Detection of growth-related QTL in turbot (Scophthalmus maximus)

Sánchez-Molano, Enrique; Cerna, Alex; Toro, M. Á.; Bouza, Carmen; Hermida, Miguel; Pardo, Belén G.; Cabaleiro, Santiago; Fernández, Jesús; Martı́nez, Paulino

doi:10.1186/1471-2164-12-473

Cited by 70 publications

(69 citation statements)

References 38 publications

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“…QTL for both weight and length were detected on Chr-12 (Sept. XX male) and Chr-10 and -17 (Dec. XY male). Overlapping weight and length QTL have also been found in other species of fish (Wang et al 2013;Sánchez-Molano et al 2011;McClelland and Naish 2010), and these results suggest that many genes have pleiotropic effects in the regulation of weight and length. The coupling of length and weight QTL is not surprising given that genetic correlations for these two traits are high (Fishback et al 2002), but interestingly, these traits appear largely uncoupled to genes influencing variation in condition factor.…”

Section: Qtlmentioning

confidence: 72%

Co-localization of growth QTL with differentially expressed candidate genes in rainbow trout

Kocmarek

Ferguson

Danzmann

2015

Genome

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Abstract:We tested whether genes differentially expressed between large and small rainbow trout co-localized with familial QTL regions for body size. Eleven chromosomes, known from previous work to house QTL for weight and length in rainbow trout, were examined for QTL in half-sibling families produced in September (1 XY male and 1 XX neomale) and December (1 XY male). In previous studies, we identified 108 candidate genes for growth expressed in the liver and white muscle in a subset of the fish used in this study. These gene sequences were BLASTN aligned against the rainbow trout and stickleback genomes to determine their location (rainbow trout) and inferred location based on synteny with the stickleback genome. Across the progeny of all three males used in the study, 63.9% of the genes with differential expression appear to co-localize with the QTL regions on 6 of the 11 chromosomes tested in these males. Genes that co-localized with QTL in the mixed-sex offspring of the two XY males primarily showed up-regulation in the muscle of large fish and were related to muscle growth, metabolism, and the stress response.Key words: rainbow trout, QTL, neomale, growth.Résumé : Les auteurs ont voulu vérifier si des gènes montrant une expression différentielle chez des grandes et des petites truites arc-en-ciel étaient situés au même endroit dans le génome que des QTL pour la taille. Onze chromosomes, connus comme étant porteurs de QTL pour la masse et la longueur des truites, ont été examinés pour des QTL au sein de familles de demi-frères produits en septembre (1 mâle XY et 1 néo-mâle XX) et en décembre (1 mâle XY). Dans des travaux antérieurs, les auteurs avaient identifié 108 gènes candidats pour la croissance qui sont exprimés chez le foie et les muscles lisses chez un sous-ensemble des poissons analysés dans ce travail. Les séquences de ces gènes ont été alignées (BLASTN) sur les génomes de la truite arc-en-ciel et de l'épinoche pour déterminer leur position (truite arc-en-ciel) ou position inférée sur la base de la synténie avec le génome de l'épinoche. Parmi les progénitures des trois mâles employés dans ce travail, 63,9 % des gènes affichant une expression différentielle ont semblé présenter une co-localisation avec des QTL sur 6 des 11 chromosomes testés chez ces mâles. Les gènes qui co-localisaient avec les QTL au sein des progénitures des deux sexes des deux mâles XY étaient principalement surexprimés chez le muscle des grands poissons et étaient impliqués dans la croissance musculaire, le métabolisme et la réponse aux stress. [Traduit par la Rédaction]

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Section: Qtlmentioning

confidence: 72%

Co-localization of growth QTL with differentially expressed candidate genes in rainbow trout

Kocmarek

Ferguson

Danzmann

2015

Genome

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“…LG, linkage group; Selection: type of selection and geographical region; Gene/Function: official gene symbol and function (IG: immunoglobulin); data mining: relevant genes identified related to growth (G), VHSV resistance (VH), Aeromonas salmonicida resistance (AS), reproduction (R) and osmoregulation (OS); QTLs and previous outliers from 1 Sánchez‐Molano et al., 2011; 2 Rodríguez‐Ramilo et al., 2014; 3 Rodríguez‐Ramilo et al., 2011; V2015: outliers reported by Vilas et al., 2015.…”

Section: Resultsmentioning

confidence: 99%

“…Both outlier loci were within the confidence interval of a growth‐related QTL (Sánchez‐Molano et al., 2011) and data mining detected the presence of MTOR (mechanistic target of rapamycin), a candidate gene related to growth and A . salmonicida resistance (Figueras et al., 2016), and TWIST2 (twist family BHLH transcription factor 2), a gene related to osmoregulation (Grady et al., 2014).…”

Section: Resultsmentioning

confidence: 99%

“…As expected, F ST between BAS and BLS increased when these outliers were excluded (using only neutral markers). As mentioned above, two of these markers (7033_88 and 5397_68) are linked to several growth‐related loci (Robledo et al., 2016; Rodríguez‐Ramilo et al., 2014; Sánchez‐Molano et al., 2011), and also to some candidate genes associated with osmotic stress response (Norman et al., 2014; Ortells et al., 2012). Two other outlier loci reside close to genes related to osmoregulation: 1587_12 on LG13 near RAC1 and PRKCA (Di Ciano et al., 2002; Zhuang, Hirai, & Ohno, 2000), and 2921_40 on LG16 near NAP1L1 (Wang et al., 2014).…”

Section: Discussionmentioning

confidence: 99%

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Parallel evolution and adaptation to environmental factors in a marine flatfish: Implications for fisheries and aquaculture management of the turbot (Scophthalmus maximus)

Prado

Vera

Hermida

et al. 2018

Evolutionary Applications

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Unraveling adaptive genetic variation represents, in addition to the estimate of population demographic parameters, a cornerstone for the management of aquatic natural living resources, which, in turn, represent the raw material for breeding programs. The turbot (Scophthalmus maximus) is a marine flatfish of high commercial value living on the European continental shelf. While wild populations are declining, aquaculture is flourishing in southern Europe. We evaluated the genetic structure of turbot throughout its natural distribution range (672 individuals; 20 populations) by analyzing allele frequency data from 755 single nucleotide polymorphism discovered and genotyped by double‐digest RAD sequencing. The species was structured into four main regions: Baltic Sea, Atlantic Ocean, Adriatic Sea, and Black Sea, with subtle differentiation apparent at the distribution margins of the Atlantic region. Genetic diversity and effective population size estimates were highest in the Atlantic populations, the area of greatest occurrence, while turbot from other regions showed lower levels, reflecting geographical isolation and reduced abundance. Divergent selection was detected within and between the Atlantic Ocean and Baltic Sea regions, and also when comparing these two regions with the Black Sea. Evidence of parallel evolution was detected between the two low salinity regions, the Baltic and Black seas. Correlation between genetic and environmental variation indicated that temperature and salinity were probably the main environmental drivers of selection. Mining around the four genomic regions consistently inferred to be under selection identified candidate genes related to osmoregulation, growth, and resistance to diseases. The new insights are useful for the management of turbot fisheries and aquaculture by providing the baseline for evaluating the consequences of turbot releases from restocking and farming.

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“…LG12, LG14 and LG15) and Fulton's condition factor (LG3 and LG16) (Sánchez-Molano et al 2011) have been identified. Also, a QTL associated with turbot body length was detected on male LG7 (Ruan et al 2010).…”

Section: Genetic Maps and Detection Of Quantitative Trait Loci (Qtls)mentioning

confidence: 99%

Advances in genomics for flatfish aquaculture

Cerdà

Manchado

2012

Genes Nutr

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Fish aquaculture is considered to be one of the most sustainable sources of protein for humans. Many different species are cultured worldwide, but among them, marine flatfishes comprise a group of teleosts of high commercial interest because of their highly prized white flesh. However, the aquaculture of these fishes is seriously hampered by the scarce knowledge on their biology. In recent years, various experimental 'omics' approaches have been applied to farmed flatfishes to increment the genomic resources available. These tools are beginning to identify genetic markers associated with traits of commercial interest, and to unravel the molecular basis of different physiological processes. This article summarizes recent advances in flatfish genomics research in Europe. We focus on the new generation sequencing technologies, which can produce a massive amount of DNA sequencing data, and discuss their potentials and applications for de novo genome sequencing and transcriptome analysis. The relevance of these methods in nutrigenomics and foodomics approaches for the production of healthy animals, as well as high quality and safety products for the consumer, is also briefly discussed.

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Detection of growth-related QTL in turbot (Scophthalmus maximus)

Cited by 70 publications

References 38 publications

Co-localization of growth QTL with differentially expressed candidate genes in rainbow trout

Co-localization of growth QTL with differentially expressed candidate genes in rainbow trout

Parallel evolution and adaptation to environmental factors in a marine flatfish: Implications for fisheries and aquaculture management of the turbot (Scophthalmus maximus)

Advances in genomics for flatfish aquaculture

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