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An integrated genomic approach for the study of mandibular prognathism in the European seabass

ABSTRACT: An integrated genomic approach for the study of mandibular prognathism in the European seabass

PROVIDER: PRJNA336028 | ENA |

REPOSITORIES: ENA

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An integrated genomic approach for the study of mandibular prognathism in the European seabass

Project description:This SuperSeries is composed of the SubSeries listed below.

2017-02-12 | GSE85056 | GEO

An integrated genomic approach for the study of mandibular prognathism in the European seabass (Dicentrarchus labrax).

Project description:Skeletal anomalies in farmed fish are a relevant issue affecting animal welfare and health and causing significant economic losses. Here, a high-density genetic map of European seabass for QTL mapping of jaw deformity was constructed and a genome-wide association study (GWAS) was carried out on a total of 298 juveniles, 148 of which belonged to four full-sib families. Out of 298 fish, 107 were affected by mandibular prognathism (MP). Three significant QTLs and two candidate SNPs associated with MP were identified. The two GWAS candidate markers were located on ChrX and Chr17, both in close proximity with the peaks of the two most significant QTLs. Notably, the SNP marker on Chr17 was positioned within the Sobp gene coding region, which plays a pivotal role in craniofacial development. The analysis of differentially expressed genes in jaw-deformed animals highlighted the "nervous system development" as a crucial pathway in MP. In particular, Zic2, a key gene for craniofacial morphogenesis in model species, was significantly down-regulated in MP-affected animals. Gene expression data revealed also a significant down-regulation of Sobp in deformed larvae. Our analyses, integrating transcriptomic and GWA methods, provide evidence for putative mechanisms underlying seabass jaw deformity.

| S-EPMC5144136 | biostudies-literature

An integrated genomic approach for the study of mandibular prognathism in the European seabass (Dicentrarchus labrax) II

Project description:A sea bass oligo microarray platform was used to profile gene expression in mandibles of 58 days-old sea bass affected by prognathism, a skeletal malformation that strongly affects sea bass production. Two different conditions: i) protruding jaws, and ii) normal jaws were used for gene expression analysis. For each condition, total RNA was extracted from five (5) independent biological replicates, each consisting of pools of five (5) jaws.

2017-02-12 | GSE85054 | GEO

An integrated genomic approach for the study of mandibular prognathism in the European seabass (Dicentrarchus labrax) I

Project description:A sea bass oligo microarray platform was used to profile gene expression in whole heads of 38 days-old sea bass affected by prognathism, a skeletal malformation that strongly affects sea bass production. Two different conditions: i) prognathous individuals, and ii) normal individuals were analyzed. For each condition, total RNA was extracted from three (3) independent biological replicates, each consisting of pools of five (5) heads.

2017-02-12 | GSE85052 | GEO

Dicentrarchus labrax

Project description:An integrated genomic approach for the study of mandibular prognathism in the European seabass (Dicentrarchus labrax) I

| PRJNA336034 | ENA

Dicentrarchus labrax

Project description:An integrated genomic approach for the study of mandibular prognathism in the European seabass (Dicentrarchus labrax) II

| PRJNA336035 | ENA

Seabass Meiotic Gynogenesis ddRAD

Project description:Gene-centromere mapping in meiotic gynogenetic European seabass

| PRJEB7015 | ENA

Microarray analysis of the Asian seabass (Lates calcarifer) brains

Project description:In this study, we attempt to characterize the transcriptomic profile of the Asian seabass brains collected from the male and female sexes. The objective is to identify genes that show sexually dimorphic expression in the brain of this species. For this experiment, Asian seabass were collected from the Marine Aquaculture Center of the Agri-Food & Veterinary Authority of Singapore. There were no treatments carried out in this experiment. Four brains from adult male seabass (5 years old) with M3-type testis and four brains from adult female seabass (5 years old) with F3-type ovaries were used in this experiment. (Gonads were examined by histology and classified according to sexual maturation status as described by Guiguen and colleagues (Guiguen et al. Environmental Biology of Fishes, 1994)).

2015-01-08 | GSE53901 | GEO

Effect of poultry byproduct meal on European seabass gut microbiota

Project description:Effect of fishmeal replacement with poultry byproduct meal (PBM) on European seabass intestinal microbiota.

| PRJEB70800 | ENA

Microarray analysis of the Asian seabass (Lates calcarifer) brains

2015-01-08 | E-GEOD-53901 | biostudies-arrayexpress