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The integration of physical and high-density genetic maps is a very useful approach to achieve chromosome-level genome assemblies. Here, the genome of a male Senegalese sole (Solea senegalensis) was de novo assembled and the contigs were anchored to a high-quality genetic map for chromosome-level scaffolding. Hybrid assembled genome was 609.3 Mb long and contained 3403 contigs with a N50 of 513 kb. The linkage map was constructed using 16,287 informative SNPs derived from ddRAD sequencing in 327 sole individuals from five families. Markers were assigned to 21 linkage groups with an average number of 21.9 markers per megabase. The anchoring of the physical to the genetic map positioned 1563 contigs into 21 pseudo-chromosomes covering 548.6 Mb. Comparison of genetic and physical distances indicated that the average genome-wide recombination rate was 0.23 cM/Mb and the female-to-male ratio 1.49 (female map length: 2,698.4 cM, male: 2,036.6 cM). Genomic recombination landscapes were different between sexes with crossovers mainly concentrated toward the telomeres in males while they were more uniformly distributed in females. A GWAS analysis using seven families identified 30 significant sex-associated SNP markers located in linkage group 18. The follicle-stimulating hormone receptor appeared as the most promising locus associated with sex within a region with very low recombination rates. An incomplete penetrance of sex markers with males as the heterogametic sex was determined. An interspecific comparison with other Pleuronectiformes genomes identified a high sequence similarity between homologous chromosomes, and several chromosomal rearrangements including a lineage-specific Robertsonian fusion in S. senegalensis. This study was funded by project RTA2017-00054-C03-01 and RTA2017-00054-C03-funded from MCIU/AEI/FEDER, UE and cofunded 80% by Programa Operativo FEDER de Andalucía 2014-2020, project PP.AVA.AVA201601.9 SOLEALGAE. Moreover, the study has received funding from EU H2020 research and innovation program under grant agreement 817992 ERANET-BLUEBIO COFUND project PCI2020-111994 BestBrood/AEI/10.13039/501100011033. IGC is funded by a predoctoral fellowship from INIA. This work would not have been possible without the computer resources and the technical support provided by the Plataforma Andaluza de Bioinformática of the University of Málaga and CNAG.

Shape quality is very important in flatfish aquaculture due to the impact on commercialization. The Senegalese sole (Solea senegalensis) is a valuable flatfish with a highly elliptic body that slightly changes with age and size, and it is prone to accumulating malformations during the production cycle. The present study aims to investigate the genetic parameters of two growth traits (weight and standard length) and six shape quality predictors (ellipticity, three body heights (body height at the pectoral fin base [BHP], body maximum height [BMH] and caudal peduncle height [CPH]) and two ratios (BMH/BHP and BMH/CPH)). These traits were measured before the on-growing stage (age ~400 days (d)) and at harvest (~800 d). Phenotypic data, heritabilities and genetic and phenotypic correlations between the traits are presented and discussed. High or very high heritabilities (0.433–0.774) were found for growth traits, body heights and ellipticity and they were higher at 400 than 800 d. In contrast, the ratios of BMH/BHP and BMH/CPH were less heritable (0.144–0.306). Positive and very high (&gt, 0.95) correlations between growth traits and the three heights were found and decreased with age. In contrast, ellipticity had negative and medium-high genetic correlations with growth traits and heights, indicating fish selected for bigger size would also become rounder. The ratio of BMH/CPH showed low genetic correlations with all traits and provided complementary information to ellipticity for a better fitting to the expected lanceolate body morphology of sole. The genetic correlations for all traits at both ages were very high, indicating that selection before entering the growth-out stage in recirculation aquaculture systems is recommended to accelerate genetic gains.

Breeding programs are essential for aquaculture. The present study was conducted to investigate the genetic parameters of four growth traits in Senegalese sole. Families were produced by mass spawning (n = 2171 offspring) from an industrial broodstock. Weight, total area, standard length and width (the two latter measured directly on the fish and by image analysis) were determined before the on-growing stage (age ~ 400 d) and at harvest (~800 d) in RAS. Phenotypic data are presented and discussed. Females grew faster than males and a high variation of sex ratios by family was observed. Heritabilities were high for all traits ranging from 0.568 to 0.609 at 400 d and from 0.424 to 0.500 at 800d. The genetic correlations between traits were very high (>0.94) at both ages. Genetic estimates for traits measured in vivo and by digital image analysis were similar. To investigate genomic regions associated with these growth traits, a low-density array using a set of 60 single nucleotide polymorphisms (SNPs) distributed in 17 linkage groups was designed. Using samples from wild fish, a total of 49 assays for SNP analysis were validated. The association analysis was carried out using two fast-growth families and two slow-growth families (n = 279). Two significantly-associated SNPs with most of the traits at both ages were detected. They were located in the general transcription factor 3C polypeptide 4 (gtf3c4) and the mitochondrial fission process protein 1 (mtfp1). Results are of high relevance for genetic breeding programs in this species.

International audience; Internal electronic tagging is a major issue in flatfish species due to the small size of abdominal cavity. In this study, three tag types, referred to as Nonatec, nano and mini, were evaluated in three weight classes of Senegalese sole: small (0.3 g), middle (0.8 g) and large (2.0 g). Tags were injected from the blind side and fish were carefully handled to minimize sharp movements. Tag losses were 8% in the small size class, between 5.2 and 15.1% in the middle size class and 2-4% in the large size class. The mortality rates ranged between 2.0 and 15.0% with the lowest values in the large size class. No negative effects of tags on growth (tagged vs non-tagged fish using a middle size class) were found after 57 days of culture. Four additional trials using mini tags in a large size class at industrial scale validated our experimental results. With respect to morphology, no differences in the area, ellipticity and circularity were found except for a slight higher aspect ratio index in mini- and nano-tagged soles when compared with untagged fish. A longitudinal analysis of growth using the tag type, sex and tag position (anterior, medium or posterior) as fixed factors revealed a significant and strong effect of sex, with females appearing significantly heavier (13.6%) than males. In addition, the significant interactions between tag position and tag type with the time indicated a delayed growth of Nonatec-tagged fish and specimens with tags in the posterior section of abdomen. Expression analysis of stress-related genes revealed an activation of HPI axis and cellular stress defenses at 2 days just after tagging (dat) not evident at 11 dat. All these data indicate that soles can be successfully tagged at very small sizes both at experimental and industrial scales if tag type is properly selected and fish correctly handled. Moreover, sex and tag position are significant factors affecting growth that need to be controlled in longitudinal studies and selective breeding programs.