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

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

Genetic differentiation and phylogeography of Mediterranean-North Eastern Atlantic blue shark (Prionace glauca, L. 1758) using mitochondrial DNA: Panmixia or complex stock structure?

Background The blue shark (Prionace glauca, Linnaeus 1758) is one of the most abundant epipelagic shark inhabiting all the oceans except the poles, including the Mediterranean Sea, but its genetic structure has not been confirmed at basin and interoceanic distances. Past tagging programs in the Atlantic Ocean failed to find evidence of migration of blue sharks between the Mediterranean and the adjacent Atlantic, despite the extreme vagility of the species. Although the high rate of by-catch in the Mediterranean basin, to date no genetic study on Mediterranean blue shark was carried out, which constitutes a significant knowledge gap, considering that this population is classified as “Critically Endangered”, unlike its open-ocean counterpart. Methods Blue shark phylogeography and demography in the Mediterranean Sea and North-Eastern Atlantic Ocean were inferred using two mitochondrial genes (Cytb and control region) amplified from 207 and 170 individuals respectively, collected from six localities across the Mediterranean and two from the North-Eastern Atlantic. Results Although no obvious pattern of geographical differentiation was apparent from the haplotype network, Φst analyses indicated significant genetic structure among four geographical groups. Demographic analyses suggest that these populations have experienced a constant population expansion in the last 0.4–0.1 million of years. Discussion The weak, but significant, differences in Mediterranean and adjacent North-eastern Atlantic blue sharks revealed a complex phylogeographic structure, which appears to reject the assumption of panmixia across the study area, but also supports a certain degree of population connectivity across the Strait of Gibraltar, despite the lack of evidence of migratory movements observed by tagging data. Analyses of spatial genetic structure in relation to sex-ratio and size could indicate some level of sex/stage biased migratory behaviour

Full-length sequence and expression analysis of Toll-like receptor 9 in the gilthead seabream (Sparus aurata L.)

Toll-Like Receptors (TLRs) have recently emerged as key sensors of invading microbes, acting through recognition of pathogen-associated molecular patterns. It has been demonstrated that TLR9 is involved in the recognition of unmethylated CpG motifs in mice, humans, and pigs. We report here the full-length sequence of TLR9 cDNA in the gilthead sea bream (Sparus aurata L.). The predicted protein (1063 amino acids) was similar to mammalian TLR9s, showing 21 leucine-rich repeats in the extracellular region and a typical Toll/IL-1R (TIR) domain in the intracellular region. Comparative analysis of TLR9 sequences indicated that critical residues for ligand-binding are conserved across vertebrate lineages, although evidence of functional divergence was observed. Analysis of the genomic structure of sea bream TLR9 gene revealed the presence of two intervening sequences. Retention of the second intron produced an alternatively spliced mRNA (TLR9B) showing differential expression among tissues or developmental stages compared to the wild-type isoform (TLR9A). RT-PCR analysis indicated a broad expression of TLR9A, especially in immune-related organs (spleen, head-kidney) and mucosal-epithelial barriers (gills, gut, skin). Using quantitative Real-Time RT-PCR, no statistically significant variation was observed for TLR9 mRNAs expression in the spleen of experimentally infected animals compared to healthy controls. Comparing sequence and expression profile of sea bream TLR9 with mammalian TLR9s suggested that the main function of TLR9 might be conserved across vertebrates, although species-specific features are present (modulation of ligand-binding specificity, alternative splicing)

Data imputation and machine learning improve association analysis and genomic prediction for resistance to fish photobacteriosis in the gilthead sea bream

Disease resistance represents a key trait for breeding programs in aquaculture species. Here we re-analysed 2bRAD sequence data from two experimental challenges of gilthead sea bream with Photobacterium damsealae piscicida. Using a high quality reference genome, we carried out variant calling and data imputation with Beagle to obtain a large set of SNPs (80,744). This allowed the identification of eight novel QTLs for resistance to photobacteriosis across different chromosomes and revealed a highly polygenic genetic architecture.Bayesian regression approaches and machine learning methods (support vector machines and linear bagging) were compared to evaluate relative performance to classify susceptible-resistant individuals. Both data sets showed higher Matthew Correlation Coefficient (MCC) and accuracy values for machine learning methods, particularly linear bagging, with 20–70 % increase in prediction performance. Overall, machine learning methods should be explored in parallel with parametric regression approaches to increase the chances of highly effective genomic prediction

CONTRIBUTION OF ADVENTITIAL FIBROBLASTS TO NEOINTIMA FORMATION AND VASCULAR REMODELING: FROM AN INNOCENT BYSTANDER TO ACTIVE PARTICIPANT

The adventitial layer surrounding the blood vessels has long been exclusively considered a supporting tissue the main function of which is to provide adequate nourishment to the muscle layers of tunica media. Although functionally interconnected, the adventitial and medial layers are structurally interfaced at the external elastic lamina level, clearly distinguishable at the maturational phase of vascular morphogenesis. Over the last few years the \u201cpassive\u201d role that the adventitia seemed to play in experimental and spontaneous vascular pathologies involving proliferation, migration, differentiation, and apoptosis of vascular smooth muscle cells (VSMCs) has been questioned. It has been demonstrated that fibroblasts from the adventitia display an important partnership with the resident medial VSMCs in terms of phenotypic conversion, proliferation, apoptotic, and migratory properties the result of which is neointima formation and vascular remodeling. This article is an attempt at reviewing the major themes and more recent findings dealing with the phenotypic conversion process that leads adventitial \u201cpassive\u201d (static) fibroblasts to become \u201cactivated\u201d (mobile) myofibroblasts. This event shows some facets in common with vascular morphogenesis, ie, the process of recruitment, incorporation, and phenotypic conversion of cells surrounding the primitive endothelial tube in the definitive vessel wall. We hypothesize that during the response to vascular injuries in the adult, \u201cactivation\u201d of adventitial fibroblasts is, at least in part, reminiscent of a developmental program that also invests, although with distinct spatiotemporal features, medial VSMC

High mortality of juvenile gilthead sea bream (Sparus aurata) from photobacteriosis is associated with alternative macrophage activation and anti-inflammatory response: Results of gene expression profiling of early responses in the head kidney

The halophilic bacterium Photobacterium damselae subsp. piscicida (Phdp) represents a substantial health problem for several fish species in aquaculture. Bacteria that reside free and inside phagocytes cause acute and chronic forms of photobacteriosis. Infections of juveniles rapidly kill up to 90-100% fish. Factors underlying failure of the immune protection against bacteria remain largely unknown. The reported study used a transcriptomic approach to address this issue. juvenile sea breams (0.5 g) were challenged by immersion in salt water containing 2.89 x 10(8) CFU of a virulent Phdp and the head kidney was sampled after 24- and 48-h. Analyses were performed using the second version of a 44 k oligonucleotide DNA microarray that represents 19,734 sea bream unique transcripts and covers diverse immune pathways. Expression changes of selected immune genes were validated with qPCR. Results suggested rapid recognition of the pathogen, as testified by up-regulation of lectins and antibacterial proteins (bactericidal permeability-increasing protein lectins, lysozyme, intracellular and extracellular proteases), chemokines and chemokine receptors. Increased expression of proteins involved in iron and heme metabolism also could be a response against bacteria that are dependent on iron. However, negative regulators of immune/inflammatory response were preponderant among the up-regulated genes. A remarkable finding was the increased expression of IL-10 in concert with up-regulation of arginase I and II and proteins of the polyamine biosynthesis pathway that diverts the arginine flux from the production of reactive nitrogen species. Such expression changes are characteristic for alternatively activated macrophages that do not develop acute inflammatory responses. Immune suppression can be induced by the host to reduce tissue damages or by the pathogen to evade host response. (C) 2013 Elsevier Ltd. All rights reserved