Dataset Information

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

ABSTRACT: 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. Currently, genomic resources for southern flounder do not exist. Here, we used two hatchery-reared families and double-digest, restriction-site-associated DNA (ddRAD) sequencing to create a reduced-representation genomic library consisting of several thousand single nucleotide polymorphisms (SNPs) located throughout the genome.The relative position of each SNP-containing locus was determined to create a high-density genetic map spanning the 24 linkage groups of the southern flounder genome. The consensus map was used to identify regions of shared synteny between southern flounder and seven other fish species for which genome assemblies are available. Finally, syntenic blocks were used to localize genes identified from transcripts in European flounder as potentially being involved in ecotoxicological and osmoregulatory responses, as well as QTLs associated with growth and disease resistance in Japanese flounder, on the southern flounder linkage map.The information provided by the linkage map will enrich restoration efforts by providing a foundation for interpreting spatial genetic variation within the species, ultimately furthering an understanding of the adaptive potential and resilience of southern flounder to future changes in local environmental conditions. Further, the map will facilitate the use of genetic markers to enhance restoration and commercial aquaculture.

SUBMITTER: O'Leary SJ

PROVIDER: S-EPMC5824557 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature

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

O'Leary Shannon J SJ Hollenbeck Christopher M CM Vega Robert R RR Gold John R JR Portnoy David S DS

BMC genomics 20180223 1

<h4>Background</h4>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 aqu ...[more]

PMID: 29471804

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Project description:Physiological information is rarely used in descriptions of maturity for managed, wild fish species; however, the use of physiological data holds great promise to provide important detail on the complexities of oocyte development and maturity. Investigating southern flounder (Paralichthys lethostigma)-an overfished commercial and recreational fishery resource-we examined pre-spawn physiological changes in females to provide further detail of the maturation process. Given that adults of this species complete maturation and spawn in unknown offshore locations, information on pre-spawn physiological changes is particularly informative for both size- and age-based patterns of maturity. We evaluated seasonal and ontogenetic changes in hormone concentrations in blood plasma that are commonly associated with sexual maturation, in addition to quantifying and classifying lipid stored in liver tissue. We found a strong positive relationship between body weight and lipid content during all months, as well as evidence for mobilization of lipids among larger females in September and October, presumably for gonadal development. Throughout the sampling period, the lipid content of smaller individuals was dominated by structural lipids (as opposed to storage lipids). In contrast, larger individuals possessed greater amounts of storage lipids. This suggests that larger, putatively maturing individuals were accumulating storage lipids for later production of vitellogenin. Females sampled for blood sex steroids and ovarian histology showed different testosterone and estradiol concentrations between putatively maturing and immature fish, and temporal variation with peaks in October and November. Overall, emerging patterns of liver lipid content and composition and blood steroid concentrations describe a multi-month maturation process that is often managed one dimensionally over short time periods. Insights from this work will improve our understanding of the life history of southern flounder, with the potential for better understanding of the dynamics of offshore spawning migration and informing subsequent species management.

Project description:BACKGROUND: Japanese flounder (Paralichthys olivaceus) is one of the most economically important marine species in Northeast Asia. Information on genetic markers associated with quantitative trait loci (QTL) can be used in breeding programs to identify and select individuals carrying desired traits. Commercial production of Japanese flounder could be increased by developing disease-resistant fish and improving commercially important traits. Previous maps have been constructed with AFLP markers and a limited number of microsatellite markers. In this study, improved genetic linkage maps are presented. In contrast with previous studies, these maps were built mainly with a large number of codominant markers so they can potentially be used to analyze different families and populations. RESULTS: Sex-specific genetic linkage maps were constructed for the Japanese flounder including a total of 1,375 markers [1,268 microsatellites, 105 single nucleotide polymorphisms (SNPs) and two genes]; 1,167 markers are linked to the male map and 1,067 markers are linked to the female map. The lengths of the male and female maps are 1,147.7 cM and 833.8 cM, respectively. Based on estimations of map lengths, the female and male maps covered 79 and 82% of the genome, respectively. Recombination ratio in the new maps revealed F:M of 1:0.7. All linkage groups in the maps presented large differences in the location of sex-specific recombination hot-spots. CONCLUSIONS: The improved genetic linkage maps are very useful for QTL analyses and marker-assisted selection (MAS) breeding programs for economically important traits in Japanese flounder. In addition, SNP flanking sequences were blasted against Tetraodon nigroviridis (puffer fish) and Danio rerio (zebrafish), and synteny analysis has been carried out. The ability to detect synteny among species or genera based on homology analysis of SNP flanking sequences may provide opportunities to complement initial QTL experiments with candidate gene approaches from homologous chromosomal locations identified in related model organisms.

Dataset Information

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

Publications

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

Similar Datasets

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