A high-resolution linkage map for comparative genome analysis and QTL fine mapping in Asian seabass, Lates calcarifer

Abstract

BackgroundHigh density linkage maps are essential for comparative analysis of synteny, fine mapping of quantitative trait loci (QTL), searching for candidate genes and facilitating genome sequence assembly. However, in most foodfish species, marker density is still low. We previously reported a first generation linkage map with 240 DNA markers and its application to preliminarily map QTL for growth traits in Asian seabass (Lates calcarifer). Here, we report a high-resolution linkage map with 790 microsatellites and SNPs, comparative analysis of synteny, fine-mapping of QTL and the identification of potential candidate genes for growth traits.ResultsA second generation linkage map of Asian seabass was developed with 790 microsatellite and SNP markers. The map spanned a genetic length of 2411.5 cM, with an average intermarker distance of 3.4 cM or 1.1 Mb. This high density map allowed for comparison of the map with Tetraodon nigroviridis genome, which revealed 16 synteny regions between the two species. Moreover, by employing this map we refined QTL to regions of 1.4 and 0.2 cM (or 400 and 50 kb) in linkage groups 2 and 3 in a population containing 380 progeny; potential candidate genes for growth traits in QTL regions were further identified using comparative genome analysis, whose effects on growth traits were investigated. Interestingly, a QTL cluster at Lca371 underlying growth traits of Asian seabass showed similarity to the cathepsin D gene of human, which is related to cancer and Alzheimer's disease.ConclusionsWe constructed a high resolution linkage map, carried out comparative mapping, refined the positions of QTL, identified candidate genes for growth traits and analyzed their effects on growth. Our study developed a framework that will be indispensable for further identification of genes and analysis of molecular variation within the refined QTL to enhance understanding of the molecular basis of growth and speed up genetic improvement of growth performance, and it also provides critical resource for future genome sequence assembly and comparative genomics studies on the evolution of fish genomes.

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

“…Compared with other popular molecular markers, microsatellite, or simple sequence repeat (SSR) marker is one of the best options for linkage map construction because of its many merits, such as abundance in genome, uniformly distribution, high polymorphism, co-dominant inheritance, long flanking sequences, ease of detection by PCR, and easy accession by other laboratories via published primer sequences (Liu and Cordes, 2004). Several high-density genetic linkage maps have been constructed based on microsatellites for aquaculture species, such as Asian seabass (Wang et al, 2011a), Japanese flounder (Song et al, 2012b), halfsmooth tongue sole (Song et al, 2012a). 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).…”

Genetic and genomic analyses for economically important traits and their applications in molecular breeding of cultured fish

“…These five major QTLs have been confirmed in two other Asian seabass populations [22]. Further QTL fine mapping of the Asian seabass growth trait identified three candidate "growth genes" (cathepsin D, KCTD15, and csmd2) affecting body weight, body length, and total length [10]. The [20] function of the cathepsin D gene in humans involves cell proliferation and cell growth; therefore, cathepsin D may also be a major "growth gene" in Asian seabass.…”

Microsatellite-centromere mapping in common carp through half-tetrad analysis in diploid meiogynogenetic families

“…However, these markers were difficult to localize centromeres along chromosomes owing to the limitation of their polymorphisms and numbers of loci. Recently, wellestablished genetic linkage maps have been constructed based on microsatellites in many teleost fishes (Guo et al 2013;Song et al 2012a, b;Wang et al 2011;Xia et al 2010;Xu et al 2013), and the numbers of LGs are exactly or almost coincident with the chromosome numbers of haploid genome. The localizations of centromeres onto all LGs according to estimated G-C distances have been successfully reported in zebrafish (Johnson et al 1996), turbot (Scophthalmus maximus) (Martinez et al 2008), Atlantic halibut (Hippoglossus hippoglossus L.) (Reid et al 2007), rainbow trout (Guyomard et al 2006), and bighead carp .…”

“…Song et al 2012a, b;Wang et al 2011;Xia et al 2010;Zhang et al 2013a). Genetic linkage maps have become essential tools in various fields of genetic research, such as identifying quantitative trait loci (QTLs) related with target traits (Sun and Liang 2004), positional or candidate gene cloning (Donovan et al 2000), genome assembly (Kong et al 2002), and comparative genome mapping (Solinastoldo et al 1995).…”