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

Shannon J O’Leary,John R Gold,David S Portnoy,Christopher M Hollenbeck,Robert R Vega

doi:10.1186/s12864-018-4541-0

Abstract

BackgroundSouthern 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.ResultsThe 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.ConclusionsThe 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.

Highlights

Southern flounder, Paralichthys lethostigma, historically support a substantial fishery along the Atlantic and Gulf coasts of the southern United States
Reference construction, genotyping and Single-nucleotide polymorphism (SNP) filtering The final reduced-representation reference genome consisted of 52,831 RAD fragments
Black ticks indicate the positions of loci mapped on southern flounder linkage groups; loci mapped to the same location are stacked

Summary

Introduction

Paralichthys lethostigma, historically support a substantial fishery along the Atlantic and Gulf coasts of the southern United States. Current management of the resource includes releasing hatchery-raised juveniles to restock bays and estuaries; there is a growing interest in the potential for commercial aquaculture of the species. Current management of the resource includes spawning wild-caught adults, rearing fingerlings in hatcheries, and releasing juveniles to augment natural recruitment [6, 7] It is possible, given the species’ life history, that differences in environmental conditions (e.g., temperature, salinity) across estuaries and bays inhabited by southern flounder [8, 9] may have resulted in localized adaptation, in which case offspring from wild-caught adults adapted to those conditions would need to be. A highly dense linkage map, where genetic markers are localized onto individual linkage groups (chromosomes) and relative positions of the markers are summarized, can fulfill many of the purposes of a fully assembled and annotated genome by giving insight into genome structure and organization and further providing a resource for comparative bioinformatics [12, 14]

Methods

Results

Discussion

Conclusion