginica) populations are influenced by two lethal parasites that cause Dermo and MSX diseases. As part of the US National Science Foundation Ecology of Infectious Diseases initiative, a program developed for Delaware Bay focuses on understanding how oyster population genetics and population dynamics interact with the environment and these parasites to structure he host populations, and how these interactions might modified by climate change. Laboratory and field studies undertaken during this program include identifying genes related to MSX and Dermo disease resistance, potential regions for refugia and the mechanisms that allow them to exist, phenotypic and genotypic differences in oysters from putative refugia and high-disease areas, and spatial and temporal variability in the effective size of the spawning populations. Resulting data provide inputs to oyster genetics, population dynamics, and larval growth models that interface with a three-dimensional circulation model developed for Delaware Bay. Reconstruction of Lagrangian particle tracks is used to infer transport pathways of oyster larvae and MSX and Dermo disease pathogens. Results emerging from laboratory, field, and modeling studies are providing an understanding of long-term changes in Delaware Bay oyster populations that occur as the oyster population responds to climate, environmental, and biological variability

A Scientific Name for Pacific Oysters

WOS:000447083800041International audienc

Multi-model study of mercury dispersion in the atmosphere : Atmospheric processes and model evaluation

Current understanding of mercury (Hg) behavior in the atmosphere contains significant gaps. Some key characteristics of Hg processes, including anthropogenic and geogenic emissions, atmospheric chemistry, and air-surface exchange, are still poorly known. This study provides a complex analysis of processes governing Hg fate in the atmosphere involving both measured data from ground-based sites and simulation results from chemical transport models. A variety of long-term measurements of gaseous elemental Hg (GEM) and reactive Hg (RM) concentration as well as Hg wet deposition flux have been compiled from different global and regional monitoring networks. Four contemporary global-scale transport models for Hg were used, both in their state-of-the-art configurations and for a number of numerical experiments to evaluate particular processes. Results of the model simulations were evaluated against measurements. As follows from the analysis, the interhemispheric GEM gradient is largely formed by the prevailing spatial distribution of anthropogenic emissions in the Northern Hemisphere. The contributions of natural and secondary emissions enhance the south-to-north gradient, but their effect is less significant. Atmospheric chemistry has a limited effect on the spatial distribution and temporal variation of GEM concentration in surface air. In contrast, RM air concentration and wet deposition are largely defined by oxidation chemistry. The Br oxidation mechanism can reproduce successfully the observed seasonal variation of the RM=GEM ratio in the near-surface layer, but it predicts a wet deposition maximum in spring instead of in summer as observed at monitoring sites in North America and Europe. Model runs with OH chemistry correctly simulate both the periods of maximum and minimum values and the amplitude of observed seasonal variation but shift the maximum RM=GEM ratios from spring to summer. O3 chemistry does not predict significant seasonal variation of Hg oxidation. Hence, the performance of the Hg oxidation mechanisms under study differs in the extent to which they can reproduce the various observed parameters. This variation implies possibility of more complex chemistry and multiple Hg oxidation pathways occurring concurrently in various parts of the atmosphere

The oyster genome reveals stress adaptation and complexity of shell formation

The Pacific oyster Crassostrea gigas belongs to one of the most species-rich but genomically poorly explored phyla, the Mollusca. Here we report the sequencing and assembly of the oyster genome using short reads and a fosmid-pooling strategy, along with transcriptomes of development and stress response and the proteome of the shell. The oyster genome is highly polymorphic and rich in repetitive sequences, with some transposable elements still actively shaping variation. Transcriptome studies reveal an extensive set of genes responding to environmental stress. The expansion of genes coding for heat shock protein 70 and inhibitors of apoptosis is probably central to the oyster's adaptation to sessile life in the highly stressful intertidal zone. Our analyses also show that shell formation in molluscs is more complex than currently understood and involves extensive participation of cells and their exosomes. The oyster genome sequence fills a void in our understanding of the Lophotrochozoa. © 2012 Macmillan Publishers Limited. All rights reserved

QUANTIFYING AND MINIMIZING RISK THAT HATCHERY-ENHANCEMENT WILL REDUCE GENETIC DIVERSITY OF WHITE SEABASS

Demand for seafood on a global scale is projected to increase by 70 percent in the next 30 years, though most fisheries are at or beyond their sustainable yields and many are in decline (Botsford et al. 1997). Fisheries management must be augmented by new strategies for protecting and enhancing marine resources, such as “no-take” marine reserves (Allison et al. 1998; Hastings and Botsford 1999) or enhancing natural stocks through artificial hatchery propagation. Despite criticisms from conservationists and fisheries biologists alike (e.g. Meffe 1992; MacCall 1989), large-scale hatchery supplementation programs are already in place for many anadromous and marine fisheries (Travis et al. 1998), and in Japan, a substantial fraction of marine production is attributable to enhancement programs (Masuda and Tsukamoto 1998). The global extent of enhancement of wild fisheries is poorly documented, however, especially for marine species (A.F. Born, A.J. Immink, and D.M. Bartley, FAO Fisheries, pers. com.). In Japan, to take just one example, nearly 70 marine species are supplemented, some at very high levels. To date there have been very few analyses of the potential genetic impact of these marine supplementation programs

MEIOSIS IN TETRAPLOID PACIFIC OYSTERS, THEIR TRIPLOID MOTHERS, AND DIPLOID GRANDMOTHERS

The Pacific oyster occurs on all continents but Antarctica (Mann 1979) and for the past several years has had the highest annual production of any freshwater or marine organism (4.2 million metric tons in 2002, worth $3.5 billion; FAO 2004). About 92 million pounds of Pacific oyster meat were produced on the West Coast in 2000, with a farm-gate value of nearly$70 million (Toba and Chew 1999). West Coast production exceeds the harvest of Eastern oysters on either the Gulf or Atlantic Coasts, primarily because diseases have wiped out those natural stocks. As the Pacific oyster does not naturally reproduce along much of the West Coast, seed was imported from Japan for decades (Chew 1984). In the early 1980s, however, the industry adopted hatchery techniques and now relies mainly on hatchery seed. This sets the stage not only for commercial breeding programs, which industry identifies as a top priority (Pacific Shellfish Institute 1999), but also for development in the future of a mature seed industry servicing global markets

Linkage Maps of Microsatellite DNA Markers for the Pacific Oyster Crassostrea gigas

We constructed male and female consensus linkage maps for the Pacific oyster Crassostrea gigas, using a total of 102 microsatellite DNA markers typed in 11-day-old larvae from three families. We identified 11 and 12 linkage groups in the male and female consensus maps, respectively. Alignment of these separate maps, however, suggests 10 linkage groups, which agrees with the haploid chromosome number. The male linkage map comprises 88 loci and spans 616.1 cM, while the female map comprises 86 loci and spans 770.5 cM. The male and the female maps share 74 loci; 2 markers remain unlinked. The estimated coverages for the consensus linkage maps are 79% for the male and 70–75% for the female, on the basis of two estimates of genome length. Ninety-five percent of the genome is expected to lie within 16 and 21 cM of markers on the male and female maps, respectively, while 95% of simulated minimum distances to the male and female maps are within 10.1 and 13.6 cM, respectively. Females have significantly more recombination than males, across 118 pairs of linked markers in common to the parents of the three families. Significant differences in recombination and orders of markers are also evident among same-sex parents of different families as well as sibling parents of opposite sex. These observations suggest that polymorphism for chromosomal rearrangements may exist in natural populations, which could have profound implications for interpreting the evolutionary genetics of the oyster. These are the first linkage maps for a bivalve mollusc that use microsatellite DNA markers, which should enable them to be transferred to other families and to be useful for further genetic analyses such as QTL mapping