An Expressed Sequence Tag (EST)-enriched genetic map of turbot (Scophthalmus maximus): a useful framework for comparative genomics across model and farmed teleosts

Abstract

BackgroundThe turbot (Scophthalmus maximus) is a relevant species in European aquaculture. The small turbot genome provides a source for genomics strategies to use in order to understand the genetic basis of productive traits, particularly those related to sex, growth and pathogen resistance. Genetic maps represent essential genomic screening tools allowing to localize quantitative trait loci (QTL) and to identify candidate genes through comparative mapping. This information is the backbone to develop marker-assisted selection (MAS) programs in aquaculture. Expressed sequenced tag (EST) resources have largely increased in turbot, thus supplying numerous type I markers suitable for extending the previous linkage map, which was mostly based on anonymous loci. The aim of this study was to construct a higher-resolution turbot genetic map using EST-linked markers, which will turn out to be useful for comparative mapping studies.ResultsA consensus gene-enriched genetic map of the turbot was constructed using 463 SNP and microsatellite markers in nine reference families. This map contains 438 markers, 180 EST-linked, clustered at 24 linkage groups. Linkage and comparative genomics evidences suggested additional linkage group fusions toward the consolidation of turbot map according to karyotype information. The linkage map showed a total length of 1402.7 cM with low average intermarker distance (3.7 cM; ~2 Mb). A global 1.6:1 female-to-male recombination frequency (RF) ratio was observed, although largely variable among linkage groups and chromosome regions. Comparative sequence analysis revealed large macrosyntenic patterns against model teleost genomes, significant hits decreasing from stickleback (54%) to zebrafish (20%). Comparative mapping supported particular chromosome rearrangements within Acanthopterygii and aided to assign unallocated markers to specific turbot linkage groups.ConclusionsThe new gene-enriched high-resolution turbot map represents a useful genomic tool for QTL identification, positional cloning strategies, and future genome assembling. This map showed large synteny conservation against model teleost genomes. Comparative genomics and data mining from landmarks will provide straightforward access to candidate genes, which will be the basis for genetic breeding programs and evolutionary studies in this species.

Chromosomal manipulation in Senegalese sole (Solea senegalensis Kaup, 1858): induction of triploidy and gynogenesis

“…Additionally, being highly homozygotic, they are useful in other genetic and genomic applications for producing cloned fish lines (Thorgaard et al 2002) or in developing genetic maps to calculate the distance of the markers to the centromere by half tetrad analyses, for example in flatfishes such as turbot (Martínez et al 2008), halibut (Reid et al 2007), tongue solea (Ji et al 2009), and Senegalese sole (Molina-Luzón et al 2014). In the same sense, although they are not viable, the haploid gynogenetic embryos are used to estimate the distance between molecular markers in these types of studies in turbot (Bouza et al 2007(Bouza et al , 2012 and Senegalese sole (Molina-Luzón et al 2014). …”

Highly dense linkage maps from 31 full-sibling families of turbot (Scophthalmus maximus) provide insights into recombination patterns and chromosome rearrangements throughout a newly refined genome assembly

“…Those markers showing consistent deviations from Mendelian segregation ( P  < 0.01) across families or extreme departures from Hardy–Weinberg equilibrium (HWE) in the parental population ( P  < 0.001) due to heterozygote excess ( F IS  < −0.5, P  < 0.0001; paralogous genes) or deficit ( F IS  > 0.5, P  < 0.0001; null alleles) were filtered out. Finally, RAD-tags containing SNPs were mapped against the turbot gene catalog 38 using Blastn (E-value < e−20) to obtain sequence annotations.…”

“…When markers of a specific scaffold were assigned to more than one LG, the scaffold was split into fragments pertaining to different LGs or to the same LG but in different positions (see Results). To establish the most confident splitting of these scaffolds, we compared the sequence of the gap between the flanking markers assigned to different LGs with the two model fish genomes, Gasterosteus aculeatus and Oryzias latipes , which had demonstrated large synteny with turbot 34 , 38 . Then, we looked for the turbot genes in the gap assigned to different LGs in the model species in order to narrow down as much as possible the gap (Supplementary Fig.…”

“…Nowadays, a broad battery of genetic markers and genomic tools are available in turbot, which can aid to understand the genetic basis of the main economically important traits (growth rate, disease resistance, sex control) and for applying a more efficient selection 30–35 . The first genetic maps in turbot, based on anonymous or gene-associated microsatellites and SNPs, 36–38 were later integrated in a consensus map 38 . More recently, a high-density map was reported by Wang et al, 21 but the scarce information provided on genetic marker-associated sequences made it not feasible to integrate with previously reported maps 9 .…”

“…Centromeres have been located in the turbot genetic map using half-tetrad analysis 40 , and recently, a high coverage draft genome has been assembled and anchored to the reported consensus map 36 . Moreover, the development of genomic resources for other important flatfish species 41–43 and their integration in a common framework has allowed comparative analyses to transfer genomic information on production-related traits between species and to look for insights into flatfish evolution 9 , 38 …”