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

Abstract

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.

Epimutations in Developmental Genes Underlie the Onset of Domestication in Farmed European Sea Bass

“…2014). In this context, it is interesting to note that glutamate receptors were also found differentially expressed in the lower jaw of European sea bass with mandibular prognathism (Babbucci et al. 2016).…”

“…This, along with the observation that farmed sea bass also shares some of the characteristics of the domestication syndrome, for example, changes in morphology (Arechavala-Lopez et al. 2012), jaw malformation (Babbucci et al. 2016), indicates that this species constitutes a suitable model to study the first steps of domestication in vertebrates.…”

Genome-wide survey of single-nucleotide polymorphisms reveals fine-scale population structure and signs of selection in the threatened Caribbean elkhorn coral,Acropora palmata

“…In a study that used three orders of magnitude more loci (905,561 SNPs) failed to reveal population structure in A. digitifera collected from the Ryukyu Archipelago of Japan using Bayesian clustering based methods ( Shinzato et al, 2015 ). Low coverage, 5× in this study, is also a concern however this depth of coverage has been used in other non-model species ( Babbucci et al, 2016 ; Blanco-Bercial & Bucklin, 2016 ; Laporte et al, 2016 ). Yet in the coral Platygyra daedalea, 5× coverage was sufficient to assign samples to two distinct clusters based on their geographic origin, the Persian Gulf or Sea of Oman and was consistent with their 20× coverage data set ( Howells et al, 2016 ).…”

Individual-based population genomics reveal different drivers of adaptation in sympatric fish

“…Individual-based information is used in genome-wide association studies (GWAS), which can identify signals of adaptation to both environmental conditions (EAAs) and phenotypic traits through phenotype association analysis (PAAs). This methodology has proven to be a powerful tool to study interesting phenotypic traits and adaptation in model species such as humans, plants and captive fish [11][12][13] . While the use of individual-based information is common in model species, the application in wild populations is rare and has been only used in a few studies combined with environmental data information 14 .…”