Characterization and refinement of growth related quantitative trait loci in European sea bass (Dicentrarchus labrax) using a comparative approach

Abstract

The identification of genetic markers for traits of interest for aquaculture, such as growth, is an important step for the establishment of breeding programmes. As more genomic information becomes available the possibility of applying comparative genomics to identify and refine quantitative trait locus (QTLs) and potentially identify candidate genes responsible for the QTL effect may accelerate genetic improvement in established and new aquaculture species. Here we report such an approach on growth related traits in the European sea bass (Dicentrarchus labrax), an important species for European aquaculture. A genetic map was generated with markers targeted to previously identified QTL for growth which reduced distance and improved resolution in these regions. A total of 36 significant QTL were identified when morphometric traits were considered individually in maternal half sibs, paternal half sibs and sib pair analysis. Twenty seven new markers targeted to the growth QTLs, obtained by comparative mapping, reduced the average distance between markers from 23.4, 9.1, and 5.8 cM in the previous map to 3.4, 2.2, and 5.2 cM, on linkage group (LG) LG4, LG6 and LG15 respectively. Lists of genes embedded in the QTL-591 genes in LG4, 234 genes in LG6 and 450 genes in LG15-were obtained from the European sea bass genome. Comparative mapping revealed conserved gene synteny across teleost fishes. Functional protein association network analysis with the gene products of the 3 linkage groups revealed a large global association network including 42 gene products. Strikingly the association network was populated with genes of known biological importance for growth and body weight in terrestrial farm animals, such as elements of the signalling pathways for Jak-STAT, MAPK, adipocytokine and insulin, growth hormone, IGFI and II. This study demonstrates the feasibility of a comparative genomics 3 combined with functional gene annotation to refine the resolution of QTL and the establishment of hypothesis to accelerate discovery of putative responsible genes.

QTL fine mapping and identification of candidate genes for growth-related traits in bighead carp ( Hypophthalmichehys nobilis )

“…QTL for disease resistance, salinity and temperature tolerance, sex determination and growth traits have been identified in various fish species based on microsatellitebased genetic maps (Laghari et al, 2014;Yue, 2014). Given the importance of production in aquaculture, QTL for growth traits have been investigated in over 20 aquaculture species, such as rainbow trout (Wringe et al, 2010), Atlantic salmon (Gutierrez et al, 2012), Arctic charr (Kuttner et al, 2011), European sea bass (Louro et al, 2016), large yellow croaker , Japanese flounder (Song et al, 2012a), small abalone (Ren et al, 2016), triangle pearl mussel (Bai et al, 2015) and Chinese mitten crab (Qiu et al, 2016). A lot of candidate genes and molecular markers have been identified based on the results of QTL mapping and provide useful tools for MAS programs to improve the efficiency and precision of fish breeding Wang et al, 2015b;Xia et al, 2013).…”

Genetic Variation of Insulin-like Growth Factor II (IGF-II) Gene and its Associations with Growth Traits in European sea bass (Dicentrarchus labrax)

“…Louro et al (2018) revealed a candidate function of IGF-II in growth regulation of European sea bass. In another study, Louro et al (2016) found that the sea bass LG6 (linkage group 6) has a high quantitative effect on the growth axis such as IGF-II and leptin. Therefore, in our study we have chosen to identify IGF-II gene located on LG6 (HG916846).…”

“…In the last few decades, molecular markers have been utilized to improve economic traits that were required for a fast and effective production (Schlicht et al, 2019). Therefore, using molecular markers in relation to growth traits is an essential step for the success of selective breeding programs for the European sea bass production (Louro et al, 2016).…”

Untitled

“…There has been a continuous effort for marker development, studies on genetic structures of population and quantitative trait loci (QTL) mapping of D. labrax (Chatziplis et al, 2007;Massault et al, 2010;Louro et al, 2016). To this date, few hatcheries have already initiated specific breeding programs in order to develop genetic improvements of this species for sustainable aquaculture practice (Chavanne et al, 2016).…”